Citrus Sinensis ID: 036599

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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-------19
Protein Sequence
HEPPVNQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSLMKKETVIEDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHcccccccccEEEEcccEEEEEEEEcccccHHHHHHHHHHHcccEEEEEEEEEccccEEEEEEEEEEccccccccHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHcccccccccEEEEEEEcccEEEEEEEEcccccHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEcccccccccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
heppvnqtkmrehrsdsedkavykskNLEAERRRRQKLNDRLLKLRSLMKKETVIEDAITYIRQLKGRVLFLCDqvlqvepleeeetkpkidENAAEEMKNcgieedvkvtnmggnklrINIIFGKKRGNFTKLVEAMNALGfvfgdtsvttlkGATLFSSVLegthggdriiRVEETRELLLKIIRGI
Flexible Loop (DISEMBL)
heppvnqtkmrehrsdsedkavyksknleaerrrrQKLNdrllklrslmkketviEDAITYIRQLKGRVLFLCDQVLqvepleeeetkpkidenaaEEMKNCgieedvkvtnmggnKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSsvlegthggdriirveetRELLLKIIRGI
Low Complexity Region (SEG)
HEPPVNQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSLMKKETVIEDAITYIRQLKGRVLFLCDqvlqvepleeeetkpkIDENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI
Disordered region (IsUnstruct)
*****************************************LLKLRSLMKKETVIEDAITYIRQLKGRVLFLCDQVLQV**********************CGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII***
Disordered Region (DISOPRED)
**************************************NDRLLKLRSLMKKETVIEDAITYIRQLK*********************************************NMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGD*IIRVEETRELLLKIIRG*
Disordered Region (DISEMBL)
********************AVYKSKNLEAERRRRQKLNDRLLKLRSLMKKETVIEDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI
Disordered Region (DISPRO)
*********************VYKSKNLEAERRRRQKLNDRLLKLRSLMKKETVIEDAITYIRQLKGRVLFLCDQVLQV*********************NCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
HEPPVNQTKMREHRSDSEDKAVYKSKNxxxxxxxxxxxxxxxxxxxxxMKKETVIEDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI
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	189	2.2.26 [Sep-21-2011]
O81900	207	Transcription factor DYSF	yes	no	0.957	0.874	0.385	9e-26
Q9ZVX2	571	Transcription factor ABOR	no	no	0.846	0.280	0.28	9e-13
Q2HIV9	248	Transcription factor bHLH	no	no	0.878	0.669	0.273	3e-07
Q9LSE2	494	Transcription factor ICE1	no	no	0.714	0.273	0.248	1e-06
Q9LPW3	450	Transcription factor SCRE	no	no	0.703	0.295	0.277	3e-06
Q9FIP9	592	Transcription factor ATR2	no	no	0.730	0.233	0.266	6e-05
Q39204	623	Transcription factor MYC2	no	no	0.312	0.094	0.4	9e-05
Q700E3	263	Transcription factor bHLH	no	no	0.693	0.498	0.270	0.0001
Q9ZPY8	566	Transcription factor ABA-	no	no	0.380	0.127	0.357	0.0001
Q8S3F1	320	Transcription factor NAI1	no	no	0.211	0.125	0.521	0.0001

>sp|O81900|DYT1_ARATH Transcription factor DYSFUNCTIONAL TAPETUM 1 OS=Arabidopsis thaliana GN=DYT1 PE=2 SV=1

 Score =  116 bits (291), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 77/200 (38%), Positives = 116/200 (58%), Gaps = 19/200 (9%)

Query: 4   PVNQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIED 57
           PV  ++ ++   + E+   +KS NLEAERRRR+KL+ RL+ LRS       M K +++ED
Sbjct: 10  PVRMSRRKQVTKEKEEDENFKSPNLEAERRRREKLHCRLMALRSHVPIVTNMTKASIVED 69

Query: 58  AITYIRQLKGRVLFLCDQVLQVEP----LEEEETKPKI-----DENAAEEMKNCGIEEDV 108
           AITYI +L+  V  L +   ++E     ++EE+T P I       +  EEMK  GIEE+V
Sbjct: 70  AITYIGELQNNVKNLLETFHEMEEAPPEIDEEQTDPMIKPEVETSDLNEEMKKLGIEENV 129

Query: 109 KVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHG 168
           ++  +G  K  + II  K+ G FTK +E M  LGF   D S+TT  GA L S+ ++    
Sbjct: 130 QLCKIGERKFWLKIITEKRDGIFTKFMEVMRFLGFEIIDISLTTSNGAILISASVQTQEL 189

Query: 169 GDRIIRVEETRELLLKIIRG 188
            D    VE+T++ LL+++R 
Sbjct: 190 CD----VEQTKDFLLEVMRS 205

Transcription factor. Involved in the control of tapetum development. Required for male fertility and pollen differentiation, especially during callose deposition.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVX2|AMS_ARATH Transcription factor ABORTED MICROSPORES OS=Arabidopsis thaliana GN=AMS PE=1 SV=2

 Score = 73.2 bits (178), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 99/200 (49%), Gaps = 40/200 (20%)

Query: 24  KSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQVL 77
           ++KNL AERRRR+KLNDRL  LRSL      + + +++ DAI Y+++L+     L D++ 
Sbjct: 312 QAKNLMAERRRRKKLNDRLYALRSLVPRITKLDRASILGDAINYVKELQNEAKELQDELE 371

Query: 78  QVEPLEEEETKPK-----------------------------ID-ENAAEEMKNCGIEED 107
           +    E+   +P+                             +D EN+ ++ +   +E  
Sbjct: 372 ENSETEDGSNRPQGGMSLNGTVVTGFHPGLSCNSNVPSVKQDVDLENSNDKGQE--MEPQ 429

Query: 108 VKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTH 167
           V V  + G +  + +I   K G FT+L+EA+++LG     T+  T +  +L S+V +   
Sbjct: 430 VDVAQLDGREFFVKVICEYKPGGFTRLMEALDSLGLEV--TNANTTRYLSLVSNVFKVEK 487

Query: 168 GGDRIIRVEETRELLLKIIR 187
             + +++ E  R  LL+I R
Sbjct: 488 NDNEMVQAEHVRNSLLEITR 507

Transcription factor. Plays a crucial role in tapetum development. Required for male fertility and pollen differentiation, especially during the post-meiotic transcriptional regulation of microspore development within the developing anther.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2HIV9|BH035_ARATH Transcription factor bHLH35 OS=Arabidopsis thaliana GN=BHLH35 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 92/201 (45%), Gaps = 35/201 (17%)

Query: 4   PVNQTKMREHRSDSEDKAVYK--SKNLEAERRRRQKLNDRLLKLRSL------MKKETVI 55
           P+ +     + S S D A     SKN+ +ER RRQKLN RL  LRS+      M K ++I
Sbjct: 31  PLEEAISGSYDSSSPDGAASSPASKNIVSERNRRQKLNQRLFALRSVVPNITKMDKASII 90

Query: 56  EDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPK--------IDEN-----AAEEMKNC 102
           +DAI+YI  L+       ++ L+ E + E E+ PK         D +      +++MK  
Sbjct: 91  KDAISYIEGLQYE-----EKKLEAE-IRELESTPKSSLSFSKDFDRDLLVPVTSKKMKQL 144

Query: 103 G-------IEE-DVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK 154
                   IE  ++KVT MG   + +++   K+     KL E   +L      +++T+  
Sbjct: 145 DSGSSTSLIEVLELKVTFMGERTMVVSVTCNKRTDTMVKLCEVFESLNLKILTSNLTSFS 204

Query: 155 GATLFSSVLEGTHGGDRIIRV 175
           G    +  +E       ++R+
Sbjct: 205 GMIFHTVFIEADEEEQEVLRL 225

Arabidopsis thaliana (taxid: 3702)

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

 Score = 53.1 bits (126), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/157 (24%), Positives = 73/157 (46%), Gaps = 22/157 (14%)

Query: 24  KSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQVL 77
            +KNL AERRRR+KLNDRL  LRS+      M + +++ DAI Y+++L  R+  L +++ 
Sbjct: 305 PAKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDLHNELE 364

Query: 78  QVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMG---------------GNKLRIN 121
              P     T           +  +C ++E++  +++                G  + I+
Sbjct: 365 STPPGSLPPTSSSFHPLTPTPQTLSCRVKEELCPSSLPSPKGQQARVEVRLREGRAVNIH 424

Query: 122 IIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATL 158
           +  G++ G     ++A++ LG       ++   G  L
Sbjct: 425 MFCGRRPGLLLATMKALDNLGLDVQQAVISCFNGFAL 461

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)

>sp|Q9LPW3|SCRM2_ARATH Transcription factor SCREAM2 OS=Arabidopsis thaliana GN=SCRM2 PE=1 SV=1

 Score = 51.6 bits (122), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 70/155 (45%), Gaps = 22/155 (14%)

Query: 24  KSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQVL 77
            +KNL AERRRR+KLNDRL  LRS+      M + +++ DAI Y+++L  R+  L  ++ 
Sbjct: 265 PAKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDLHTELE 324

Query: 78  QVEPLEEE-----ETKPKIDENAAEEMKNC---------GIEEDVKVTNMGGNKLRINII 123
              P          T   +     EE+  C         G +  V+V    G  + I++ 
Sbjct: 325 STPPSSSSLHPLTPTPQTLSYRVKEEL--CPSSSLPSPKGQQPRVEVRLREGKAVNIHMF 382

Query: 124 FGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATL 158
            G++ G     + A++ LG       ++   G  L
Sbjct: 383 CGRRPGLLLSTMRALDNLGLDVQQAVISCFNGFAL 417

Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIP9|ATR2_ARATH Transcription factor ATR2 OS=Arabidopsis thaliana GN=ATR2 PE=1 SV=1

 Score = 47.4 bits (111), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 48/180 (26%), Positives = 83/180 (46%), Gaps = 42/180 (23%)

Query: 2   EPPVNQTKMREHR-SDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETV 54
           EPP  + + R  + ++  ++ +    ++EAER+RR+KLN R   LR++      M K ++
Sbjct: 393 EPPEKKPRKRGRKPANGREEPL---NHVEAERQRREKLNQRFYSLRAVVPNVSKMDKASL 449

Query: 55  IEDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDENAAE--EMKNCG--------- 103
           + DAI+YI +LK +        LQ    ++EE + K+D  + E    K CG         
Sbjct: 450 LGDAISYINELKSK--------LQQAESDKEEIQKKLDGMSKEGNNGKGCGSRAKERKSS 501

Query: 104 ----------IEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL 153
                     +E DVK+    G  + I +  GKK     + +EA+  L       S++ +
Sbjct: 502 NQDSTASSIEMEIDVKII---GWDVMIRVQCGKKDHPGARFMEALKELDLEVNHASLSVV 558

Involved in tryptophan and other stress-responsive gene regulation.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 46.6 bits (109), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 6/65 (9%)

Query: 27  NLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE 80
           ++EAER+RR+KLN R   LR++      M K +++ DAI YI +LK +V+    + LQ++
Sbjct: 453 HVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIK 512

Query: 81  PLEEE 85
              EE
Sbjct: 513 NQLEE 517

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|Q700E3|BH027_ARATH Transcription factor bHLH27 OS=Arabidopsis thaliana GN=BHLH27 PE=2 SV=1

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 78/181 (43%), Gaps = 50/181 (27%)

Query: 25  SKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQVLQ 78
           SKN+ +ER RRQKLN RL  LRS+      + K +VI+D+I Y+++L  +     ++ L+
Sbjct: 53  SKNVVSERNRRQKLNQRLFALRSVVPNISKLDKASVIKDSIDYMQELIDQ-----EKTLE 107

Query: 79  VEPLEEEETKPKIDENAAEEMKNCGIEE-------------------------------- 106
            E + E E++  + EN   +  +C   E                                
Sbjct: 108 AE-IRELESRSTLLENPVRDY-DCNFAETHLQDFSDNNDMRSKKFKQMDYSTRVQHYPIE 165

Query: 107 --DVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDT---SVTTLKGATLFSS 161
             ++KVT MG   + + I   KKR    +L + + +L      T   S T+    TLF  
Sbjct: 166 VLEMKVTWMGEKTVVVCITCSKKRETMVQLCKVLESLNLNILTTNFSSFTSRLSTTLFLQ 225

Query: 162 V 162
           V
Sbjct: 226 V 226

Arabidopsis thaliana (taxid: 3702)

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

 Score = 46.2 bits (108), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 12/84 (14%)

Query: 27  NLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE 80
           ++EAER+RR+KLN R   LRS+      M K +++ DAI+YI++L+ +V  + D+ +  +
Sbjct: 396 HVEAERQRREKLNQRFYALRSVVPNISKMDKASLLGDAISYIKELQEKVKIMEDERVGTD 455

Query: 81  -PLEEEET-----KPKIDENAAEE 98
             L E  T      P++D  A  E
Sbjct: 456 KSLSESNTITVEESPEVDIQAMNE 479

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 46.2 bits (108), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 34/46 (73%), Gaps = 6/46 (13%)

Query: 30  AERRRRQKLNDRLLKLRSLMK------KETVIEDAITYIRQLKGRV 69
           AER+RRQKLN+RL+ L +L+       K TV+EDAI +++QL+ RV
Sbjct: 136 AERKRRQKLNERLIALSALLPGLKKTDKATVLEDAIKHLKQLQERV 181

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

Arabidopsis thaliana (taxid: 3702)

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	189
359496224	204	PREDICTED: transcription factor DYSFUNCT	0.873	0.808	0.591	5e-42
147791425	204	hypothetical protein VITISV_006000 [Viti	0.873	0.808	0.591	6e-42
359496236	204	PREDICTED: transcription factor DYSFUNCT	0.873	0.808	0.586	3e-41
255555099	207	DNA binding protein, putative [Ricinus c	0.910	0.830	0.519	1e-35
224078792	209	predicted protein [Populus trichocarpa]	0.941	0.851	0.489	3e-34
356557627	218	PREDICTED: transcription factor DYSFUNCT	0.984	0.853	0.425	4e-30
356557625	213	PREDICTED: transcription factor DYSFUNCT	0.941	0.835	0.427	5e-29
356546706	208	PREDICTED: transcription factor DYSFUNCT	0.920	0.836	0.464	3e-28
356546704	194	PREDICTED: LOW QUALITY PROTEIN: transcri	0.867	0.845	0.438	2e-27
356519517	223	PREDICTED: transcription factor DYSFUNCT	0.814	0.690	0.469	2e-25

>gi|359496224|ref|XP_003635181.1| PREDICTED: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Vitis vinifera]

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 103/174 (59%), Positives = 127/174 (72%), Gaps = 9/174 (5%)

Query: 23  YKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQV 76
           YKSKNL+AERRRRQKL+DRLL LR+L      M K T+IEDAITYI++L+  V  L DQ+
Sbjct: 33  YKSKNLQAERRRRQKLSDRLLALRALVPIITNMNKATIIEDAITYIKELQKNVKDLSDQL 92

Query: 77  LQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLV 135
           L++E   EEE K + +  +AAEEM  CGIEEDVKVTN+ GNK  + I+  KKR +FTKLV
Sbjct: 93  LEMEASSEEEAKQRSETIDAAEEMNKCGIEEDVKVTNIDGNKFWLKIVIQKKRSSFTKLV 152

Query: 136 EAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI 189
           EAMN LGF F DTSVTT KGA L ++ +EG +G +      ETRELL +II+GI
Sbjct: 153 EAMNFLGFEFTDTSVTTSKGAILITACVEGIYGEN--FAAAETRELLQEIIKGI 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147791425|emb|CAN76852.1| hypothetical protein VITISV_006000 [Vitis vinifera]

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 103/174 (59%), Positives = 126/174 (72%), Gaps = 9/174 (5%)

Query: 23  YKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQV 76
           YKSKNL+AERRRRQKL+DRLL LR+L      M K T+IEDAITYI++L+  V  L DQ+
Sbjct: 33  YKSKNLQAERRRRQKLSDRLLALRALVPIITNMNKATIIEDAITYIKELQKNVKDLSDQL 92

Query: 77  LQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLV 135
           L++E   EEE K + +  +AAEEM  CGIEEDVKVTN+ GNK  + I+  KKR +FTKLV
Sbjct: 93  LEMEASSEEEAKQRSETIDAAEEMNKCGIEEDVKVTNIDGNKFWLKIVIQKKRSSFTKLV 152

Query: 136 EAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI 189
           EAMN LGF F DTSVTT KGA L ++ +EG +G        ETRELL +II+GI
Sbjct: 153 EAMNFLGFEFTDTSVTTSKGAILITACVEGIYG--EXFAAAETRELLQEIIKGI 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496236|ref|XP_003635187.1| PREDICTED: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Vitis vinifera]

 Score =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 102/174 (58%), Positives = 126/174 (72%), Gaps = 9/174 (5%)

Query: 23  YKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDQV 76
           YKSKNL+AERRRRQKL+DRLL LR+L      M K T+IEDAITYI++L+  V  L DQ+
Sbjct: 33  YKSKNLQAERRRRQKLSDRLLALRALVPIITNMNKATIIEDAITYIKELQKNVKDLSDQL 92

Query: 77  LQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLV 135
           L++E   EEE K + +  +AAEEM  CGIEEDV+VTN+ GNK  + I+  KKR +FTKLV
Sbjct: 93  LEMEASSEEEAKQRSETIDAAEEMNKCGIEEDVEVTNIDGNKFWLKIVIQKKRSSFTKLV 152

Query: 136 EAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRGI 189
           EAMN LGF F DTSVTT KGA L ++ +EG +G        ETRELL +II+GI
Sbjct: 153 EAMNFLGFEFTDTSVTTSKGAILITACVEGIYG--ETFAAAETRELLQEIIKGI 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555099|ref|XP_002518587.1| DNA binding protein, putative [Ricinus communis] gi|223542432|gb|EEF43974.1| DNA binding protein, putative [Ricinus communis]

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 94/181 (51%), Positives = 125/181 (69%), Gaps = 9/181 (4%)

Query: 16  DSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRV 69
           D +D   YKSKNL AERRRR+KL++RLL LR+       M K T+IEDAITYI++L+  V
Sbjct: 29  DYDDTKEYKSKNLGAERRRRKKLSERLLALRASVPIITNMNKATIIEDAITYIQELQKHV 88

Query: 70  LFLCDQVLQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKR 128
             L DQ+L+++ L EE  K + DE + AEEMK CGI EDV+VT +   KL I II  KKR
Sbjct: 89  KHLSDQLLEMDELSEEAVKTRSDEFDPAEEMKQCGIMEDVQVTYVDETKLWIKIILEKKR 148

Query: 129 GNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRG 188
           G FT+L+EA++ LG    +T+VTT +GA L SS +EG +G    + V++T+E LL+IIR 
Sbjct: 149 GRFTRLIEALSYLGLELTETTVTTYRGAMLVSSFVEGAYGD--TLTVQQTKEYLLEIIRT 206

Query: 189 I 189
           I
Sbjct: 207 I 207

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224078792|ref|XP_002305631.1| predicted protein [Populus trichocarpa] gi|222848595|gb|EEE86142.1| predicted protein [Populus trichocarpa]

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 93/190 (48%), Positives = 126/190 (66%), Gaps = 12/190 (6%)

Query: 9   KMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYI 62
           +M   R+  +D   YKSKNL AERRRR+KL++RLL LR+L      M K T+IEDAITYI
Sbjct: 23  RMGRKRTSYDDTVGYKSKNLHAERRRREKLSNRLLTLRALVPIITNMNKGTIIEDAITYI 82

Query: 63  RQLKGRVLFLCDQVLQVEPLEEEET--KPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLR 119
           ++LK  V  L D +LQ       E   K +++E +A+EEMK CGI+EDV+VTN+ G+KL 
Sbjct: 83  QELKKNVEALTD-MLQEMEASSSEEEFKTRVNEIDASEEMKLCGIKEDVQVTNIEGDKLW 141

Query: 120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETR 179
           I II  KKRG F +L+E M   G    D++VTT KGA L ++ +EG  G    + V++T+
Sbjct: 142 IKIILEKKRGGFARLMEKMACFGLELIDSNVTTSKGAMLVTACVEGAFGD--TLTVQQTK 199

Query: 180 ELLLKIIRGI 189
           ELL +II+GI
Sbjct: 200 ELLTQIIKGI 209

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557627|ref|XP_003547117.1| PREDICTED: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Glycine max]

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 83/195 (42%), Positives = 123/195 (63%), Gaps = 9/195 (4%)

Query: 2   EPPVNQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVI 55
           E   ++ +M   R+  +D  VYKSKNLE ERRRR+KL+ RLL LRS+      M + T+I
Sbjct: 21  ENVSSRQRMSRKRNYDDDTRVYKSKNLEIERRRREKLSTRLLMLRSINPIITNMNRGTII 80

Query: 56  EDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMG 114
            DAITYI +L+  V  L  ++ Q+E   E+  + K+DE +A E+MK+ GI+ +V+V  + 
Sbjct: 81  VDAITYIEKLQHEVQRLSQELHQLEATSEKTAEAKVDEIDAVEDMKHWGIQAEVRVAQID 140

Query: 115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR 174
            NKL + II  KKRG F+KL+EA+N  G    DT+ TT KGA L +S ++    G+R + 
Sbjct: 141 ENKLWVKIIIEKKRGRFSKLMEALNNFGIELIDTNFTTTKGAFLITSCIQ-VKDGER-LE 198

Query: 175 VEETRELLLKIIRGI 189
           + +++ LL +II  I
Sbjct: 199 IHQSKSLLQEIINDI 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557625|ref|XP_003547116.1| PREDICTED: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Glycine max]

 Score =  132 bits (333), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 80/187 (42%), Positives = 116/187 (62%), Gaps = 9/187 (4%)

Query: 10  MREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIR 63
           M   R+  +D   YKSKNLE ERRRR+KL+ RLL LRS+      M K T++EDAITYI 
Sbjct: 29  MSRKRNYDDDTREYKSKNLETERRRREKLSSRLLMLRSMVPIITNMNKATIVEDAITYIE 88

Query: 64  QLKGRVLFLCDQVLQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLRINI 122
           +L+ +V  L  ++ Q+E    E  + KI E +A E+MKN GI+E+V+V  +  NKL + I
Sbjct: 89  KLQDKVQNLSQELHQMEATSVETAETKIVEIDAVEDMKNWGIQEEVRVAQINENKLWVKI 148

Query: 123 IFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELL 182
           I  KKRG F +L++A+N  G    DT++TT KG+ L +S ++    G+R   + + + LL
Sbjct: 149 IIEKKRGRFNRLMQALNNFGIELIDTNLTTTKGSFLITSCIK-CKNGER-FEIHQAKNLL 206

Query: 183 LKIIRGI 189
             +I  I
Sbjct: 207 QDVINHI 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546706|ref|XP_003541764.1| PREDICTED: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Glycine max]

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 85/183 (46%), Positives = 119/183 (65%), Gaps = 9/183 (4%)

Query: 14  RSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKG 67
           R+  +D   YKSKNLE ERRRR+KL+ RLL LRS+      M K  ++EDAITYI +L+ 
Sbjct: 28  RNFDDDTKEYKSKNLETERRRREKLSSRLLMLRSIVPIITNMNKAMIVEDAITYIEKLQD 87

Query: 68  RVLFLCDQVLQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGK 126
           +V  L  ++ Q+E   EE  + KI E +AAE+MKN GI+E+V V  +  NKL + II  K
Sbjct: 88  KVQSLSQELHQMEATSEETAETKIVEIDAAEDMKNWGIQEEVIVEEINENKLWVKIIVEK 147

Query: 127 KRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII 186
           KRG F++L+EA+N  G    DT++TT KGA L +S ++G   G+R + + +T+ LL  II
Sbjct: 148 KRGRFSRLMEALNNFGIELIDTNLTTTKGAFLITSFIKG-KNGER-LEIHQTKNLLQDII 205

Query: 187 RGI 189
             I
Sbjct: 206 NDI 208

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546704|ref|XP_003541763.1| PREDICTED: LOW QUALITY PROTEIN: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Glycine max]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 75/171 (43%), Positives = 107/171 (62%), Gaps = 7/171 (4%)

Query: 2   EPPVNQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVI 55
           E   ++ +M   R+  +D  VYKSKNLE E RRR+KL+  LL LRS+      M + T+I
Sbjct: 22  ENVSSRQRMSRKRNYDDDTRVYKSKNLEIEGRRREKLSASLLMLRSMNPIITNMNRGTII 81

Query: 56  EDAITYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMG 114
            DAITYI +L+  V  L  ++ Q+E   E+    KIDE +A E+MKN GI+ +V+V  + 
Sbjct: 82  VDAITYIEKLQYEVQRLSQELHQLEANSEKTAXAKIDEIDAVEDMKNWGIQAEVRVAKID 141

Query: 115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEG 165
            NKL + II  KKRG F+KL+EA+N  G    DT++ T KGA+L +S ++ 
Sbjct: 142 ENKLWVKIIIEKKRGRFSKLMEALNNFGIELIDTNLATTKGASLITSCIQA 192

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519517|ref|XP_003528419.1| PREDICTED: transcription factor DYSFUNCTIONAL TAPETUM 1-like [Glycine max]

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/166 (46%), Positives = 105/166 (63%), Gaps = 12/166 (7%)

Query: 6   NQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAI 59
           N+ +MR    D  D  V+KSKNLE ERRRR+KL+ R+L LRSL      M K T++EDAI
Sbjct: 25  NRERMRRKNYDY-DTQVFKSKNLEVERRRREKLSTRILLLRSLVPIITKMNKATIVEDAI 83

Query: 60  TYIRQLKGRVLFLCDQVLQVEPLEEEETKPKIDE-NAAEEMKNCGIEEDVKVTNMGGNKL 118
           TYI   +  V  L  ++ ++E   EE  KPK +E +AAEEM   GI   V+ T + GNKL
Sbjct: 84  TYIETQQNIVQSLSYELHEMEATSEE-IKPKKEEIDAAEEMNKLGI---VQATKIDGNKL 139

Query: 119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE 164
            + +I  KKRG F KL+EAM+ +G    DT+VTTLK A L ++ ++
Sbjct: 140 WVKMIIEKKRGRFKKLMEAMDNIGIELIDTNVTTLKKAYLVTTFMQ 185

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	189
TAIR|locus:2141206	207	DYT1 "AT4G21330" [Arabidopsis	0.962	0.879	0.353	1.3e-22
TAIR|locus:2039445	571	AMS "AT2G16910" [Arabidopsis t	0.312	0.103	0.438	5e-12
UNIPROTKB|Q58GE3	234	UDT1 "Undeveloped tapetum 1" [	0.857	0.692	0.282	2.8e-11
UNIPROTKB|Q6YUS3	552	OSJNBb0088N06.15 "BHLH protein	0.433	0.148	0.305	5.6e-11
UNIPROTKB|Q8H8E4	430	OJ1006F06.1 "Putative bHLH tra	0.830	0.365	0.255	2e-07
TAIR|locus:2155725	351	bHLH093 "AT5G65640" [Arabidops	0.825	0.444	0.264	8e-06
TAIR|locus:2123954	263	AT4G29930 "AT4G29930" [Arabido	0.328	0.235	0.394	2e-05
UNIPROTKB|Q84LF9	310	RERJ1 "Transcription Factor" [	0.253	0.154	0.444	8.9e-05
TAIR|locus:2142419	315	AT5G10570 "AT5G10570" [Arabido	0.793	0.476	0.269	0.0001
TAIR|locus:2090847	494	ICE1 "AT3G26744" [Arabidopsis	0.238	0.091	0.490	0.00039

TAIR|locus:2141206 DYT1 "AT4G21330" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 71/201 (35%), Positives = 107/201 (53%)

Query:     2 EPPVNQTKMREHRSDSEDKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVI 55
             + PV  ++ ++   + E+   +KS NLEAERRRR+KL+ RL+ LRS       M K +++
Sbjct:     8 QEPVRMSRRKQVTKEKEEDENFKSPNLEAERRRREKLHCRLMALRSHVPIVTNMTKASIV 67

Query:    56 EDAITYIRQLKGRVLFLCDXXXXXXXXXXXXXXXXID---------ENAAEEMKNCGIEE 106
             EDAITYI +L+  V  L +                 D          +  EEMK  GIEE
Sbjct:    68 EDAITYIGELQNNVKNLLETFHEMEEAPPEIDEEQTDPMIKPEVETSDLNEEMKKLGIEE 127

Query:   107 DVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGT 166
             +V++  +G  K  + II  K+ G FTK +E M  LGF   D S+TT  GA L S+ ++  
Sbjct:   128 NVQLCKIGERKFWLKIITEKRDGIFTKFMEVMRFLGFEIIDISLTTSNGAILISASVQT- 186

Query:   167 HGGDRIIRVEETRELLLKIIR 187
                  +  VE+T++ LL+++R
Sbjct:   187 ---QELCDVEQTKDFLLEVMR 204

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=IMP;TAS

GO:0048658 "tapetal layer development" evidence=IMP

TAIR|locus:2039445 AMS "AT2G16910" [Arabidopsis thaliana (taxid:3702)]

 Score = 114 (45.2 bits), Expect = 5.0e-12, Sum P(2) = 5.0e-12
 Identities = 32/73 (43%), Positives = 42/73 (57%)

Query:    16 DSEDKAVYK--------SKNLEAERRRRQKLNDRLLKLRSLMKKET------VIEDAITY 61
             D ED   YK        +KNL AERRRR+KLNDRL  LRSL+ + T      ++ DAI Y
Sbjct:   296 DDEDDPKYKKKSGKGSQAKNLMAERRRRKKLNDRLYALRSLVPRITKLDRASILGDAINY 355

Query:    62 IRQLKGRVLFLCD 74
             +++L+     L D
Sbjct:   356 VKELQNEAKELQD 368

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:0009555 "pollen development" evidence=IMP

GO:0048658 "tapetal layer development" evidence=IMP

UNIPROTKB|Q58GE3 UDT1 "Undeveloped tapetum 1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 48/170 (28%), Positives = 79/170 (46%)

Query:    23 YKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDXX 76
             +KSKNLEAERRRR +LN  +  LR++      M KE  + DAI +I+ L+  VL L    
Sbjct:    62 FKSKNLEAERRRRGRLNGNIFALRAVVPKITKMSKEATLSDAIEHIKNLQNEVLELQRQL 121

Query:    77 XXXXXXXXXXXXXXIDENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVE 136
                               +    +N   +  V++ ++G +K  + I + K+ G FTK++E
Sbjct:   122 GDSPGEAWEKQGSASCSESFVPTENAHYQGQVELISLGSSKYNLKIFWTKRAGLFTKVLE 181

Query:   137 AMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII 186
             A+    +     S+ T+       S       G++ + + E R LL  I+
Sbjct:   182 AL--CSYKVQVLSLNTISFYGYAESFFTIEVKGEQDVVMVELRSLLSSIV 229

GO:0005634 "nucleus" evidence=IDA

GO:0048656 "tapetal layer formation" evidence=IMP

GO:0048658 "tapetal layer development" evidence=IMP

UNIPROTKB|Q6YUS3 OSJNBb0088N06.15 "BHLH protein-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 107 (42.7 bits), Expect = 5.6e-11, Sum P(2) = 5.6e-11
 Identities = 26/85 (30%), Positives = 48/85 (56%)

Query:   104 IEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVL 163
             +E  ++V  + GN+L + +++  K G F +L++AMNALG    + +VTT K  TL  +V 
Sbjct:   414 MEPQLEVRQVQGNELFVQVLWEHKPGGFVRLMDAMNALGLEVINVNVTTYK--TLVLNVF 471

Query:   164 EG-THGGDRIIRVEETRELLLKIIR 187
                    +  ++ +  R+ LL++ R
Sbjct:   472 RVMVRDSEVAVQADRVRDSLLEVTR 496

GO:0003677 "DNA binding" evidence=IMP

GO:0005634 "nucleus" evidence=IC

GO:0048653 "anther development" evidence=IMP

GO:0048654 "anther morphogenesis" evidence=IMP

GO:0048657 "tapetal cell differentiation" evidence=IMP

UNIPROTKB|Q8H8E4 OJ1006F06.1 "Putative bHLH transcription protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 127 (49.8 bits), Expect = 2.0e-07, P = 2.0e-07
 Identities = 43/168 (25%), Positives = 73/168 (43%)

Query:    25 SKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDXXXX 78
             SKNL AERRRR++LNDRL  LRS+      M + +++ D I Y+++L  R+  L +    
Sbjct:   181 SKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDTIDYVKELTERIKTLEEEIGV 240

Query:    79 XXXXXXXXXXXXIDENAAEEMKNCGIEEDVK--VTNMGGNKLRINIIFGKKRGNFTKLVE 136
                         + ++++       +    K  V N G    RI I      G     V 
Sbjct:   241 TPEELDLLNT--MKDSSSGNNNEMLVRNSTKFDVENRGSGNTRIEICCPANPGVLLSTVS 298

Query:   137 AMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLK 184
             A+  LG       V+      + +S L+   G  +++  +E ++ L +
Sbjct:   299 ALEVLGLEIEQCVVSCFSDFGMQASCLQ-EDGKRQVVSTDEIKQTLFR 345

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2155725 bHLH093 "AT5G65640" [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 8.0e-06, P = 8.0e-06
 Identities = 45/170 (26%), Positives = 73/170 (42%)

Query:    25 SKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRVLFLCDXXXX 78
             SKNL AERRRR++LNDRL  LRS+      M + +++ DAI Y+++L  ++  L D    
Sbjct:   177 SKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDAIDYMKELLDKINKLQDEEQE 236

Query:    79 XXXXXXXXXXXXI----DENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKL 134
                              D NA E +     + ++   +      R++I    K G     
Sbjct:   237 LGNSNNSHHSKLFGDLKDLNANEPLVRNSPKFEI---DRRDEDTRVDICCSPKPGLLLST 293

Query:   135 VEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLK 184
             V  +  LG       ++     +L +S  EG    D  I  E+ ++ L +
Sbjct:   294 VNTLETLGLEIEQCVISCFSDFSLQASCSEGAEQRD-FITSEDIKQALFR 342

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2123954 AT4G29930 "AT4G29930" [Arabidopsis thaliana (taxid:3702)]

 Score = 100 (40.3 bits), Expect = 2.0e-05, Sum P(2) = 2.0e-05
 Identities = 28/71 (39%), Positives = 40/71 (56%)

Query:     4 PVNQTKMREHRSDSEDKAVYK---SKNLEAERRRRQKLNDRLLKLRSL------MKKETV 54
             P+ +       S S D A      SKN+ +ER RRQKLN RL  LRS+      + K +V
Sbjct:    29 PMEEAFSGSGESSSPDGAATSPASSKNVVSERNRRQKLNQRLFALRSVVPNISKLDKASV 88

Query:    55 IEDAITYIRQL 65
             I+D+I Y+++L
Sbjct:    89 IKDSIDYMQEL 99

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

UNIPROTKB|Q84LF9 RERJ1 "Transcription Factor" [Oryza sativa (taxid:4530)]

 Score = 95 (38.5 bits), Expect = 8.9e-05, Sum P(2) = 8.9e-05
 Identities = 24/54 (44%), Positives = 36/54 (66%)

Query:    19 DKAVYKSKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLK 66
             D A   +KN+  ER RR+KLN++L  LRS+      M K ++I+DAI YI++L+
Sbjct:    86 DDAGGANKNILMERDRRRKLNEKLYALRSVVPNITKMDKASIIKDAIEYIQRLQ 139

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2142419 AT5G10570 "AT5G10570" [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 0.00010, P = 0.00010
 Identities = 45/167 (26%), Positives = 72/167 (43%)

Query:    25 SKNLEAERRRRQKLNDRLLKLRSLMKKET------VIEDAITYIRQLKGRVLFLCDXXXX 78
             SKNL AERRRR++LNDRL  LRS++ K T      ++ DAI Y+++L  ++  L +    
Sbjct:   150 SKNLMAERRRRKRLNDRLSLLRSIVPKITKMDRTSILGDAIDYMKELLDKINKLQEDEQE 209

Query:    79 XXXXXXXXXXXXIDENAAEEMKNCGIEEDVKVTNMGGNKLRINIIFGKKRGNFTKLVEAM 138
                          +      +K    E D +  N       I+I    K G     V  +
Sbjct:   210 LGSNSHLSTLITNESMVRNSLK---FEVDQREVNT-----HIDICCPTKPGLVVSTVSTL 261

Query:   139 NALGFVFGDTSVTTLKGATLFSSVLEGTHGGDR-IIRVEETRELLLK 184
               LG       ++     +L +S  E   G  R ++  E T++ L++
Sbjct:   262 ETLGLEIEQCVISCFSDFSLQASCFEV--GEQRYMVTSEATKQALIR 306

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:2090847 ICE1 "AT3G26744" [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 0.00039, P = 0.00039
 Identities = 25/51 (49%), Positives = 36/51 (70%)

Query:    25 SKNLEAERRRRQKLNDRLLKLRSL------MKKETVIEDAITYIRQLKGRV 69
             +KNL AERRRR+KLNDRL  LRS+      M + +++ DAI Y+++L  R+
Sbjct:   306 AKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRI 356

GO:0003677 "DNA binding" evidence=ISS;IDA;TAS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009409 "response to cold" evidence=IEP

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

GO:0050826 "response to freezing" evidence=RCA;IMP

GO:0010440 "stomatal lineage progression" evidence=IMP

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

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010182 "sugar mediated signaling pathway" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O81900	DYT1_ARATH	No assigned EC number	0.385	0.9576	0.8743	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	189
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-05
smart00353	53	smart00353, HLH, helix loop helix domain	4e-05
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	4e-05

>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 = 39.9 bits (94), Expect = 3e-05
 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 9/52 (17%)

Query: 24 KSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLK 66
          +  +   ERRRR+++ND   +LRSL         + K  ++  A+ YI+ L+
Sbjct: 5  REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQ 56

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

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

 Score = 39.5 bits (93), Expect = 4e-05
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 9/50 (18%)

Query: 29 EAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRV 69
            ERRRR+K+N+   +LRSL         + K  ++  AI YI+ L+  +
Sbjct: 2  ARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEEL 51

Length = 53

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

 Score = 39.4 bits (93), Expect = 4e-05
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 8/46 (17%)

Query: 29 EAERRRRQKLNDRLLKLRSLM------K--KETVIEDAITYIRQLK 66
          E ERRRR ++ND   +LR L+      K  K  ++  AI YI+ L+
Sbjct: 7  ERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	189
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.26
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.24
smart00353	53	HLH helix loop helix domain.	99.24
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	98.82
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.63
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	98.62
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	98.58
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	98.52
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	98.51
KOG1318	411	consensus Helix loop helix transcription factor EB	98.46
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	98.37
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.28
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	98.17
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.8
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	97.79
KOG4304	250	consensus Transcriptional repressors of the hairy/	97.77
PRK05007	884	PII uridylyl-transferase; Provisional	97.77
PRK00275	895	glnD PII uridylyl-transferase; Provisional	97.75
PRK04374	869	PII uridylyl-transferase; Provisional	97.68
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	97.67
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	97.6
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	97.55
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.55
PRK05092	931	PII uridylyl-transferase; Provisional	97.54
PRK03059	856	PII uridylyl-transferase; Provisional	97.51
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.5
PRK03381	774	PII uridylyl-transferase; Provisional	97.45
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	97.42
PRK00194	90	hypothetical protein; Validated	97.37
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	97.35
PRK03381	774	PII uridylyl-transferase; Provisional	97.34
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.3
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	97.26
PRK05007	884	PII uridylyl-transferase; Provisional	97.21
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.19
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	97.16
PLN03217	93	transcription factor ATBS1; Provisional	97.15
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	97.13
KOG0561	373	consensus bHLH transcription factor [Transcription	97.11
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	97.11
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	97.01
PRK00275	895	glnD PII uridylyl-transferase; Provisional	97.01
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.99
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	96.96
PRK05092	931	PII uridylyl-transferase; Provisional	96.94
PRK03059	856	PII uridylyl-transferase; Provisional	96.93
PRK04374	869	PII uridylyl-transferase; Provisional	96.91
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	96.83
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	96.52
KOG4029	228	consensus Transcription factor HAND2/Transcription	96.37
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	96.3
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	96.2
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	96.17
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	95.8
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	95.72
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	95.61
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	95.6
PRK04435	147	hypothetical protein; Provisional	95.56
cd02116	60	ACT ACT domains are commonly involved in specifica	95.42
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	95.41
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	95.4
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	95.2
PRK08577	136	hypothetical protein; Provisional	95.0
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	94.98
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	94.86
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	94.65
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	94.59
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	94.27
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	94.18
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	94.12
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	94.12
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	94.1
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	94.0
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	93.84
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	93.5
PRK11589	190	gcvR glycine cleavage system transcriptional repre	93.48
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	93.41
PRK06737	76	acetolactate synthase 1 regulatory subunit; Valida	93.21
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	93.16
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	92.85
TIGR00119	157	acolac_sm acetolactate synthase, small subunit. ac	92.82
PRK13562	84	acetolactate synthase 1 regulatory subunit; Provis	92.79
PF13710	63	ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.	92.29
PRK07334	403	threonine dehydratase; Provisional	92.26
CHL00100	174	ilvH acetohydroxyacid synthase small subunit	92.22
COG0788	287	PurU Formyltetrahydrofolate hydrolase [Nucleotide	92.0
PRK11895	161	ilvH acetolactate synthase 3 regulatory subunit; R	91.96
COG3830	90	ACT domain-containing protein [Signal transduction	91.66
KOG3910	632	consensus Helix loop helix transcription factor [T	91.33
cd04930	115	ACT_TH ACT domain of the nonheme iron-dependent ar	91.0
PF05088	1528	Bac_GDH: Bacterial NAD-glutamate dehydrogenase	90.95
PRK00227	693	glnD PII uridylyl-transferase; Provisional	90.94
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	90.42
PRK11152	76	ilvM acetolactate synthase 2 regulatory subunit; P	90.36
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	90.0
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	89.95
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	89.63
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	88.51
cd04885	68	ACT_ThrD-I Tandem C-terminal ACT domains of threon	87.21
COG4492	150	PheB ACT domain-containing protein [General functi	86.98
PRK11899	279	prephenate dehydratase; Provisional	86.84
PRK11589	190	gcvR glycine cleavage system transcriptional repre	86.61
PRK08178	96	acetolactate synthase 1 regulatory subunit; Review	86.13
PRK10872	743	relA (p)ppGpp synthetase I/GTP pyrophosphokinase;	85.08
TIGR00691	683	spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (	84.92
cd04922	66	ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctiona	84.11
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	83.94
PRK11092	702	bifunctional (p)ppGpp synthetase II/ guanosine-3',	83.71

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

Probab=99.26  E-value=8.3e-12  Score=82.05  Aligned_cols=48  Identities=33%  Similarity=0.580  Sum_probs=44.8

Q ss_pred             hhhhhchHHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHH
Q 036599           22 VYKSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRV   69 (189)
Q Consensus        22 ~~~~~h~~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv   69 (189)
                      ..+..|...||+||++||..|..|+++         +||++||..||+||+.|+.++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            356789999999999999999999999         699999999999999999876

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=99.24  E-value=1.2e-11  Score=80.45  Aligned_cols=43  Identities=44%  Similarity=0.770  Sum_probs=40.9

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc-----------ccccchHHHHHHHHHHHH
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL-----------MKKETVIEDAITYIRQLK   66 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl-----------~DKaSIl~dAI~YIk~Lq   66 (189)
                      +..|+..||+||++||+.|..|+.+           +||++||..||+||++||
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            4689999999999999999999999           789999999999999997

; 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=99.24  E-value=1.2e-11  Score=79.54  Aligned_cols=42  Identities=40%  Similarity=0.666  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHH
Q 036599           29 EAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVL   70 (189)
Q Consensus        29 ~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~   70 (189)
                      ..||+||++||+.|..|+++         +||++||.+||+||++|+.+++
T Consensus         2 ~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        2 ARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999         6899999999999999999875

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

Probab=98.82  E-value=7.1e-08  Score=66.88  Aligned_cols=69  Identities=9%  Similarity=0.086  Sum_probs=58.0

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccC---HHHHHHHHHHHHhc
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR---VEETRELLLKIIRG  188 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s---~~~lk~~L~~~i~~  188 (189)
                      +|+|.|+++||+|.+|..+|-.+|++|.+|.|+|.++.+..+|.|.-. .|....+   .+.|+++|..+|.+
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~-~g~kl~~~~~~~~l~~~L~~al~~   74 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHK-DGRTLSTEGERQRVIKCLEAAIER   74 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcC-CCCccCCHHHHHHHHHHHHHHHhc
Confidence            689999999999999999999999999999999999999999999833 3333333   35778888888764

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.

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

Probab=98.63  E-value=4.6e-07  Score=62.33  Aligned_cols=47  Identities=11%  Similarity=0.128  Sum_probs=45.3

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEe
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEG  165 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~  165 (189)
                      .|+|.++++||+|.+|.++|..+||+|..|.|+|.++.+..+|.|.-
T Consensus         3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d   49 (72)
T cd04895           3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTD   49 (72)
T ss_pred             EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEEC
Confidence            68999999999999999999999999999999999999999999983

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=98.62  E-value=4e-07  Score=63.01  Aligned_cols=67  Identities=18%  Similarity=0.280  Sum_probs=53.1

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCcccc---CHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRII---RVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~---s~~~lk~~L~~~i  186 (189)
                      +.++|.|+++||+|.++..+|..+|++|..|.|++ .++.++.+|.|. ..++ ...   ..+.|+++|.+++
T Consensus         1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~-d~~~-~~~~~~~~~~l~~~L~~~L   71 (76)
T cd04927           1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFIT-DARE-LLHTKKRREETYDYLRAVL   71 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEe-CCCC-CCCCHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999997 899999999997 3222 222   2334556665554

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.

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

Probab=98.58  E-value=9.5e-07  Score=61.23  Aligned_cols=67  Identities=7%  Similarity=0.017  Sum_probs=56.4

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEE--eeCCeEEEEEEEEeeeCCcccc-C---HHHHHHHHHHHHhc
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVT--TLKGATLFSSVLEGTHGGDRII-R---VEETRELLLKIIRG  188 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is--~~~~~~l~~~~vk~~~~~~~~~-s---~~~lk~~L~~~i~~  188 (189)
                      .|.|.|.++||+|.+|.++|..+|++|..|.|+  |.++++..+|.+. ..+ . .+ +   .+.|+++|..++.+
T Consensus         2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~-~~g-~-kl~d~~~~~~L~~~L~~~l~~   74 (75)
T cd04896           2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQ-SDG-K-KIMDPKKQAALCARLREEMVC   74 (75)
T ss_pred             EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEe-CCC-C-ccCCHHHHHHHHHHHHHHhcC
Confidence            588999999999999999999999999999999  9999999999994 333 2 33 3   45788888877653

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.

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

Probab=98.52  E-value=2.3e-06  Score=58.75  Aligned_cols=69  Identities=16%  Similarity=0.217  Sum_probs=56.1

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccc---cCHHHHHHHHHHHHh
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRI---IRVEETRELLLKIIR  187 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~---~s~~~lk~~L~~~i~  187 (189)
                      .|+|.++++||+|.+|..+|..+|++|..|.+++.++.++.+|.|.-..++...   ...+.|+++|.+++.
T Consensus         2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~~l~   73 (74)
T cd04925           2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGAPIDDPIRLASIEDRLDNVLR   73 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHHHhc
Confidence            588999999999999999999999999999999999999999999732212222   234678888887765

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.

>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=98.51  E-value=2.3e-06  Score=58.45  Aligned_cols=46  Identities=24%  Similarity=0.333  Sum_probs=43.4

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL-KGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~-~~~~l~~~~vk  164 (189)
                      .|.|.|+++||+|.++..+|..+|++|..|.+.+. +|.++.+|.+.
T Consensus         3 ~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~   49 (73)
T cd04900           3 EVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVL   49 (73)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEE
Confidence            57899999999999999999999999999999887 79999999998

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.

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

Probab=98.46  E-value=5.4e-07  Score=80.12  Aligned_cols=50  Identities=34%  Similarity=0.567  Sum_probs=45.6

Q ss_pred             hhhhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHHHH
Q 036599           21 AVYKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGRVL   70 (189)
Q Consensus        21 ~~~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~kv~   70 (189)
                      ...+..|++.||+||++||+++..|-.|          ..|.+||.-+.+||++||+..+
T Consensus       231 r~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  231 RRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            4457899999999999999999999999          4699999999999999998776

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

Probab=98.37  E-value=6.7e-06  Score=55.95  Aligned_cols=64  Identities=22%  Similarity=0.254  Sum_probs=54.9

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .|-|.|+++||+|.++..+|..+||+|+.|++.+ .+|.++.+|.|....++    ....|.++|+.++
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~~~----~~~~~~~~~~~~~   67 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWKRG----ETAALGHALQKEI   67 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCCcc----chHHHHHHHHHhh
Confidence            5778899999999999999999999999999997 48899999999854443    4678888888765

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.

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.28  E-value=1.5e-06  Score=69.50  Aligned_cols=57  Identities=21%  Similarity=0.355  Sum_probs=51.4

Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHHhc-------------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           23 YKSKNLEAERRRRQKLNDRLLKLRSL-------------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        23 ~~~~h~~~ER~RR~kln~~f~~LRsl-------------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      .+..|..+||+||+.||.-|..|..|             ..||-||..||+||..|..++..-+++...|
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L  131 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL  131 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36789999999999999999999999             4688899999999999999998888887655

>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=98.17  E-value=3.4e-05  Score=51.44  Aligned_cols=48  Identities=10%  Similarity=0.146  Sum_probs=44.1

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEee
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGT  166 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~  166 (189)
                      .|.|.|++++|+|.+|+.+|.+++++|.++++.+.++.++..|.+...
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~   49 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDA   49 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECC
Confidence            578899999999999999999999999999999988888888999843

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.

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

Probab=97.80  E-value=0.00049  Score=46.78  Aligned_cols=46  Identities=9%  Similarity=0.174  Sum_probs=42.1

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .|.|.+++++|+|.+|..+|.+++++|+++.+.+.++..+.+|.+.
T Consensus         3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~   48 (72)
T cd04926           3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVT   48 (72)
T ss_pred             EEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEE
Confidence            5677889999999999999999999999999999988888888887

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.

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

Probab=97.79  E-value=0.00035  Score=47.97  Aligned_cols=66  Identities=14%  Similarity=0.154  Sum_probs=54.2

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      .+.|++.++++||++..+..+|.++|.++.+++.++.++.+...+.+.+.     .-+.++|+.+|..+-+
T Consensus         2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~-----~~~~~~l~~~L~~l~~   67 (76)
T PF13740_consen    2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP-----EDSLERLESALEELAE   67 (76)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES-----HHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC-----cccHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999777777732     2267889999887654

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

Probab=97.77  E-value=3.5e-05  Score=64.95  Aligned_cols=54  Identities=24%  Similarity=0.365  Sum_probs=47.1

Q ss_pred             cchhhhhhchHHHHHHHHHHHHHHHHHHhc--------------ccccchHHHHHHHHHHHHHHHHHH
Q 036599           19 DKAVYKSKNLEAERRRRQKLNDRLLKLRSL--------------MKKETVIEDAITYIRQLKGRVLFL   72 (189)
Q Consensus        19 ~~~~~~~~h~~~ER~RR~kln~~f~~LRsl--------------~DKaSIl~dAI~YIk~Lq~kv~~L   72 (189)
                      .....+..+-+-||+||.+||.-|..|+.|              ++||=||.-|++|++.|+..-..-
T Consensus        28 ~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~~   95 (250)
T KOG4304|consen   28 TRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQAA   95 (250)
T ss_pred             hHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccccc
Confidence            345567889999999999999999999999              689999999999999998765443

>PRK05007 PII uridylyl-transferase; Provisional

Probab=97.77  E-value=0.00021  Score=69.90  Aligned_cols=81  Identities=16%  Similarity=0.211  Sum_probs=63.6

Q ss_pred             CccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccC---HHHHHH
Q 036599          105 EEDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR---VEETRE  180 (189)
Q Consensus       105 ~~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s---~~~lk~  180 (189)
                      ++.|.+... .+.-..|+|.|.++||+|.+|.++|.++|++|.+|.|+|.++.+..+|.|. ... +..++   .+.|++
T Consensus       795 ~~~V~~d~~~s~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~-~~~-g~~l~~~~~~~l~~  872 (884)
T PRK05007        795 PTEVSFLPTHTDRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILA-TAD-RRALNEELQQELRQ  872 (884)
T ss_pred             CCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEE-cCC-CCcCCHHHHHHHHH
Confidence            345665432 234468999999999999999999999999999999999999999999998 332 33555   356777


Q ss_pred             HHHHHHh
Q 036599          181 LLLKIIR  187 (189)
Q Consensus       181 ~L~~~i~  187 (189)
                      +|..++.
T Consensus       873 ~L~~~l~  879 (884)
T PRK05007        873 RLTEALN  879 (884)
T ss_pred             HHHHHHh
Confidence            7776653

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=97.75  E-value=0.00038  Score=68.21  Aligned_cols=82  Identities=9%  Similarity=0.125  Sum_probs=64.1

Q ss_pred             CccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccC---HHHHHH
Q 036599          105 EEDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR---VEETRE  180 (189)
Q Consensus       105 ~~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s---~~~lk~  180 (189)
                      .+.|.+... .++-..|.|.+.++||+|.+|..+|..+||+|..|.|+|.++.++.+|.|. ...+....+   .+.|++
T Consensus       801 ~~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~-d~~g~~l~~~~~~~~l~~  879 (895)
T PRK00275        801 PTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFIT-DADNQPLSDPQLCSRLQD  879 (895)
T ss_pred             CCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEE-CCCCCCCCCHHHHHHHHH
Confidence            345555543 234578999999999999999999999999999999999999999999998 322322223   356888


Q ss_pred             HHHHHHh
Q 036599          181 LLLKIIR  187 (189)
Q Consensus       181 ~L~~~i~  187 (189)
                      +|.+++.
T Consensus       880 ~L~~~L~  886 (895)
T PRK00275        880 AICEQLD  886 (895)
T ss_pred             HHHHHHh
Confidence            8888774

>PRK04374 PII uridylyl-transferase; Provisional

Probab=97.68  E-value=0.00055  Score=66.90  Aligned_cols=82  Identities=12%  Similarity=0.201  Sum_probs=65.4

Q ss_pred             CccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccC---HHHHHH
Q 036599          105 EEDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR---VEETRE  180 (189)
Q Consensus       105 ~~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s---~~~lk~  180 (189)
                      ++.|.+... .++-..|.|.+.++||+|.+|..+|.++|++|..|.|+|.++.++.+|.|. ...+. .++   .+.|++
T Consensus       783 ~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~-d~~g~-~~~~~~~~~l~~  860 (869)
T PRK04374        783 APRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQIT-DEHDR-PLSESARQALRD  860 (869)
T ss_pred             CCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEE-CCCCC-cCChHHHHHHHH
Confidence            456666553 234578999999999999999999999999999999999999999999998 32222 232   368888


Q ss_pred             HHHHHHhc
Q 036599          181 LLLKIIRG  188 (189)
Q Consensus       181 ~L~~~i~~  188 (189)
                      +|..++..
T Consensus       861 ~L~~~l~~  868 (869)
T PRK04374        861 ALCACLDP  868 (869)
T ss_pred             HHHHHhcc
Confidence            88887754

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

Probab=97.67  E-value=0.00071  Score=46.62  Aligned_cols=64  Identities=17%  Similarity=0.220  Sum_probs=54.7

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      +.|.+.|+++||+...|.+.|.+.|..|..++....++.|+..+.+...     ..+.+.|.+.|..+-
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~-----~~~~~~l~~~l~~~~   65 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS-----WDAIAKLEAALPGLA   65 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec-----cccHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999999998777777732     247888888887653

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

>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=97.60  E-value=0.001  Score=43.29  Aligned_cols=63  Identities=17%  Similarity=0.219  Sum_probs=47.2

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG-ATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~-~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      +.|.+.|+++||+|.+++.+|.++|++|.++.+....+ .....+... ..    ....+.+.++|.++
T Consensus         1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~-~~----~~~~~~~~~~l~~~   64 (66)
T PF01842_consen    1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIV-VD----EEDLEKLLEELEAL   64 (66)
T ss_dssp             EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEE-EE----GHGHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEE-CC----CCCHHHHHHHHHcc
Confidence            36889999999999999999999999999999999877 222122222 11    34577777777665

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

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

Probab=97.55  E-value=0.002  Score=42.34  Aligned_cols=46  Identities=13%  Similarity=0.221  Sum_probs=41.3

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .|.|.|++++|+|.+|+.+|.++++.|.++.+.+.++.....|.+.
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~   47 (70)
T cd04873           2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVT   47 (70)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEE
Confidence            4778999999999999999999999999999999877766677777

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

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

Probab=97.55  E-value=8.7e-05  Score=71.12  Aligned_cols=46  Identities=28%  Similarity=0.430  Sum_probs=43.5

Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHH
Q 036599           23 YKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGR   68 (189)
Q Consensus        23 ~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~k   68 (189)
                      .+..|..+||+||++||..+..|.+|          +||.+||-.||.+|+.+++.
T Consensus        20 ~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   20 KRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            37899999999999999999999999          89999999999999999885

>PRK05092 PII uridylyl-transferase; Provisional

Probab=97.54  E-value=0.0011  Score=65.32  Aligned_cols=81  Identities=16%  Similarity=0.151  Sum_probs=63.7

Q ss_pred             ccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccC---HHHHHHH
Q 036599          106 EDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR---VEETREL  181 (189)
Q Consensus       106 ~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s---~~~lk~~  181 (189)
                      +.|.+... .++...|.|.|.++||+|.+|..+|.++|++|..|.|+|.++.+..+|.|... .+....+   .+.|+++
T Consensus       831 ~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~-~g~~i~~~~~~~~l~~~  909 (931)
T PRK05092        831 PRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDL-FGLKITNEARQAAIRRA  909 (931)
T ss_pred             CEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCC-CCCcCCCHHHHHHHHHH
Confidence            45666543 23457899999999999999999999999999999999999999999999833 2222223   3578888


Q ss_pred             HHHHHh
Q 036599          182 LLKIIR  187 (189)
Q Consensus       182 L~~~i~  187 (189)
                      |..+|.
T Consensus       910 L~~~L~  915 (931)
T PRK05092        910 LLAALA  915 (931)
T ss_pred             HHHHhc
Confidence            888774

>PRK03059 PII uridylyl-transferase; Provisional

Probab=97.51  E-value=0.00082  Score=65.61  Aligned_cols=80  Identities=11%  Similarity=0.112  Sum_probs=61.4

Q ss_pred             ccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          106 EDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       106 ~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      +.|.+... .++-..|.|.|+++||+|.+|..+|..+|++|..|.|+|.++.++.+|.|... .....-..+.|+++|.+
T Consensus       774 ~~V~~~~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~~-~~~~~~~~~~l~~~L~~  852 (856)
T PRK03059        774 PRVDLRPDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDGS-GLSDNRLQIQLETELLD  852 (856)
T ss_pred             ceEEEEEcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcCC-CCCCHHHHHHHHHHHHH
Confidence            34555443 23457899999999999999999999999999999999999999999999521 11112234677777777


Q ss_pred             HH
Q 036599          185 II  186 (189)
Q Consensus       185 ~i  186 (189)
                      +|
T Consensus       853 ~L  854 (856)
T PRK03059        853 AL  854 (856)
T ss_pred             Hh
Confidence            65

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.50  E-value=0.00069  Score=66.09  Aligned_cols=80  Identities=11%  Similarity=0.188  Sum_probs=62.4

Q ss_pred             CccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCH---HHHHH
Q 036599          105 EEDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRV---EETRE  180 (189)
Q Consensus       105 ~~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~---~~lk~  180 (189)
                      ++.|.+... .+.-..|.|.+.++||+|.+|.++|.++|++|..|.|+|.++.+..+|.|. ... +..++.   +.|++
T Consensus       770 ~~~V~~dn~~s~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~-~~~-g~~l~~~~~~~l~~  847 (854)
T PRK01759        770 KTEVRFLNEEKQEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILT-NQQ-GQALDEEERKALKS  847 (854)
T ss_pred             CCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEE-CCC-CCcCChHHHHHHHH
Confidence            345665442 233478999999999999999999999999999999999999999999998 322 234543   56777


Q ss_pred             HHHHHH
Q 036599          181 LLLKII  186 (189)
Q Consensus       181 ~L~~~i  186 (189)
                      +|..+|
T Consensus       848 ~L~~~l  853 (854)
T PRK01759        848 RLLSNL  853 (854)
T ss_pred             HHHHHh
Confidence            776654

>PRK03381 PII uridylyl-transferase; Provisional

Probab=97.45  E-value=0.0015  Score=63.19  Aligned_cols=72  Identities=15%  Similarity=0.237  Sum_probs=60.8

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHhc
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRG  188 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~~  188 (189)
                      .+.+.|.|.|+++||+|.+|..+|..+|++|++|.+.+.+|.++.+|.|.... + .....+.|+++|.+++.+
T Consensus       597 ~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~~-~-~~~~~~~l~~~L~~~L~~  668 (774)
T PRK03381        597 PHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPRF-G-SPPDAALLRQDLRRALDG  668 (774)
T ss_pred             CCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCC-C-CcchHHHHHHHHHHHHcC
Confidence            35678999999999999999999999999999999999999999999998332 2 234468899999888753

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

Probab=97.42  E-value=0.00049  Score=57.35  Aligned_cols=61  Identities=18%  Similarity=0.290  Sum_probs=51.3

Q ss_pred             cchhhhhhchHHHHHHHHHHHHHHHHHHhc-------c--cccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           19 DKAVYKSKNLEAERRRRQKLNDRLLKLRSL-------M--KKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        19 ~~~~~~~~h~~~ER~RR~kln~~f~~LRsl-------~--DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      .....+..|+.-||+||..|.+.|..|+-+       .  +.++||.-|..||+.|+.+..+.+..++++
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l  124 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDL  124 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHH
Confidence            345667899999999999999999999999       2  257899999999999999887777666543

>PRK00194 hypothetical protein; Validated

Probab=97.37  E-value=0.0015  Score=45.97  Aligned_cols=67  Identities=19%  Similarity=0.153  Sum_probs=54.3

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .+.|.+.|+++||++..+..+|.+.|++|.+.+..+.++.+.-.+.+...   ....+.++|++.|..+-
T Consensus         3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~---~~~~~~~~l~~~l~~l~   69 (90)
T PRK00194          3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDIS---ESKKDFAELKEELEELG   69 (90)
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEec---CCCCCHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999888877655666622   11356788888887654

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

Probab=97.35  E-value=0.0013  Score=46.15  Aligned_cols=66  Identities=15%  Similarity=0.143  Sum_probs=54.4

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      +.|.+.|+++||++..|.+.|-++|++|.+++..+.++.+.-.+.+..   .....+.++|++.|..+-
T Consensus         2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~---~~~~~~~~~L~~~l~~l~   67 (88)
T cd04872           2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDI---SESNLDFAELQEELEELG   67 (88)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEe---CCCCCCHHHHHHHHHHHH
Confidence            579999999999999999999999999999999998887765666662   112467889998887654

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.

>PRK03381 PII uridylyl-transferase; Provisional

Probab=97.34  E-value=0.0016  Score=62.95  Aligned_cols=58  Identities=14%  Similarity=0.103  Sum_probs=50.4

Q ss_pred             cEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          107 DVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       107 ~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .|.+... +++-..|.|.|.++||+|.+|..+|..+|++|.+|.|+|.++.++.+|.|.
T Consensus       696 ~v~~~~~~~~~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~  754 (774)
T PRK03381        696 RVLWLDGASPDATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVT  754 (774)
T ss_pred             EEEEEECCCCCeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEE
Confidence            4444432 223588999999999999999999999999999999999999999999998

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

Probab=97.30  E-value=0.00069  Score=56.67  Aligned_cols=56  Identities=23%  Similarity=0.315  Sum_probs=48.7

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      +..-.+.||+|=+|.|+-|-+|.--        ..|.-||-.||.||..||.=++++......+
T Consensus       119 RKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  119 RKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            3445678999999999999999766        7899999999999999999999998777654

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=97.26  E-value=0.0026  Score=62.03  Aligned_cols=72  Identities=22%  Similarity=0.294  Sum_probs=58.4

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEE-eeCCeEEEEEEEEeeeCCccccC----HHHHHHHHHHHHhc
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVT-TLKGATLFSSVLEGTHGGDRIIR----VEETRELLLKIIRG  188 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is-~~~~~~l~~~~vk~~~~~~~~~s----~~~lk~~L~~~i~~  188 (189)
                      .+...|.|.++++||+|.+|..+|..+||+|..|.|+ +.+|.++.+|.|.... +. .++    .+.|+++|.+++.+
T Consensus       666 ~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~-g~-~~~~~~~~~~i~~~L~~~L~~  742 (850)
T TIGR01693       666 SGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLF-GS-PPAAERVFQELLQGLVDVLAG  742 (850)
T ss_pred             CCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCC-CC-CCCcHHHHHHHHHHHHHHHcC
Confidence            3456899999999999999999999999999999999 6799999999998432 22 332    34577788777753

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=97.21  E-value=0.0053  Score=60.24  Aligned_cols=80  Identities=13%  Similarity=0.115  Sum_probs=60.7

Q ss_pred             ccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEEeeeCCccccCH---HHHHH
Q 036599          106 EDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL-KGATLFSSVLEGTHGGDRIIRV---EETRE  180 (189)
Q Consensus       106 ~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~-~~~~l~~~~vk~~~~~~~~~s~---~~lk~  180 (189)
                      +-|.+... ..+...|.|.|++++|+|..|..+|..+||+|..|.|.+. +|.++.+|.|... .+ ..++.   +.|++
T Consensus       689 p~V~i~~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~-~g-~~~~~~~~~~I~~  766 (884)
T PRK05007        689 PLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEP-DG-SPLSQDRHQVIRK  766 (884)
T ss_pred             CeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECC-CC-CCCCHHHHHHHHH
Confidence            44555432 2356789999999999999999999999999999999886 5599999999832 22 23443   34777


Q ss_pred             HHHHHHh
Q 036599          181 LLLKIIR  187 (189)
Q Consensus       181 ~L~~~i~  187 (189)
                      .|.+++.
T Consensus       767 ~L~~aL~  773 (884)
T PRK05007        767 ALEQALT  773 (884)
T ss_pred             HHHHHHc
Confidence            8877764

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.19  E-value=0.0055  Score=59.90  Aligned_cols=81  Identities=20%  Similarity=0.250  Sum_probs=61.9

Q ss_pred             CccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCccccCH---HHHH
Q 036599          105 EEDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRIIRV---EETR  179 (189)
Q Consensus       105 ~~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~s~---~~lk  179 (189)
                      .+.|.+... ..+...|.|.|+++||+|.+|..+|..+||+|..|.|.+ .+|.++.+|.|.-. . +..++.   +.|+
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~-~-g~~~~~~~~~~l~  741 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTEL-N-GKLLEFDRRRQLE  741 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCC-C-CCCCCHHHHHHHH
Confidence            344555432 234578999999999999999999999999999999987 89999999999832 2 223343   3577


Q ss_pred             HHHHHHHh
Q 036599          180 ELLLKIIR  187 (189)
Q Consensus       180 ~~L~~~i~  187 (189)
                      ++|.+++.
T Consensus       742 ~~L~~aL~  749 (854)
T PRK01759        742 QALTKALN  749 (854)
T ss_pred             HHHHHHHc
Confidence            77777764

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

Probab=97.16  E-value=0.0065  Score=41.08  Aligned_cols=66  Identities=8%  Similarity=-0.059  Sum_probs=48.6

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      .|.+.|+++||++.+|.+.|.++|+.+......+  .++.+  .+.+++. .+....+..+++++|..+-.
T Consensus         1 ii~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f--~~~~~~~-~~~~~~~~~~l~~~l~~l~~   68 (74)
T cd04875           1 ILTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRF--FMRVEFE-LEGFDLSREALEAAFAPVAA   68 (74)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeE--EEEEEEE-eCCCCCCHHHHHHHHHHHHH
Confidence            3789999999999999999999999999998886  33332  3333322 12113678999998887543

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.

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.15  E-value=0.0012  Score=46.44  Aligned_cols=47  Identities=30%  Similarity=0.473  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHhc---------ccccc---hHHHHHHHHHHHHHHHHHHHhhhhhhccc
Q 036599           36 QKLNDRLLKLRSL---------MKKET---VIEDAITYIRQLKGRVLFLCDQVLQVEPL   82 (189)
Q Consensus        36 ~kln~~f~~LRsl---------~DKaS---Il~dAI~YIk~Lq~kv~~Le~~~~~l~~~   82 (189)
                      +.||+..+.|++|         .||+|   +|.||-+||+.|+..|..|.+...++-+.
T Consensus        20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6899999999999         46776   89999999999999999999999887543

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=97.13  E-value=0.0039  Score=60.85  Aligned_cols=80  Identities=11%  Similarity=0.122  Sum_probs=61.8

Q ss_pred             CccEEEEEec-CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccC---HHHHHH
Q 036599          105 EEDVKVTNMG-GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIR---VEETRE  180 (189)
Q Consensus       105 ~~~V~V~~~~-~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s---~~~lk~  180 (189)
                      ++.|.+.... ++-..|.|.|.++||+|.+|.++|.++|++|.++.|+|.++.....|.+....  +..++   .+.|++
T Consensus       766 ~~~V~~d~~~s~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~--g~~~~~~~~~~l~~  843 (850)
T TIGR01693       766 PPRVTILNTASRKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLF--GLKLTDEEEQRLLE  843 (850)
T ss_pred             CCeEEEccCCCCCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCC--CCCCCHHHHHHHHH
Confidence            3456665432 23578999999999999999999999999999999999999999999998322  22443   456777


Q ss_pred             HHHHHH
Q 036599          181 LLLKII  186 (189)
Q Consensus       181 ~L~~~i  186 (189)
                      +|..++
T Consensus       844 ~L~~~l  849 (850)
T TIGR01693       844 VLAASV  849 (850)
T ss_pred             HHHHHh
Confidence            776654

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.

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.11  E-value=0.00036  Score=59.77  Aligned_cols=49  Identities=35%  Similarity=0.512  Sum_probs=42.0

Q ss_pred             chHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHHHHHhh
Q 036599           27 NLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVLFLCDQ   75 (189)
Q Consensus        27 h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~~Le~~   75 (189)
                      -+.-||+|=+-||.-|..||+|        ..||.||+.+.+||.+|+...-+|-.+
T Consensus        64 ANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~q  120 (373)
T KOG0561|consen   64 ANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQ  120 (373)
T ss_pred             hcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccc
Confidence            3446999999999999999999        689999999999999999877665433

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

Probab=97.11  E-value=0.0092  Score=40.72  Aligned_cols=63  Identities=13%  Similarity=0.097  Sum_probs=50.6

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC------CeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK------GATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~------~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      |.+.|+++||++.+|.+.|.+.|++|.+.+..+.+      +.+.-.+.+..   . ...+...++..|..+-
T Consensus         2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~---p-~~~~~~~l~~~l~~l~   70 (81)
T cd04869           2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLAL---P-AGTDLDALREELEELC   70 (81)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEec---C-CCCCHHHHHHHHHHHH
Confidence            67999999999999999999999999999999987      55544455552   2 2467889998887654

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

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

Probab=97.01  E-value=0.018  Score=39.38  Aligned_cols=49  Identities=14%  Similarity=0.226  Sum_probs=40.9

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEEe
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLEG  165 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk~  165 (189)
                      .+.|+|.|.+++|+|.+|..+|.+.++.|.++++...  ++.+.-.|.+++
T Consensus         6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V   56 (80)
T PF13291_consen    6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEV   56 (80)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEE
T ss_pred             EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEE
Confidence            4678899999999999999999999999999999995  677776788884

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=97.01  E-value=0.0054  Score=60.27  Aligned_cols=71  Identities=27%  Similarity=0.307  Sum_probs=56.5

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCcccc----CHHHHHHHHHHHHh
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRII----RVEETRELLLKIIR  187 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~----s~~~lk~~L~~~i~  187 (189)
                      +...|.|.|+++||+|.++..+|..+||+|..|.|.+ .+|.++.+|.|.... +....    -.+.|.++|.+++.
T Consensus       703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~-g~~~~~~~~r~~~i~~~L~~~L~  778 (895)
T PRK00275        703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDD-GEPIGDNPARIEQIREGLTEALR  778 (895)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCC-CCCccchHHHHHHHHHHHHHHHc
Confidence            5678999999999999999999999999999999855 688999999998332 22212    23457788887764

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

Probab=96.99  E-value=0.01  Score=40.41  Aligned_cols=64  Identities=17%  Similarity=0.128  Sum_probs=52.6

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      |.+.++++||+...+.++|.++|+++.+...++.++.+.-.+.+...    ...+.++|+++|...-.
T Consensus         2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p----~~~~~~~l~~~l~~l~~   65 (75)
T cd04870           2 ITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIP----DSADSEALLKDLLFKAH   65 (75)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcC----CCCCHHHHHHHHHHHHH
Confidence            67889999999999999999999999999999998887555666521    13678999999887653

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.

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

Probab=96.96  E-value=0.0042  Score=59.77  Aligned_cols=78  Identities=17%  Similarity=0.228  Sum_probs=61.2

Q ss_pred             CCccEEEEEec-CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHH
Q 036599          104 IEEDVKVTNMG-GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELL  182 (189)
Q Consensus       104 ~~~~V~V~~~~-~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L  182 (189)
                      +.+.|.+.... .+...+++.+.++||+|..+..+|..++|++.+|.|+|++..+..+|.|....  +..+ ..++++.|
T Consensus       777 i~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~--~~~l-~~~~~q~l  853 (867)
T COG2844         777 IPPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDAD--GQAL-NAELRQSL  853 (867)
T ss_pred             cCCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEeccc--cccC-CHHHHHHH
Confidence            35677776542 23578999999999999999999999999999999999999999999998432  3355 33445554


Q ss_pred             HH
Q 036599          183 LK  184 (189)
Q Consensus       183 ~~  184 (189)
                      .+
T Consensus       854 ~~  855 (867)
T COG2844         854 LQ  855 (867)
T ss_pred             HH
Confidence            44

>PRK05092 PII uridylyl-transferase; Provisional

Probab=96.94  E-value=0.012  Score=58.11  Aligned_cols=81  Identities=15%  Similarity=0.187  Sum_probs=61.0

Q ss_pred             ccEEEEEe-cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCcc---ccCHHHHHH
Q 036599          106 EDVKVTNM-GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDR---IIRVEETRE  180 (189)
Q Consensus       106 ~~V~V~~~-~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~---~~s~~~lk~  180 (189)
                      +.|.+... +.+...|.|.|++++|+|.+|..+|..+|++|..|.|++ .+|.++.+|.|.... +..   .-..+.|.+
T Consensus       720 ~~v~~~~~~~~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~-g~~~~~~~~~~~l~~  798 (931)
T PRK05092        720 LATEVRPDPARGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAF-GRDEDEPRRLARLAK  798 (931)
T ss_pred             cEEEEEecCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCC-CCCCCCHHHHHHHHH
Confidence            44555442 235689999999999999999999999999999999988 688888889997322 211   123556777


Q ss_pred             HHHHHHh
Q 036599          181 LLLKIIR  187 (189)
Q Consensus       181 ~L~~~i~  187 (189)
                      +|.+++.
T Consensus       799 ~L~~~l~  805 (931)
T PRK05092        799 AIEDALS  805 (931)
T ss_pred             HHHHHHc
Confidence            7777763

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.93  E-value=0.005  Score=60.24  Aligned_cols=73  Identities=16%  Similarity=0.159  Sum_probs=57.3

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCcc--ccCHHHHHHHHHHHHhc
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDR--IIRVEETRELLLKIIRG  188 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~--~~s~~~lk~~L~~~i~~  188 (189)
                      .+...|.|.|+++||+|..+..+|..+||+|+.|.|.+ .+|.++.+|.|.. ..+..  .--.+.|++.|.+++.+
T Consensus       676 ~~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~-~~~~~~~~~~~~~i~~~l~~~l~~  751 (856)
T PRK03059        676 GEGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLD-PEEDVHYRDIINLVEHELAERLAE  751 (856)
T ss_pred             CCeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeC-CCCCCChHHHHHHHHHHHHHHHcC
Confidence            35678999999999999999999999999999999955 6999999999983 22220  11245677777777643

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.91  E-value=0.0071  Score=59.27  Aligned_cols=73  Identities=12%  Similarity=0.123  Sum_probs=58.6

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHhc
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRG  188 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~~  188 (189)
                      .+...|.|.|++++|+|.+|..+|..+||+|+.|.|.+ .+|.++.+|.|... .+...-....|.+.|.+++.+
T Consensus       688 ~~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~-~~~~~~~~~~i~~~l~~~l~~  761 (869)
T PRK04374        688 NDALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQ-DTYADGDPQRLAAALRQVLAG  761 (869)
T ss_pred             CCeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCC-CCCChHHHHHHHHHHHHHHcC
Confidence            35678999999999999999999999999999999998 69999999999832 222122355577888777754

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

Probab=96.83  E-value=0.0094  Score=39.83  Aligned_cols=66  Identities=14%  Similarity=0.014  Sum_probs=54.6

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      .|.|.||++-|+-.++.+.+-++||.|....+++-+..-+-.|.|.. +..+..+.-+-||+.|..+
T Consensus         2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv~-~~~~~~~rW~lLK~RL~~~   67 (69)
T cd04894           2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVVP-RPPSIKVRWDLLKNRLMSA   67 (69)
T ss_pred             EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEec-CCCCCcccHHHHHHHHHhc
Confidence            58999999999999999999999999999999998887766777763 2334456777888887754

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.

>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=96.52  E-value=0.029  Score=37.48  Aligned_cols=46  Identities=11%  Similarity=0.200  Sum_probs=38.8

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEEe
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLEG  165 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk~  165 (189)
                      |++.+.++||+|.+|+.+|.+.|..|.+.+..... +.....|.+++
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev   48 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDA   48 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEc
Confidence            67888999999999999999999999999988764 56555677773

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.

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

Probab=96.37  E-value=0.0057  Score=50.66  Aligned_cols=57  Identities=25%  Similarity=0.310  Sum_probs=47.6

Q ss_pred             chhhhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHHHHHHHhhh
Q 036599           20 KAVYKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGRVLFLCDQV   76 (189)
Q Consensus        20 ~~~~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~   76 (189)
                      ...+...++..||+|=+-+|..|..||.+          ..|..+|.-||.||+.|+.-++.-+...
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~  172 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL  172 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence            45556677778999999999999999999          3477799999999999998877665544

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

Probab=96.30  E-value=0.042  Score=35.71  Aligned_cols=45  Identities=18%  Similarity=0.252  Sum_probs=35.3

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee-----CCeEEEEEEEE
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL-----KGATLFSSVLE  164 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~-----~~~~l~~~~vk  164 (189)
                      +.|.++++||.|.+|+.+|.+.|++|.+.+....     .+...-.+.++
T Consensus         1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~   50 (73)
T cd04886           1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLE   50 (73)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEE
Confidence            3578889999999999999999999999887764     24443345555

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.

>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=96.20  E-value=0.06  Score=35.53  Aligned_cols=47  Identities=11%  Similarity=0.133  Sum_probs=37.3

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEE
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLE  164 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk  164 (189)
                      ++|.+.+.+++|.+.+++..|.+.+..+.+.+.....  +...-.+.+.
T Consensus         1 ~yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~   49 (79)
T cd04881           1 YYLRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTH   49 (79)
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEc
Confidence            4789999999999999999999999999999877653  4443234444

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.

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

Probab=96.17  E-value=0.061  Score=36.27  Aligned_cols=63  Identities=14%  Similarity=0.106  Sum_probs=43.8

Q ss_pred             EEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          121 NIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG-ATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       121 ~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~-~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      -+..+++||.|.+++..|.+.|+.+.+....+..+ ..-+.|.++.. +.-.....+.+...|.+
T Consensus         3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~-~~~~~~~~~~~l~~l~~   66 (75)
T cd04880           3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFE-GHIDDPDVKEALEELKR   66 (75)
T ss_pred             EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEE-CCCCCHHHHHHHHHHHH
Confidence            34456789999999999999999999998888765 55567777733 31113344445555544

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

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=95.80  E-value=0.1  Score=44.75  Aligned_cols=69  Identities=14%  Similarity=0.188  Sum_probs=54.4

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      ..+.|.+.|+++||+...|.++|.++|++|.+.+.++  .+|.|.-.+.+... .  ...+.++|+++|..+=+
T Consensus         5 ~~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~-~--~~~~~~~L~~~L~~l~~   75 (286)
T PRK06027          5 QRYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGD-G--LIFNLETLRADFAALAE   75 (286)
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeC-C--CCCCHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999  88865444444421 1  13568899999887643

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

Probab=95.72  E-value=0.076  Score=35.43  Aligned_cols=62  Identities=10%  Similarity=0.128  Sum_probs=43.6

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEEeeeCCccccCHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL-KGATLFSSVLEGTHGGDRIIRVEETRELLL  183 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~-~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~  183 (189)
                      .+.+.+++++|++.+|+.+|.+.+.+|...+.+.. ++.+--.|.++..  + .....+.|.++|.
T Consensus         2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~--~-~~~~l~~l~~~L~   64 (76)
T cd04888           2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTS--T-MNGDIDELLEELR   64 (76)
T ss_pred             EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcC--c-hHHHHHHHHHHHh
Confidence            57788899999999999999999999999987654 3544445667632  1 1124455555544

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.

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=95.61  E-value=0.13  Score=44.17  Aligned_cols=67  Identities=10%  Similarity=0.046  Sum_probs=51.8

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      .+.|.+.|+++||+...+.+.|-++|++|.+.+..+  .++.|  .+.++....  ...+.++|+++|..+-.
T Consensus         7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F--~m~~~~~~p--~~~~~~~L~~~L~~l~~   75 (286)
T PRK13011          7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRF--FMRVEFHSE--EGLDEDALRAGFAPIAA   75 (286)
T ss_pred             eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeE--EEEEEEecC--CCCCHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999974  33443  344443212  24679999999987643

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=95.60  E-value=0.078  Score=45.65  Aligned_cols=69  Identities=7%  Similarity=0.084  Sum_probs=51.1

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEE--eeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVT--TLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is--~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      .+.|.+.|++++|+...|-+.|-+.|++|++++-.  +..+.++-.+.+....  ...++.++|+++|..+-+
T Consensus         9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~~--~~~~~~~~l~~~l~~l~~   79 (289)
T PRK13010          9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQS--AEAASVDTFRQEFQPVAE   79 (289)
T ss_pred             CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcCC--CCCCCHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999985  3334433232233111  125789999999987643

>PRK04435 hypothetical protein; Provisional

Probab=95.56  E-value=0.11  Score=40.32  Aligned_cols=67  Identities=13%  Similarity=0.248  Sum_probs=50.1

Q ss_pred             cCceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCccccCHHHHHHHHH
Q 036599          114 GGNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRIIRVEETRELLL  183 (189)
Q Consensus       114 ~~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~  183 (189)
                      .+..+.|.+.+.+++|+|.+|+++|.+.+.+|...+.+. .+|...-+|.++..   +.....++|-++|.
T Consensus        66 ~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs---~~~~~L~~Li~~L~  133 (147)
T PRK04435         66 KGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTS---SMEGDIDELLEKLR  133 (147)
T ss_pred             CCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeC---ChHHHHHHHHHHHH
Confidence            367899999999999999999999999999999998765 35655556777732   11234555555554

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

Probab=95.42  E-value=0.15  Score=30.18  Aligned_cols=35  Identities=11%  Similarity=0.171  Sum_probs=31.2

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK  154 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~  154 (189)
                      |.+.|+..+|.+.+++.+|...++.+.........
T Consensus         1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            46788889999999999999999999999987754

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

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

Probab=95.41  E-value=0.26  Score=30.71  Aligned_cols=45  Identities=13%  Similarity=0.110  Sum_probs=35.8

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEE
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLE  164 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk  164 (189)
                      |++.|.+++|.+..++.+|.+.++++.+..+...+ +.....+.++
T Consensus         1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~   46 (71)
T cd04876           1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLE   46 (71)
T ss_pred             CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEE
Confidence            46778899999999999999999999999887765 4443345555

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

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=95.40  E-value=0.17  Score=43.39  Aligned_cols=63  Identities=6%  Similarity=-0.022  Sum_probs=50.5

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      .|.+.|++++|+...|-..|-+.|++|++++-+..  ++.|+-.+.+..   .+...+.++|+++|..
T Consensus         2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~~---~~~~~~~~~l~~~l~~   66 (280)
T TIGR00655         2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQL---EGFRLEESSLLAAFKS   66 (280)
T ss_pred             EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEEe---CCCCCCHHHHHHHHHH
Confidence            57899999999999999999999999999998884  466653444442   2224788999999887

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.

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

Probab=95.20  E-value=0.24  Score=32.08  Aligned_cols=36  Identities=19%  Similarity=0.147  Sum_probs=31.9

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK  154 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~  154 (189)
                      .+.+.+++++|.+.+++..|.+.+..|.+.+....+
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~   37 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIER   37 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccC
Confidence            467889999999999999999999999998887653

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.

>PRK08577 hypothetical protein; Provisional

Probab=95.00  E-value=0.35  Score=36.71  Aligned_cols=66  Identities=20%  Similarity=0.225  Sum_probs=48.3

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      +.+.|.+.+.+++|+|.+|+++|.+.+.++.+.+..+..  +.+.-.+.+++. +  ......++.+.|.+
T Consensus        55 ~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~-~--~~~~l~~l~~~L~~  122 (136)
T PRK08577         55 KLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLS-K--SDIDLEELEEELKK  122 (136)
T ss_pred             cEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeC-C--chhhHHHHHHHHHc
Confidence            468899999999999999999999999999998877753  444335666632 1  11345666666653

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=94.98  E-value=0.021  Score=55.62  Aligned_cols=59  Identities=27%  Similarity=0.431  Sum_probs=51.9

Q ss_pred             hhhhhhchHHHHHHHHHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           21 AVYKSKNLEAERRRRQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        21 ~~~~~~h~~~ER~RR~kln~~f~~LRsl-------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      ...+..|+..|++=|--||+++..|+.+       +-|.+.+.-||+||++|+..-+.|......+
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l  339 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL  339 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence            4568999999999999999999999999       6799999999999999998877776665543

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

Probab=94.86  E-value=0.33  Score=32.63  Aligned_cols=43  Identities=9%  Similarity=0.174  Sum_probs=36.0

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .|+|.|.+++|++.+|+.+|.+.+..+.+.++.+. +. + .|.++
T Consensus         2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~-i-~l~i~   44 (74)
T cd04877           2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GR-I-YLNFP   44 (74)
T ss_pred             EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-Ce-E-EEEeE
Confidence            47889999999999999999999999999999775 44 2 35555

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

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

Probab=94.65  E-value=0.26  Score=31.57  Aligned_cols=58  Identities=17%  Similarity=0.147  Sum_probs=42.2

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      +.+.+++++|.+.+|+..|.+.++.|.+..+....  +.....|.+.    +  . ....+.+.|..
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~----~--~-~~~~l~~~l~~   61 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVD----S--P-VPEEVLEELKA   61 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcC----C--C-CCHHHHHHHHc
Confidence            56778899999999999999999999999988754  5554445443    1  1 24566665543

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

>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=94.59  E-value=0.55  Score=32.00  Aligned_cols=60  Identities=17%  Similarity=0.174  Sum_probs=42.6

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEEeeeCCccccCHHHHHHHHH
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLEGTHGGDRIIRVEETRELLL  183 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk~~~~~~~~~s~~~lk~~L~  183 (189)
                      +.+..++++|.|.++++.|.++|+.+.+....+.. +...+.|.+... +   ..+...+.++|.
T Consensus         4 l~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~-~---~~~~~~~~~~l~   64 (80)
T cd04905           4 IVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE-G---HIEDPNVAEALE   64 (80)
T ss_pred             EEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE-C---CCCCHHHHHHHH
Confidence            44555678999999999999999999999888763 355567777733 2   233445555443

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

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

Probab=94.27  E-value=0.62  Score=33.16  Aligned_cols=48  Identities=4%  Similarity=0.119  Sum_probs=39.0

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEEe
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLEG  165 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk~  165 (189)
                      .-|-+..++++|.|.++|..|...|+.+.+...-+.. ...-+.|.++.
T Consensus        15 tslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDi   63 (90)
T cd04931          15 ISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINL   63 (90)
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEE
Confidence            4555556788999999999999999999999999964 33456788884

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.

>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=94.18  E-value=0.27  Score=30.98  Aligned_cols=45  Identities=11%  Similarity=0.313  Sum_probs=36.3

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEE
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLE  164 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk  164 (189)
                      |.+.++++||.+.+++..|.+.|..|....+...+ +..+..|.+.
T Consensus         1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~   46 (56)
T cd04889           1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFS   46 (56)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEEC
Confidence            35678899999999999999999999988887765 5555455555

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

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

Probab=94.12  E-value=0.39  Score=30.85  Aligned_cols=33  Identities=12%  Similarity=0.206  Sum_probs=29.9

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT  152 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~  152 (189)
                      +.+.+++++|.+.+++..|.+.++++.+.....
T Consensus         2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~   34 (71)
T cd04903           2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSR   34 (71)
T ss_pred             EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEe
Confidence            567888999999999999999999999888766

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.

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

Probab=94.12  E-value=0.93  Score=29.01  Aligned_cols=46  Identities=15%  Similarity=0.328  Sum_probs=36.1

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk  164 (189)
                      .+.+.+.+++|.+.+|+..|.+.+..+...+....  ++.....|.+.
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~   49 (72)
T cd04878           2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVE   49 (72)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEE
Confidence            46778889999999999999999999999988764  34443345554

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

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

Probab=94.10  E-value=0.85  Score=29.89  Aligned_cols=59  Identities=10%  Similarity=0.109  Sum_probs=41.2

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      .|.+..+++||.|.+++..|.+.|+.+.+......  .+.....|.+..   .    +.+++.++|..
T Consensus         3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~---~----~~~~~~~~L~~   63 (72)
T cd04883           3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQT---M----NPRPIIEDLRR   63 (72)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEec---C----CHHHHHHHHHH
Confidence            56778889999999999999999999998865543  234333444441   1    23466666653

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.

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

Probab=94.00  E-value=0.62  Score=31.54  Aligned_cols=45  Identities=4%  Similarity=0.189  Sum_probs=36.9

Q ss_pred             EEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEEee
Q 036599          122 IIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG-ATLFSSVLEGT  166 (189)
Q Consensus       122 i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~-~~l~~~~vk~~  166 (189)
                      +..+++||.|.++|..|...|+.+++...-+..+ ..-+.|.++..
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            3446789999999999999999999999999755 34567888843

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

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

Probab=93.84  E-value=0.63  Score=30.46  Aligned_cols=35  Identities=6%  Similarity=0.231  Sum_probs=31.0

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL  153 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~  153 (189)
                      -+.+.++++||.|.++++.|.+.|+++........
T Consensus         3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            46778899999999999999999999998876665

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.

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

Probab=93.50  E-value=0.8  Score=30.39  Aligned_cols=34  Identities=9%  Similarity=0.173  Sum_probs=29.3

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL  153 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~  153 (189)
                      +.+.-+++||.|.++++.|.+.|..|++......
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            4556678999999999999999999999877664

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.

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=93.48  E-value=0.29  Score=39.68  Aligned_cols=66  Identities=15%  Similarity=0.143  Sum_probs=53.4

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.|++.++++||++..|.++|.++|..+..++.+..+|.|--.+.+.   +.  ..+...|+.+|...-
T Consensus         7 ~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lvs---~~--~~~~~~le~~L~~l~   72 (190)
T PRK11589          7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLS---GS--WNAITLIESTLPLKG   72 (190)
T ss_pred             cEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEEe---CC--hhHHHHHHHHHHhhh
Confidence            4578999999999999999999999999999999999999874444443   22  347788888876543

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

Probab=93.41  E-value=0.57  Score=29.92  Aligned_cols=56  Identities=16%  Similarity=0.283  Sum_probs=38.6

Q ss_pred             EEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          120 INIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       120 I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      |.+.-+++||.|.+++..|.+.|+.|.+...+...  +...  +.+...  +     .+.+.+.|.+
T Consensus         2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~--v~~~ve--~-----~~~~~~~L~~   59 (65)
T cd04882           2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKAL--LIFRTE--D-----IEKAIEVLQE   59 (65)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEE--EEEEeC--C-----HHHHHHHHHH
Confidence            45666789999999999999999999888765543  3332  334411  1     5566666653

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.

>PRK06737 acetolactate synthase 1 regulatory subunit; Validated

Probab=93.21  E-value=0.61  Score=32.28  Aligned_cols=65  Identities=6%  Similarity=0.055  Sum_probs=45.8

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      ..|.+.-.++||+|.++...|.--|+.|.+.++...++.-++-+++-+. ++  .-..+.|..-|.+.
T Consensus         3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~~~sriti~~~-~~--~~~i~qi~kQL~KL   67 (76)
T PRK06737          3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDTSGVSEMKLTAV-CT--ENEATLLVSQLKKL   67 (76)
T ss_pred             EEEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCCCCeeEEEEEEE-CC--HHHHHHHHHHHhCC
Confidence            3577778899999999999999999999999999876554445555422 33  23344555555443

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

Probab=93.16  E-value=1.2  Score=29.02  Aligned_cols=44  Identities=14%  Similarity=0.194  Sum_probs=35.9

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .|.|..+++||.|.+++.+|.+.|+.|.+.-+...++.  ..+.+.
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            46677889999999999999999999999988776663  345555

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.

>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=92.85  E-value=1.5  Score=29.88  Aligned_cols=54  Identities=13%  Similarity=0.178  Sum_probs=40.4

Q ss_pred             CCCCChHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          125 GKKRGNFTKLVEAMNALGFVFGDTSVTTL-KGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       125 ~~~~g~l~~il~aLe~l~L~V~~a~is~~-~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      ++++|.|.++|..|+..|+.+.+...-+. +...-|.|.++.. +.     .+.++++|..
T Consensus         8 ~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e-~~-----~~~i~~~l~~   62 (74)
T cd04929           8 KNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCE-CD-----QRRLDELVQL   62 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEE-cC-----HHHHHHHHHH
Confidence            67899999999999999999999999996 3445567888843 32     1255555543

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.

>TIGR00119 acolac_sm acetolactate synthase, small subunit

Probab=92.82  E-value=0.77  Score=36.09  Aligned_cols=65  Identities=14%  Similarity=0.229  Sum_probs=46.9

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .|.+.-+++||.|.+|...|...|+.+.+..+...++.-.+.+++.+. ++  .-..+.|..-|.+.+
T Consensus         3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~-~d--~~~i~qi~kQl~Kli   67 (157)
T TIGR00119         3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVV-GD--DKVLEQITKQLNKLV   67 (157)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEE-CC--HHHHHHHHHHHhcCc
Confidence            567777899999999999999999999999999876332333444422 22  345677777776654

acetohydroxyacid synthase is a synonym.

>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional

Probab=92.79  E-value=0.54  Score=33.22  Aligned_cols=66  Identities=9%  Similarity=0.067  Sum_probs=49.2

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .|.+.-.++||+|.++...|...|+.+.+.+++...+.-++-+++-+..++  .-..+.|..-|.+.+
T Consensus         4 ~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d--~~~ieqI~kQL~Kli   69 (84)
T PRK13562          4 ILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQD--DTSLHILIKKLKQQI   69 (84)
T ss_pred             EEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCC--HHHHHHHHHHHhCCc
Confidence            567777899999999999999999999999999987766666666632133  344556666665544

>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B

Probab=92.29  E-value=0.49  Score=31.27  Aligned_cols=58  Identities=17%  Similarity=0.236  Sum_probs=39.2

Q ss_pred             CCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          126 KKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       126 ~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ++||+|.+|+..|.--|+.|.+.+++..++.-++.+++.+. ++  .-.++.|..-|.+.+
T Consensus         1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~-~~--~~~i~~l~~Ql~Kli   58 (63)
T PF13710_consen    1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVS-GD--DREIEQLVKQLEKLI   58 (63)
T ss_dssp             SSTTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEE-S---CCHHHHHHHHHHCST
T ss_pred             CCcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEe-eC--chhHHHHHHHHhccC
Confidence            36999999999999999999999999944333334444422 22  345666777776654

>PRK07334 threonine dehydratase; Provisional

Probab=92.26  E-value=1.5  Score=39.12  Aligned_cols=48  Identities=15%  Similarity=0.224  Sum_probs=40.5

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee-----CCeEEEEEEEE
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL-----KGATLFSSVLE  164 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~-----~~~~l~~~~vk  164 (189)
                      .+.|.|.+.+++|+|.+|+.+|.+.+++|.++++...     ++...-.|+++
T Consensus       326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~  378 (403)
T PRK07334        326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIE  378 (403)
T ss_pred             EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEE
Confidence            4889999999999999999999999999999998764     45554456666

>CHL00100 ilvH acetohydroxyacid synthase small subunit

Probab=92.22  E-value=1.2  Score=35.52  Aligned_cols=68  Identities=15%  Similarity=0.260  Sum_probs=49.8

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHhc
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIRG  188 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~~  188 (189)
                      ..|.+.-.++||+|.+|...|...|++|.+.++....+.-+..+++- ..+++ .. .+.|...|.+.+.-
T Consensus         3 ~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~~sr~TIv-v~~~~-~~-ieqL~kQL~KLidV   70 (174)
T CHL00100          3 HTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQKGISRITMV-VPGDD-RT-IEQLTKQLYKLVNI   70 (174)
T ss_pred             EEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCCccEEEEE-EECCH-HH-HHHHHHHHHHHhHh
Confidence            35777788999999999999999999999999987433333344444 22332 22 78999999887753

>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]

Probab=92.00  E-value=1.3  Score=37.94  Aligned_cols=68  Identities=12%  Similarity=0.153  Sum_probs=52.1

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.+.++|++++|+...|-..|.+.|..|++++-.+  ..++||--..+.   .++...+.+.+.+++..+-
T Consensus         6 ~~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf~D~~~g~FFmR~~f~---~~~~~~~~~~l~~~f~~~a   75 (287)
T COG0788           6 DTFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQFDDPETGRFFMRVEFE---GEGGPLDREALRAAFAPLA   75 (287)
T ss_pred             cceEEEEecCCCCCcHHHHHHHHHHcCCceeecccccccccCeEEEEEEEe---cCCCcccHHHHHHHHHHHH
Confidence            4578999999999999999999999999999998775  245555444444   2223478888888887643

>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed

Probab=91.96  E-value=1.3  Score=34.98  Aligned_cols=64  Identities=16%  Similarity=0.300  Sum_probs=45.4

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..|.+.-+++||.|.+|...|...|+.+.+..+....  +...-++++.   ++  .-..+.|..-|.+.+
T Consensus         3 ~~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~---~~--~~~i~qi~kQl~KLi   68 (161)
T PRK11895          3 HTLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTS---GD--EQVIEQITKQLNKLI   68 (161)
T ss_pred             EEEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEE---CC--HHHHHHHHHHHhccc
Confidence            3567777899999999999999999999999988875  3333344444   22  334556665555544

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

Probab=91.66  E-value=0.44  Score=34.08  Aligned_cols=68  Identities=15%  Similarity=0.184  Sum_probs=54.0

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      -+.|+|.-.+++|+...+..+|-++|.++.+.+=+..+|+|--.+.+. .  +....+...+++.|....+
T Consensus         3 ~avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV~-~--~~~~~d~~~lr~~l~~~~~   70 (90)
T COG3830           3 RAVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVD-I--SKEVVDFAALRDELAAEGK   70 (90)
T ss_pred             eEEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeEEc-C--ChHhccHHHHHHHHHHHHH
Confidence            367888888999999999999999999999999999999884445555 2  2236778888887776554

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=91.33  E-value=0.29  Score=45.00  Aligned_cols=51  Identities=22%  Similarity=0.249  Sum_probs=43.7

Q ss_pred             hhhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHHHHHH
Q 036599           22 VYKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGRVLFL   72 (189)
Q Consensus        22 ~~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~kv~~L   72 (189)
                      ..+..++..||-|=..||+-|..|--+          -.|.-||-.|+.-|-.|++||.|-
T Consensus       525 ERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  525 ERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            345678888999989999999999777          458889999999999999999763

>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH)

Probab=91.00  E-value=2.5  Score=31.42  Aligned_cols=48  Identities=0%  Similarity=0.045  Sum_probs=37.5

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEEee
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG-ATLFSSVLEGT  166 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~-~~l~~~~vk~~  166 (189)
                      -+-+..++++|.|.++|..|...|+.+++...-+..+ ..-|.|.|...
T Consensus        43 Slifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~~eY~FfIdie   91 (115)
T cd04930          43 TLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEGGDLEVLVRCE   91 (115)
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCCceEEEEEEEE
Confidence            3444447789999999999999999999999999733 34457777743

ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.

>PF05088 Bac_GDH: Bacterial NAD-glutamate dehydrogenase

Probab=90.95  E-value=1.4  Score=45.83  Aligned_cols=71  Identities=13%  Similarity=0.205  Sum_probs=56.3

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-----CeEEEEEEEEeeeCCccccCHHHHHHHHHHHHhc
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-----GATLFSSVLEGTHGGDRIIRVEETRELLLKIIRG  188 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-----~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~~  188 (189)
                      +.+.++|.....+..|++++-.|+++||.|+...-..+.     ..++|.|.+...  ++...+...+++.|..++..
T Consensus       488 ~~~~lkiy~~~~~~~Ls~vlPilenlGl~V~~e~~~~i~~~~~~~~~i~~F~l~~~--~~~~~~~~~~~~~~~~a~~~  563 (1528)
T PF05088_consen  488 GRLRLKIYHPGEPLPLSDVLPILENLGLRVIDERPYEIRRADGRRVWIHDFGLQYP--DGDALDLDDIRERFEEAFEA  563 (1528)
T ss_pred             CeEEEEEEcCCCCcCHHHHHHHHHhCCCEEEEEecceeecCCCceEEEEEEEEecC--CCccccHHHHHHHHHHHHHH
Confidence            468999999889999999999999999999998766543     367888999843  22357788888888776653

>PRK00227 glnD PII uridylyl-transferase; Provisional

Probab=90.94  E-value=1.6  Score=42.08  Aligned_cols=67  Identities=9%  Similarity=0.068  Sum_probs=56.3

Q ss_pred             EEEEEEe-CCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          118 LRINIIF-GKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       118 v~I~i~c-~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      ..+.|.. ++++|.++++..+|--.|+.|.+|++.+ +|.....|.|....|  ...++..+.|.+...+.
T Consensus       547 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~a~~~~-~~~~~~~~~v~~~~~--~~~~~~~~~~~~~~~~~  614 (693)
T PRK00227        547 GFFTVIWHGDYPRELVRVLALIAAKGWNILSARMVA-NGPWSAEFDVRANGP--QDFDPQEFLQAYKSGVY  614 (693)
T ss_pred             CeEEEEecCCcccHHHHHHHHHHhcCceeeEeEEec-CCceEEEEEEecCCC--CCCChHHHHHHHHHhhc
Confidence            4566665 9999999999999999999999999999 888888899985433  47788999998887654

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

Probab=90.42  E-value=1.3  Score=28.92  Aligned_cols=44  Identities=14%  Similarity=0.170  Sum_probs=34.0

Q ss_pred             EEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEE
Q 036599          121 NIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLE  164 (189)
Q Consensus       121 ~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk  164 (189)
                      -+..++++|.+.++.+.|.+.|+.+.+..++.  .++.....|.+.
T Consensus         3 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~   48 (73)
T cd04902           3 VVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVD   48 (73)
T ss_pred             EEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeC
Confidence            45678899999999999999999998887665  345654445544

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

>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional

Probab=90.36  E-value=2.9  Score=28.87  Aligned_cols=65  Identities=12%  Similarity=0.106  Sum_probs=47.1

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.+.-.++||+|.+++..+.--|+.|.+.++....+.-+..+++-+.  +  .-..+.|..-|.+.+
T Consensus         4 ~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~--~--~~~i~ql~kQL~KL~   68 (76)
T PRK11152          4 HQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA--S--ERPIDLLSSQLNKLV   68 (76)
T ss_pred             EEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC--C--CchHHHHHHHHhcCc
Confidence            3566777789999999999999999999999999965544445555421  2  445666666666543

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

Probab=90.00  E-value=1.8  Score=42.29  Aligned_cols=50  Identities=14%  Similarity=0.165  Sum_probs=45.6

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEE
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLE  164 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk  164 (189)
                      .+...|-|.|+++|.+|+.+..++...|++|+.|+|.+ .+|..+.+|.|.
T Consensus       682 ~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~  732 (867)
T COG2844         682 SGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVL  732 (867)
T ss_pred             CCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEe
Confidence            35578999999999999999999999999999999988 578899999887

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=89.95  E-value=0.3  Score=43.98  Aligned_cols=36  Identities=31%  Similarity=0.526  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHH
Q 036599           29 EAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQ   64 (189)
Q Consensus        29 ~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~   64 (189)
                      -+-|+||++-|.-|+.|-.+          .||+||+-=|-.|||-
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            46799999999999999988          7999999999999984

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

Probab=89.63  E-value=0.29  Score=46.60  Aligned_cols=40  Identities=35%  Similarity=0.616  Sum_probs=35.8

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHH
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIR   63 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk   63 (189)
                      +.+-..+-|-||-|-|+-|+.|..+          .|||||+-=||.|.+
T Consensus        47 kEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   47 KEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH
Confidence            4555668899999999999999998          899999999999986

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

Probab=88.51  E-value=0.52  Score=30.61  Aligned_cols=44  Identities=7%  Similarity=-0.000  Sum_probs=33.3

Q ss_pred             EEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          121 NIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       121 ~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      -+.+.+++|++.+++..|.+.+..+...+....++...-.|.++
T Consensus         3 ~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~   46 (69)
T cd04901           3 LHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDID   46 (69)
T ss_pred             EEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcC
Confidence            45678899999999999999999997776655445554444444

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-

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

Probab=87.21  E-value=2.9  Score=27.48  Aligned_cols=59  Identities=12%  Similarity=0.108  Sum_probs=38.0

Q ss_pred             EEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          121 NIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       121 ~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      .+.-+.+||.|.++++.|.+ |.+|+..+-...+ +...-.+.++..  +  .-...+|.++|.+
T Consensus         2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~~~~v~v~ie~~--~--~~~~~~i~~~L~~   61 (68)
T cd04885           2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGDEARVLVGIQVP--D--REDLAELKERLEA   61 (68)
T ss_pred             EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCCceEEEEEEEeC--C--HHHHHHHHHHHHH
Confidence            45667899999999999999 9999988776643 111113444521  1  2345556665543

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.

>COG4492 PheB ACT domain-containing protein [General function prediction only]

Probab=86.98  E-value=5  Score=30.91  Aligned_cols=67  Identities=12%  Similarity=0.158  Sum_probs=53.1

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      +..+.+.+.-+++.|.|+++|.++...++.|.+.+=+. .+|+.--++.+...   +...+++.|..+|.+
T Consensus        70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtlsi~~s---sm~~~V~~ii~kl~k  137 (150)
T COG4492          70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGRANVTLSIDTS---SMEKDVDKIIEKLRK  137 (150)
T ss_pred             ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCceeeEEEEEEch---hhhhhHHHHHHHHhc
Confidence            45678888899999999999999999999999987665 78887666777632   345678888777764

>PRK11899 prephenate dehydratase; Provisional

Probab=86.84  E-value=6.9  Score=33.52  Aligned_cols=64  Identities=8%  Similarity=-0.056  Sum_probs=46.3

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      ..|-+..+++||.|.++|.+|...|+.++...+-+.. +.+-|.|.++.. +   ......++++|..+
T Consensus       195 tsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~F~id~e-g---~~~d~~v~~aL~~l  259 (279)
T PRK11899        195 TTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSFTATQFYADIE-G---HPEDRNVALALEEL  259 (279)
T ss_pred             EEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCCceEEEEEEEE-C---CCCCHHHHHHHHHH
Confidence            3444445789999999999999999999999999974 456677888843 3   22334456665543

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=86.61  E-value=6.8  Score=31.68  Aligned_cols=67  Identities=1%  Similarity=0.015  Sum_probs=49.9

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC----CeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK----GATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~----~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      +.|.+.-.++||++..+.++|-+.|++|.+.+.-+.+    +.-++.+.+++.-.  ......+|+++|..+=
T Consensus        96 ~~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~lP--~~~~~~~L~~~l~~l~  166 (190)
T PRK11589         96 VWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSP--ASQDAANIEQAFKALC  166 (190)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEEcC--CCCCHHHHHHHHHHHH
Confidence            7788888999999999999999999999999888865    32233444442211  2456888888887654

>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed

Probab=86.13  E-value=5.3  Score=28.90  Aligned_cols=67  Identities=9%  Similarity=0.092  Sum_probs=50.0

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      +...|.+.-.+.||+|.+|...|..-|..|.+.++...++.-++-+++- .. +  .-..+.|..-|.+.+
T Consensus         7 ~~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~~iSRmtiv-v~-~--~~~i~Qi~kQL~KLi   73 (96)
T PRK08178          7 DNVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDGDKSRIWLL-VN-D--DQRLEQMISQIEKLE   73 (96)
T ss_pred             CCEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCCCceEEEEE-Ec-C--chHHHHHHHHHhCCc
Confidence            4467888888999999999999999999999999998877666666665 32 2  235566666555543

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

Probab=85.08  E-value=8.6  Score=37.46  Aligned_cols=49  Identities=6%  Similarity=0.049  Sum_probs=40.9

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEEe
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLEG  165 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk~  165 (189)
                      .+.|.|.+.+++|+|.+|..+|.+.++.|.++++...  ++.+.-.|++++
T Consensus       666 ~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ieV  716 (743)
T PRK10872        666 SLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIEI  716 (743)
T ss_pred             EEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEEE
Confidence            3578899999999999999999999999999999775  455544677774

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

Probab=84.92  E-value=8.4  Score=37.10  Aligned_cols=49  Identities=20%  Similarity=0.199  Sum_probs=41.4

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEEe
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL-KGATLFSSVLEG  165 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~-~~~~l~~~~vk~  165 (189)
                      .+.|.|.+.+++|+|.+|+.+|-+.+..|.++++... ++.+.-.|.+++
T Consensus       610 ~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~~~~~~~~~ieV  659 (683)
T TIGR00691       610 IVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGKREAILNITVEI  659 (683)
T ss_pred             EEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCEEEEEEEEEE
Confidence            4678999999999999999999999999999999876 355544577773

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

>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH)

Probab=84.11  E-value=8.4  Score=24.38  Aligned_cols=59  Identities=7%  Similarity=0.050  Sum_probs=36.7

Q ss_pred             EEEEEeC---CCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          119 RINIIFG---KKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       119 ~I~i~c~---~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .|.+.+.   ..++.+.+++++|.+.|+.|.-...+..+..+  +|.+. .      -+.....++|++.+
T Consensus         3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~~s~~~i--s~~v~-~------~~~~~~~~~lh~~~   64 (66)
T cd04922           3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGSSERNI--SAVID-E------DDATKALRAVHERF   64 (66)
T ss_pred             EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecCcccEE--EEEEe-H------HHHHHHHHHHHHHH
Confidence            3455542   45899999999999999999776554433222  55665 1      11344455555544

This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=83.94  E-value=0.97  Score=42.16  Aligned_cols=32  Identities=38%  Similarity=0.659  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHH
Q 036599           32 RRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIR   63 (189)
Q Consensus        32 R~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk   63 (189)
                      ++-|++||.-+..|-||          .||.|||-=++.|+.
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            45689999999999999          899999999999975

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

Probab=83.71  E-value=10  Score=36.71  Aligned_cols=49  Identities=14%  Similarity=0.096  Sum_probs=40.8

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEEe
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-GATLFSSVLEG  165 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-~~~l~~~~vk~  165 (189)
                      .+.|.|.+.+++|+|.+|..+|.+.++.|.++++...+ +.+.-.|.+++
T Consensus       626 ~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ieV  675 (702)
T PRK11092        626 IAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLTA  675 (702)
T ss_pred             EEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEEE
Confidence            45789999999999999999999999999999987765 44444577774

---

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	189
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	5e-06
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	7e-04
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	9e-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 = 42.0 bits (99), Expect = 5e-06
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 7/64 (10%)

Query: 29 EAERRRRQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVEP 81
            E+R R  +ND++++L+ L       + K  V+  AI YIR L+     L  + L +  
Sbjct: 12 AIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 71

Query: 82 LEEE 85
             +
Sbjct: 72 AVHK 75

>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 = 35.8 bits (83), Expect = 7e-04
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 12/53 (22%)

Query: 29 EAERRRRQKLNDRLLKLRSLMK------------KETVIEDAITYIRQLKGRV 69
          E ERRRR K+N+ +++L  ++             K  ++  A  YI++L+   
Sbjct: 11 EVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN 63

>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 = 36.2 bits (84), Expect = 9e-04
 Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 9/49 (18%)

Query: 29 EAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGR 68
            ER+RR +L      LR             K  +++ A  YI  ++  
Sbjct: 12 VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAE 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	189
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.63
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.5
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.49
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.47
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.46
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.42
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.4
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.38
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.37
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.37
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.27
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.05
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.91
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.7
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.64
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.21
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	97.79
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.76
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.3
1u8s_A	192	Glycine cleavage system transcriptional repressor,	97.28
2nyi_A	195	Unknown protein; protein structure initiative, PSI	97.27
2nyi_A	195	Unknown protein; protein structure initiative, PSI	96.72
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	96.71
1u8s_A	192	Glycine cleavage system transcriptional repressor,	96.52
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	96.04
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	95.94
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	95.71
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	95.39
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	95.36
2f1f_A	164	Acetolactate synthase isozyme III small subunit; f	94.41
3nrb_A	287	Formyltetrahydrofolate deformylase; N-terminal ACT	93.9
2pc6_A	165	Probable acetolactate synthase isozyme III (small;	93.4
2fgc_A	193	Acetolactate synthase, small subunit; regulatory s	93.16
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	92.07
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	89.36

>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=99.63  E-value=5.4e-16  Score=108.42  Aligned_cols=60  Identities=28%  Similarity=0.466  Sum_probs=56.1

Q ss_pred             hhhhhhchHHHHHHHHHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 036599           21 AVYKSKNLEAERRRRQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE   80 (189)
Q Consensus        21 ~~~~~~h~~~ER~RR~kln~~f~~LRsl-------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l~   80 (189)
                      ...+..|+.+||+||.+||+.|..|++|       +||++||.+||+||++||.+++.|+.+...+.
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~   70 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999       89999999999999999999999999987764

>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=99.50  E-value=3.5e-14  Score=98.65  Aligned_cols=61  Identities=18%  Similarity=0.343  Sum_probs=56.1

Q ss_pred             chhhhhhchHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 036599           20 KAVYKSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE   80 (189)
Q Consensus        20 ~~~~~~~h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l~   80 (189)
                      ....+..|+..||+||..||+.|..|+++        ++|++||..||+||+.|++++++|+.+...+.
T Consensus         9 ~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A            9 DADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             hHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999999        78999999999999999999999999987653

>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=99.49  E-value=4.5e-14  Score=98.71  Aligned_cols=57  Identities=18%  Similarity=0.379  Sum_probs=53.1

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE   80 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l~   80 (189)
                      +..|+..||+||..||+.|..|+++        ++|++||.+||+||+.|+.++++|+.++..+.
T Consensus         3 R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~   67 (83)
T 1nkp_B            3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999        79999999999999999999999998887653

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

Probab=99.47  E-value=5.3e-14  Score=95.43  Aligned_cols=54  Identities=26%  Similarity=0.437  Sum_probs=49.7

Q ss_pred             chhhhhhchHHHHHHHHHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHHHHHHH
Q 036599           20 KAVYKSKNLEAERRRRQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLC   73 (189)
Q Consensus        20 ~~~~~~~h~~~ER~RR~kln~~f~~LRsl-------~DKaSIl~dAI~YIk~Lq~kv~~Le   73 (189)
                      ....+.+|+.+||+||++||+.|..|++|       +||++||..||+||+.||..+.=|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            34567899999999999999999999999       8999999999999999999987664

>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=99.46  E-value=9.1e-14  Score=98.26  Aligned_cols=59  Identities=22%  Similarity=0.295  Sum_probs=53.3

Q ss_pred             hhhhhhchHHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           21 AVYKSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        21 ~~~~~~h~~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      ...+..|+..||+||..||+.|..||++         ++|++||.+||+||++|+.+.+.|+.++..+
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L   71 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999         7899999999999999999999888776544

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

Probab=99.42  E-value=2e-13  Score=101.44  Aligned_cols=56  Identities=32%  Similarity=0.412  Sum_probs=48.0

Q ss_pred             hhhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHHHHHHHhhhh
Q 036599           22 VYKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGRVLFLCDQVL   77 (189)
Q Consensus        22 ~~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~   77 (189)
                      ..+..|+.+||+||.+||+.|..|++|          +||++||.+||+||+.||.+++.|+....
T Consensus        26 ~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~   91 (118)
T 4ati_A           26 QKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   91 (118)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356799999999999999999999999          46999999999999999999999987654

>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=99.40  E-value=8.9e-14  Score=92.44  Aligned_cols=46  Identities=37%  Similarity=0.495  Sum_probs=42.6

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc------cc-------ccchHHHHHHHHHHHHHHH
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL------MK-------KETVIEDAITYIRQLKGRV   69 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl------~D-------KaSIl~dAI~YIk~Lq~kv   69 (189)
                      +.+|..+||+||.+||..|..|++|      .|       ||+||..||+||+.||+++
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            5689999999999999999999999      34       9999999999999999765

>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=99.38  E-value=8.1e-14  Score=93.08  Aligned_cols=47  Identities=30%  Similarity=0.552  Sum_probs=43.3

Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHHhc------------ccccchHHHHHHHHHHHHHHH
Q 036599           23 YKSKNLEAERRRRQKLNDRLLKLRSL------------MKKETVIEDAITYIRQLKGRV   69 (189)
Q Consensus        23 ~~~~h~~~ER~RR~kln~~f~~LRsl------------~DKaSIl~dAI~YIk~Lq~kv   69 (189)
                      .+..|+.+||+||.+||+.|..|++|            +||++||.+||+||++||++.
T Consensus         5 rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999            389999999999999999764

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

Probab=99.37  E-value=9.5e-13  Score=91.42  Aligned_cols=56  Identities=27%  Similarity=0.287  Sum_probs=51.6

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      +..|+..||+||..||+.|..|+++         +.|++||..|++||+.|+++.+.|+.++..+
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L   66 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4679999999999999999999999         5678899999999999999999999888765

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

Probab=99.37  E-value=4e-13  Score=91.73  Aligned_cols=48  Identities=31%  Similarity=0.454  Sum_probs=44.2

Q ss_pred             chhhhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHH
Q 036599           20 KAVYKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKG   67 (189)
Q Consensus        20 ~~~~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~   67 (189)
                      ....+..|..+||+||++||+.|..|++|          +|||+||..||+||+.|+.
T Consensus         6 ~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            6 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            34567899999999999999999999999          6999999999999999974

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

Probab=99.27  E-value=3.9e-12  Score=87.42  Aligned_cols=53  Identities=21%  Similarity=0.260  Sum_probs=43.6

Q ss_pred             hhhhhchHHHHHHHHHHHHHHHHHHhc------ccc----cchHHHHHHHHHHHHHHHHHHHh
Q 036599           22 VYKSKNLEAERRRRQKLNDRLLKLRSL------MKK----ETVIEDAITYIRQLKGRVLFLCD   74 (189)
Q Consensus        22 ~~~~~h~~~ER~RR~kln~~f~~LRsl------~DK----aSIl~dAI~YIk~Lq~kv~~Le~   74 (189)
                      ..+..|+..||+||..||+.|..||.+      .||    .+||..||+||+.||+++++++.
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            356789999999999999999999999      344    46999999999999999998854

>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=99.05  E-value=1.1e-10  Score=78.53  Aligned_cols=51  Identities=27%  Similarity=0.391  Sum_probs=45.6

Q ss_pred             chhhhhhchHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHH
Q 036599           20 KAVYKSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVL   70 (189)
Q Consensus        20 ~~~~~~~h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~   70 (189)
                      ....+..|+..||+|+..||+.|..||.+        +.|+.||..||+||..|++.++
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            45567889999999999999999999999        6788899999999999998653

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

Probab=98.91  E-value=1.2e-09  Score=71.59  Aligned_cols=47  Identities=30%  Similarity=0.316  Sum_probs=42.8

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHH
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVL   70 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~   70 (189)
                      +..|+..||+|+..||+.|..||.+         +.|..+|..||+||..|++.++
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            5678999999999999999999998         6788899999999999998763

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

Probab=98.70  E-value=8.2e-09  Score=89.02  Aligned_cols=50  Identities=26%  Similarity=0.464  Sum_probs=38.0

Q ss_pred             chhhhhhchHHHHHHHHHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHHH
Q 036599           20 KAVYKSKNLEAERRRRQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRV   69 (189)
Q Consensus        20 ~~~~~~~h~~~ER~RR~kln~~f~~LRsl-------~DKaSIl~dAI~YIk~Lq~kv   69 (189)
                      ....+..|+.+||+||++||..|..|++|       +||+|||..||+||+.|+..-
T Consensus         9 ~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A            9 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            34567889999999999999999999999       899999999999999998653

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

Probab=98.64  E-value=2e-08  Score=87.55  Aligned_cols=50  Identities=30%  Similarity=0.430  Sum_probs=44.5

Q ss_pred             cchhhhhhchHHHHHHHHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHH
Q 036599           19 DKAVYKSKNLEAERRRRQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGR   68 (189)
Q Consensus        19 ~~~~~~~~h~~~ER~RR~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~k   68 (189)
                      +....+.+|..+||+||++||..|..|++|          +||+|||..||+||+.|+..
T Consensus         9 ~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B            9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            335568899999999999999999999999          89999999999999999853

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

Probab=98.21  E-value=1.9e-07  Score=62.28  Aligned_cols=39  Identities=23%  Similarity=0.365  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHH
Q 036599           29 EAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKG   67 (189)
Q Consensus        29 ~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~   67 (189)
                      ..||+|...||+-|..||.+         +.|.-+|.-||+||..||.
T Consensus        20 erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           20 EEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            45899999999999999999         5778899999999999984

>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=97.79  E-value=0.00058  Score=46.71  Aligned_cols=67  Identities=18%  Similarity=0.121  Sum_probs=56.1

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.|.+.|+++||++.+|..+|.+.|..|.+.+.....+.+.-.+.++. . +  ....+.|.++|.++-
T Consensus         4 ~~~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~-~-~--~~~l~~l~~~L~~~~   70 (91)
T 1zpv_A            4 MKAIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSS-D-E--KQDFTYLRNEFEAFG   70 (91)
T ss_dssp             EEEEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE-S-S--CCCHHHHHHHHHHHH
T ss_pred             ceEEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEe-C-C--CCCHHHHHHHHHHHH
Confidence            45789999999999999999999999999999999988887766677763 2 2  457889999988764

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

Probab=97.76  E-value=3.1e-05  Score=53.46  Aligned_cols=43  Identities=30%  Similarity=0.434  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHhc----------ccccchHHHHHHHHHHHHHHHHHHHhhhh
Q 036599           35 RQKLNDRLLKLRSL----------MKKETVIEDAITYIRQLKGRVLFLCDQVL   77 (189)
Q Consensus        35 R~kln~~f~~LRsl----------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~   77 (189)
                      |..||+++..|.+|          ..|++||.-|++||+.||+..+.+..+..
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~   56 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   56 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77899999999999          56999999999999999987777665543

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

Probab=97.30  E-value=0.0003  Score=49.90  Aligned_cols=42  Identities=24%  Similarity=0.271  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHHH
Q 036599           30 AERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLF   71 (189)
Q Consensus        30 ~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~~   71 (189)
                      .||.|=..||+-|..||.+         ..|.-+|.-||+||..|++-+++
T Consensus        32 ~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           32 DPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            3577778999999999999         56778999999999999988754

>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=97.28  E-value=0.0018  Score=50.49  Aligned_cols=66  Identities=12%  Similarity=0.143  Sum_probs=54.6

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.|.|.|+++||++..|..+|.+.|++|..+++.+..+.++-.+.+..   +  ....+.|+++|..+.
T Consensus         5 ~~~~itv~~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~---~--~~~~~~l~~~L~~~~   70 (192)
T 1u8s_A            5 QHLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG---S--PSNITRVETTLPLLG   70 (192)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE---C--HHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEcCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEec---C--CCCHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999998888766666662   2  135678888887654

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

Probab=97.27  E-value=0.0015  Score=51.41  Aligned_cols=68  Identities=9%  Similarity=0.093  Sum_probs=50.7

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      ..+.|.|.|+++||++..|..+|.++|+.|+.+.+.+..+.++-.+.+. ....+.....+.|+++|..
T Consensus         4 ~~~~ltv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~-~~~~~~~~~~~~l~~~L~~   71 (195)
T 2nyi_A            4 QSFVVSVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVS-LNAKDGKLIQSALESALPG   71 (195)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEE-ESSSSSHHHHHHHHHHSTT
T ss_pred             eEEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEE-ecCccchhHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999888775566665 2211000115666666643

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

Probab=96.72  E-value=0.0086  Score=47.01  Aligned_cols=67  Identities=10%  Similarity=0.018  Sum_probs=52.9

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC------CeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK------GATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~------~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      ..+.|.|.|+++||++..|..+|-++|+.|..+...+.+      +.|+-.+.+...  +  ..+ +.|+++|..+..
T Consensus        92 ~~~iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~~--~--~~~-~~l~~~l~~~a~  164 (195)
T 2nyi_A           92 REYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAFP--F--PLY-QEVVTALSRVEE  164 (195)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEEE--G--GGH-HHHHHHHHHHHH
T ss_pred             cEEEEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEcC--C--Ccc-HHHHHHHHHHHH
Confidence            458999999999999999999999999999999999876      555444544422  1  345 889998887654

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

Probab=96.71  E-value=0.019  Score=38.32  Aligned_cols=48  Identities=10%  Similarity=0.090  Sum_probs=39.6

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .+.|.|.++++||+|.+|..+|.+.|+.|.+.+....++.+...|.++
T Consensus         5 ~~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~   52 (88)
T 2ko1_A            5 LAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIF   52 (88)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEE
T ss_pred             EEEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEE
Confidence            467889999999999999999999999999999988776333344444

>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=96.52  E-value=0.032  Score=43.30  Aligned_cols=68  Identities=9%  Similarity=0.018  Sum_probs=53.2

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--------CeEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--------GATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--------~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      ..+.|.+.|++++|++..|..+|.+.|++|..+...+.+        +.|+-.+.+. . .  ...+.+.|+++|..+..
T Consensus        92 ~~~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~~-~-~--~~~~~~~l~~~l~~~~~  167 (192)
T 1u8s_A           92 YTVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISAR-V-D--SGCNLMQLQEEFDALCT  167 (192)
T ss_dssp             EEEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEE-E-C--TTSCHHHHHHHHHHHHH
T ss_pred             ceEEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEEe-C-C--CCCCHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999998764        2443334443 2 2  25688999999987654

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

Probab=96.04  E-value=0.055  Score=45.64  Aligned_cols=68  Identities=13%  Similarity=0.114  Sum_probs=53.4

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      ...+.+.+.|++++|+...|...|-+.|..|+.++-+..  +|.|+-.+.+.   ..+...+.++|+++|..+
T Consensus        20 ~~~~iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~FfMr~~~~---~~~~~~~~~~L~~~l~~l   89 (302)
T 3o1l_A           20 MRTFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHEIR---ADTLPFDLDGFREAFTPI   89 (302)
T ss_dssp             CCEEEEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEEEEEEEE---GGGSSSCHHHHHHHHHHH
T ss_pred             cceEEEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEEEEEEEe---cCCCCCCHHHHHHHHHHH
Confidence            456899999999999999999999999999999998864  66664334343   122247899999998754

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

Probab=95.94  E-value=0.033  Score=48.04  Aligned_cols=68  Identities=10%  Similarity=0.064  Sum_probs=55.3

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.|++.|+++||+...|...|-+.|..|+.++-...++.|+-.+.+...   +...+.+.|+++|..+-
T Consensus        11 ~~~~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~---~~~~~~~~l~~~l~~~~   78 (415)
T 3p96_A           11 VSVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCP---ADVADGPALRHDVEAAI   78 (415)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEEC---HHHHTSHHHHHHHHHHH
T ss_pred             CeEEEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEec---CCcCCHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999999988656666522   11335688888887653

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

Probab=95.71  E-value=0.086  Score=44.09  Aligned_cols=69  Identities=12%  Similarity=0.119  Sum_probs=53.6

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ...+.+.+.|++++|+...|...|-+.|+.|..++-.+  .+|.|+-.+.+..   .+...+.++|+++|..+-
T Consensus         4 ~~~~iLtv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~---~~~~~~~~~L~~~f~~la   74 (288)
T 3obi_A            4 HHQYVLTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVVFNA---AAKVIPLASLRTGFGVIA   74 (288)
T ss_dssp             CCEEEEEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEE---SSCCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEEEEc---CCCCCCHHHHHHHHHHHH
Confidence            34688999999999999999999999999999998863  4666654455542   122478999999987653

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

Probab=95.39  E-value=0.1  Score=43.67  Aligned_cols=70  Identities=14%  Similarity=0.218  Sum_probs=52.0

Q ss_pred             CceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          115 GNKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       115 ~~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      ...+.+.+.|++++|+...|...|-+.|+.|..++-.+  .+|.|+-.+.+... .++...+.++|+++|..+
T Consensus         8 ~~~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~-~~~~~~~~~~L~~~f~~l   79 (292)
T 3lou_A            8 PHQFVLTLSCPSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFFVRCVFHAT-DDADALRVDALRREFEPI   79 (292)
T ss_dssp             CCEEEEEEEEESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEEC-C----CCHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceEEEEEEEcc-CcccCCCHHHHHHHHHHH
Confidence            34688999999999999999999999999999999884  56666534444321 002246789999988654

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

Probab=95.36  E-value=0.13  Score=42.93  Aligned_cols=67  Identities=7%  Similarity=-0.050  Sum_probs=52.7

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..+.+.+.|++++|+...|...|-+.|+.|..++-++  .++.|+-.+.+.   .++ ..+.++|+++|..+-
T Consensus         7 ~~~vLtv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~---~~~-~~~~~~L~~~f~~la   75 (286)
T 3n0v_A            7 DTWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFR---QPD-DFDEAGFRAGLAERS   75 (286)
T ss_dssp             CCEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEE---CCS-SCCHHHHHHHHHHHH
T ss_pred             CcEEEEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeEEEEEEe---cCC-CCCHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999883  566664334443   122 478999999987653

>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=94.41  E-value=0.094  Score=40.37  Aligned_cols=66  Identities=14%  Similarity=0.308  Sum_probs=47.2

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..|.|..+++||+|.+|...|...|+.|.+.++....+.-+..+++.+. ++  .-..+.|...|.+++
T Consensus         4 ~~IsV~v~NrpGvLarIt~lfs~rg~NI~Sl~v~~t~d~~~sriti~V~-~d--~~~leqI~kqL~Kl~   69 (164)
T 2f1f_A            4 RILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTV-GD--EKVLEQIEKQLHKLV   69 (164)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEEEE-SC--HHHHHHHHHHHHHST
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHHCCCCeeeceeeecCCCCEEEEEEEEe-cc--HHHHHHHHHHHcCCC
Confidence            4678888999999999999999999999999998765422234444422 33  345666666666543

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

Probab=93.90  E-value=0.3  Score=40.75  Aligned_cols=65  Identities=9%  Similarity=0.063  Sum_probs=47.8

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT--LKGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~--~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      ..+.+.+.|++++|+...|...|-+.|..|..++-..  .+|.|+-.+.+.   .+  ..+..+|+++|..+
T Consensus         6 ~~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~---~~--~~~~~~L~~~f~~l   72 (287)
T 3nrb_A            6 NQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVE---IP--VAGVNDFNSAFGKV   72 (287)
T ss_dssp             TEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEE---CC--C---CHHHHHHHHH
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHCCCCEEeeeeeecCCCCeEEEEEEEE---cC--CCCHHHHHHHHHHH
Confidence            4689999999999999999999999999999998863  466664333333   12  13345888888654

>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=93.40  E-value=0.12  Score=39.91  Aligned_cols=64  Identities=20%  Similarity=0.284  Sum_probs=47.8

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ..|.|..+++||+|.+|...|...|+.|.+.++....  +...-+|.+.   ++  .-..+.|...|.+++
T Consensus         5 ~~IsV~veNrpGvL~rI~~lfs~rg~NI~Sl~v~~t~d~g~sritivV~---~d--~~~leql~kQL~Kl~   70 (165)
T 2pc6_A            5 HIISLLMENEAGALSRVAGLFSARGYNIESLSVAPTEDPTLSRMTLVTN---GP--DEIVEQITKQLNKLI   70 (165)
T ss_dssp             EEEEEEEECSTTHHHHHHHHHHHHTCCCCEEEEEECSSTTEEEEEEEEE---EC--HHHHHHHHHHHHHST
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHHCCCcEEEEEEEecCCCCEEEEEEEEe---cc--HHHHHHHHHHhcCCC
Confidence            5688888899999999999999999999999998765  4443345554   22  345667777776654

>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=93.16  E-value=0.24  Score=39.12  Aligned_cols=65  Identities=14%  Similarity=0.253  Sum_probs=49.0

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC--eEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG--ATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~--~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      ..|.|..+++||.|.+|...|...|+.|.+..+....+  ...-++.+.   ++  .-..+.|...|.+++.
T Consensus        30 ~~LsVlVeN~pGvLaRItglfsrRG~NI~SLtV~~ted~gisRitIvV~---g~--e~~ieqL~kQL~KLid   96 (193)
T 2fgc_A           30 HLVSMLVHNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVK---GD--DKTIEQIEKQAYKLVE   96 (193)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEE---EC--TTHHHHHHHHHTTSTT
T ss_pred             EEEEEEECCCChHHHHHHHHHHHCCceEEEEEeeccCCCCEEEEEEEEE---CC--HHHHHHHHHHhcCcCc
Confidence            56788888999999999999999999999999987554  333344454   22  4557788888877553

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

Probab=92.07  E-value=0.45  Score=35.26  Aligned_cols=37  Identities=14%  Similarity=0.328  Sum_probs=33.7

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCe
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGA  156 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~  156 (189)
                      .|.|.|.+++|++.+|+.+|.+.++++..+++.+. |.
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            47899999999999999999999999999999776 44

>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=89.36  E-value=1  Score=36.22  Aligned_cols=61  Identities=20%  Similarity=0.108  Sum_probs=43.0

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC-----CeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK-----GATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~-----~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      .+.|.|.+.+++|+|.+|+.+|-+.+..|.+.+.+...     +..  .++++..  +  . ..++|-+.|.+
T Consensus         4 ~VtL~I~a~DRpGLLsDIt~vLAe~kiNIltIn~~~~~kG~~ng~A--~I~IEV~--d--~-~Le~LL~kLrk   69 (223)
T 1y7p_A            4 LRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKA--LIYFEIE--G--G-DFEKILERVKT   69 (223)
T ss_dssp             CEEEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEE--EEEEEEC--S--S-CHHHHHHHHHT
T ss_pred             eEEEEEEEcCCCCHHHHHHHHHHHcCCCceEEEEEccccCCcCCEE--EEEEEEC--C--C-CHHHHHHHHhC
Confidence            46788899999999999999999999999999999864     343  3337732  2  3 67777766653

---

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	189
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	4e-05
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	4e-05
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	5e-05
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	3e-04
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	3e-04
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	5e-04
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	7e-04
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	0.002

>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 = 38.3 bits (89), Expect = 4e-05
 Identities = 10/65 (15%), Positives = 27/65 (41%), Gaps = 8/65 (12%)

Query: 24 KSKNLEAERRRRQKLNDRLLKLRSLMK--------KETVIEDAITYIRQLKGRVLFLCDQ 75
          ++ +   ER+RR  + D    LR  +         +  +++ A  YI+ ++ +       
Sbjct: 3  RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 62

Query: 76 VLQVE 80
          +  ++
Sbjct: 63 IDDLK 67

>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 = 37.9 bits (88), Expect = 4e-05
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 8/54 (14%)

Query: 24 KSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRV 69
          +      ERRR  K+N+    L+          + K  ++ +AI YI  L+  +
Sbjct: 13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL 66

>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 = 37.5 bits (87), Expect = 5e-05
 Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 13/59 (22%)

Query: 24 KSKNLEAERRRRQKLNDRLLKLRSL-------------MKKETVIEDAITYIRQLKGRV 69
          +  +  AE+ RR +L   L +L SL               K T +E A  YIR L+   
Sbjct: 3  RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

>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 = 35.7 bits (82), Expect = 3e-04
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 18 EDKAVYKSKNLEAERRRRQKLNDRLLKLRSLMK-------KETVIEDAITYIRQLKGRVL 70
          + +   ++ +   E+R R  +ND++++L+ L+        K  V+  AI YIR L+    
Sbjct: 1  QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQ 60

Query: 71 FLCDQVLQVEPLEEE 85
           L  + L +     +
Sbjct: 61 KLKQENLSLRTAVHK 75

>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 = 35.5 bits (82), Expect = 3e-04
 Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 12/55 (21%)

Query: 24 KSKNLEAERRRRQKLNDRLLKLRSLMK------------KETVIEDAITYIRQLK 66
          ++++ E ERRRR K+N+ +++L  ++             K  ++  A  YI++L+
Sbjct: 6  RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

>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 = 35.1 bits (81), Expect = 5e-04
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 7/53 (13%)

Query: 35 RQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE 80
          R  +ND++++L+ L       M K  V+  AI YI+ L+     L  + + ++
Sbjct: 1  RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK 53

>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 = 35.3 bits (81), Expect = 7e-04
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 9/66 (13%)

Query: 24 KSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLFLCD 74
          +  +   ER+RR +L      LR             K  +++ A  YI  ++     L  
Sbjct: 7  RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS 66

Query: 75 QVLQVE 80
          +   + 
Sbjct: 67 EEDLLR 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 = 33.7 bits (77), Expect = 0.002
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 10/74 (13%)

Query: 29 EAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV 79
          E E+ RR  L   L KL+ L             +++  A  +I++L+        Q+ Q+
Sbjct: 7  EMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL 66

Query: 80 EPLEEEETKPKIDE 93
          +  E+   K ++++
Sbjct: 67 QR-EQRHLKRQLEK 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	189
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.47
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.45
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.43
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.3
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.28
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	97.96
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	97.73
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	97.08
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	95.82
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	95.32
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	95.3
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	94.48
d2f1fa1	76	Acetolactate synthase small subunit, IlvH {Escheri	92.17
d2pc6a2	77	Acetolactate synthase small subunit, IlvH {Nitroso	90.87
d1phza1	97	Phenylalanine hydroxylase N-terminal domain {Rat (	90.75
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	90.57
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	88.87
d1ygya3	78	Phosphoglycerate dehydrogenase, regulatory (C-term	87.11

>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=99.53  E-value=7.1e-15  Score=100.52  Aligned_cols=60  Identities=28%  Similarity=0.466  Sum_probs=54.9

Q ss_pred             hhhhhhchHHHHHHHHHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 036599           21 AVYKSKNLEAERRRRQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE   80 (189)
Q Consensus        21 ~~~~~~h~~~ER~RR~kln~~f~~LRsl-------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l~   80 (189)
                      ...+..|+.+||+||.+||+.|..|++|       +||++||.+||+||+.|+++++.|..+...+.
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk   70 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999       79999999999999999999999998887653

>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=99.49  E-value=2e-14  Score=97.94  Aligned_cols=57  Identities=26%  Similarity=0.292  Sum_probs=52.8

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE   80 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l~   80 (189)
                      +..|+..||+||.+||+.|..|+++         ++|++||.+||+||+.|+.+++.|..+...+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~   67 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999         78999999999999999999999998886553

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

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

Probab=99.47  E-value=1.1e-14  Score=96.58  Aligned_cols=53  Identities=26%  Similarity=0.376  Sum_probs=47.4

Q ss_pred             ccchhhhhhchHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHH
Q 036599           18 EDKAVYKSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVL   70 (189)
Q Consensus        18 ~~~~~~~~~h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~   70 (189)
                      ......+..|+..||+||.+||+.|..|+++        +||++||..||+||+.||+.++
T Consensus         7 ~~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           7 TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3445567889999999999999999999999        7999999999999999998764

>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=99.45  E-value=6.3e-14  Score=97.24  Aligned_cols=58  Identities=22%  Similarity=0.301  Sum_probs=53.4

Q ss_pred             hhhhhchHHHHHHHHHHHHHHHHHHhc---------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           22 VYKSKNLEAERRRRQKLNDRLLKLRSL---------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        22 ~~~~~h~~~ER~RR~kln~~f~~LRsl---------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      ..+..|+..||+||++||+.|..|+++         ++|++||..||+||+.|++++++|..+...+
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   71 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999         6899999999999999999999999887654

>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=99.45  E-value=6.5e-14  Score=96.16  Aligned_cols=56  Identities=18%  Similarity=0.379  Sum_probs=52.3

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc--------ccccchHHHHHHHHHHHHHHHHHHHhhhhhh
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL--------MKKETVIEDAITYIRQLKGRVLFLCDQVLQV   79 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl--------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l   79 (189)
                      +..|+..||+||.+||+.|..|+++        ++|++||..||+||+.|+.++..|+.+...+
T Consensus         3 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   66 (83)
T d1nkpb_           3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999        7999999999999999999999999887654

>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=99.43  E-value=2.1e-14  Score=93.91  Aligned_cols=46  Identities=37%  Similarity=0.475  Sum_probs=43.1

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc-------------ccccchHHHHHHHHHHHHHHH
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL-------------MKKETVIEDAITYIRQLKGRV   69 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl-------------~DKaSIl~dAI~YIk~Lq~kv   69 (189)
                      +..|+.+||+||++||+.|..|++|             +||++||..||+||+.||+++
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            4689999999999999999999999             589999999999999999865

>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=99.30  E-value=5.7e-13  Score=86.38  Aligned_cols=46  Identities=30%  Similarity=0.523  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 036599           35 RQKLNDRLLKLRSL-------MKKETVIEDAITYIRQLKGRVLFLCDQVLQVE   80 (189)
Q Consensus        35 R~kln~~f~~LRsl-------~DKaSIl~dAI~YIk~Lq~kv~~Le~~~~~l~   80 (189)
                      |++||++|..||++       +|||+||.+||+||+.||.+++.|+.+...+.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999       79999999999999999999999999987654

>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=99.28  E-value=4.3e-13  Score=88.01  Aligned_cols=45  Identities=31%  Similarity=0.606  Sum_probs=42.1

Q ss_pred             hhhchHHHHHHHHHHHHHHHHHHhc------------ccccchHHHHHHHHHHHHHH
Q 036599           24 KSKNLEAERRRRQKLNDRLLKLRSL------------MKKETVIEDAITYIRQLKGR   68 (189)
Q Consensus        24 ~~~h~~~ER~RR~kln~~f~~LRsl------------~DKaSIl~dAI~YIk~Lq~k   68 (189)
                      +..|+..||+||.+||+.|..|+++            ++|++||..||+||+.||++
T Consensus         6 R~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            5679999999999999999999999            78999999999999999865

>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=97.96  E-value=8.1e-05  Score=49.32  Aligned_cols=65  Identities=17%  Similarity=0.125  Sum_probs=55.3

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      +.|++.|+++||++..|..+|.+.|..|..++-.+.++.+.-.+.+. .. +  ..+.+.|+++|..+-
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~-~~-~--~~~~~~l~~~l~~la   67 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVS-SD-E--KQDFTYLRNEFEAFG   67 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEE-ES-S--CCCHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEE-Ee-c--CCCHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999886666666 32 2  567899999987653

>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=97.73  E-value=0.00016  Score=48.32  Aligned_cols=65  Identities=12%  Similarity=0.174  Sum_probs=55.0

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      ..+.|.+.|+++||++..+..+|-+.|..|..+.....++.+...+.+.+.     .-+.+.|...|.++
T Consensus         4 ~~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~-----~~~~~~l~~~L~~l   68 (86)
T d1u8sa1           4 QHLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGS-----PSNITRVETTLPLL   68 (86)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEEC-----HHHHHHHHHHHHHH
T ss_pred             cEEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcC-----cccHHHHHHHHHHH
Confidence            468899999999999999999999999999999999999998777777732     22577888877664

>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=97.08  E-value=0.0023  Score=42.94  Aligned_cols=67  Identities=9%  Similarity=0.004  Sum_probs=50.7

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC--------eEEEEEEEEeeeCCccccCHHHHHHHHHHHHh
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG--------ATLFSSVLEGTHGGDRIIRVEETRELLLKIIR  187 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~--------~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i~  187 (189)
                      .+.|.|.|+++||++..|...|-+.|+.|.+.+..+..+        .|.-.+.+..  ..  ..+..+|+++|..+-.
T Consensus         6 tv~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~--p~--~~~~~~l~~~l~~l~~   80 (93)
T d1u8sa2           6 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARV--DS--GCNLMQLQEEFDALCT   80 (93)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEE--CT--TSCHHHHHHHHHHHHH
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEc--Cc--cccHHHHHHHHHHHHH
Confidence            567889999999999999999999999999998876432        2333344442  22  5789999999987643

>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=95.82  E-value=0.0045  Score=40.17  Aligned_cols=63  Identities=14%  Similarity=-0.022  Sum_probs=40.0

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTT-LKGATLFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~-~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      -|+|.|.+++|+|.+|+.+|-+.+..|.+++..+ .+|..-..|.+.....   ....+.|-++|.+
T Consensus         3 ~i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~~---~~~l~~ll~kL~~   66 (77)
T d1y7pa2           3 GLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIE---GGDFEKILERVKT   66 (77)
T ss_dssp             EEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEEC---SSCHHHHHHHHHT
T ss_pred             eEEEEEecCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEcC---cccHHHHHHHHHc
Confidence            5889999999999999999999999999999876 3332222344442211   2246666666653

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

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

Probab=95.32  E-value=0.089  Score=33.20  Aligned_cols=45  Identities=11%  Similarity=0.294  Sum_probs=39.8

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVL  163 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~v  163 (189)
                      .|.|..+++||.|.++..+|...|+.+....+....++-+..+.+
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Riiv   49 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGILRGIV   49 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEEEE
Confidence            578888999999999999999999999999999988887655544

>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=95.30  E-value=0.1  Score=32.90  Aligned_cols=44  Identities=14%  Similarity=0.123  Sum_probs=37.3

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      .|.|..+++||.|.+++++|.+.|+.|...-+....+.-+  +.+.
T Consensus         1 ViaV~v~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~--~vl~   44 (71)
T d2f06a1           1 VVGISCPNVPGALAKVLGFLSAEGVFIEYMYSFANNNVAN--VVIR   44 (71)
T ss_dssp             EEEEEEESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEE--EEEE
T ss_pred             CEEEEecCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEE--EEEE
Confidence            3667778999999999999999999999999988888764  4444

>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=94.48  E-value=0.076  Score=34.35  Aligned_cols=67  Identities=16%  Similarity=0.236  Sum_probs=47.2

Q ss_pred             eEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          117 KLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       117 ~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      ...|.+...++||+|.++...|...|+.+.+.++....+.-++-+++-+. ++  .-..+.|..-|.+.+
T Consensus         3 ~~tisvlv~n~pGvL~Ri~~lF~rRg~NI~SL~v~~te~~~iSR~tivv~-g~--~~~i~qi~kQl~Kli   69 (78)
T d2fgca2           3 EHLVSMLVHNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVK-GD--DKTIEQIEKQAYKLV   69 (78)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEE-EC--TTHHHHHHHHHTTST
T ss_pred             eEEEEEEEeCCCcHHHHHHHHHhhCCcceEEEEEeecCCCCeEEEEEEEE-cC--HHHHHHHHHHHhCCc
Confidence            35788888899999999999999999999999999865544444444422 33  234566655555443

>d2f1fa1 d.58.18.6 (A:2-77) Acetolactate synthase small subunit, IlvH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Escherichia coli [TaxId: 562]

Probab=92.17  E-value=0.21  Score=31.94  Aligned_cols=65  Identities=15%  Similarity=0.332  Sum_probs=46.3

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .|.+.-+++||+|.++...|...|+.+.+.++....+.-++.+++- ..++  .-..+.|..-|.+.+
T Consensus         3 tlsv~v~N~~GVL~RisglF~rRg~NI~Sl~v~~te~~~iSR~tiv-v~~~--~~~i~qi~kQL~Kli   67 (76)
T d2f1fa1           3 ILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQ-TVGD--EKVLEQIEKQLHKLV   67 (76)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEE-EESC--HHHHHHHHHHHHHST
T ss_pred             EEEEEEECCCcHHHHHHHHHHhcCcceEEEEEcccCCCCeeEEEEE-EECC--HHHHHHHHHHHhCCC
Confidence            4566667899999999999999999999988888766555555555 2233  234555666665544

>d2pc6a2 d.58.18.6 (A:1-77) Acetolactate synthase small subunit, IlvH {Nitrosomonas europaea [TaxId: 915]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Nitrosomonas europaea [TaxId: 915]

Probab=90.87  E-value=0.2  Score=32.16  Aligned_cols=63  Identities=21%  Similarity=0.298  Sum_probs=43.9

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEEeeeCCccccCHHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLK--GATLFSSVLEGTHGGDRIIRVEETRELLLKII  186 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~--~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~i  186 (189)
                      .|.+.-+++||+|.+|...|...|+.+.+.++....  |..--++++.   ++  .-..+.|..-|.+.+
T Consensus         4 tisv~veN~pGvL~Ris~lF~rRg~NI~Sltv~~te~~~iSRmtivv~---~~--~~~i~qi~kQL~Klv   68 (77)
T d2pc6a2           4 IISLLMENEAGALSRVAGLFSARGYNIESLSVAPTEDPTLSRMTLVTN---GP--DEIVEQITKQLNKLI   68 (77)
T ss_dssp             EEEEEEECSTTHHHHHHHHHHHHTCCCCEEEEEECSSTTEEEEEEEEE---EC--HHHHHHHHHHHHHST
T ss_pred             EEEEEEECCccHHHHHHHHHhccCcceEEEEEeccCCCCeEEEEEEEE---CC--HHHHHHHHHHHhCCc
Confidence            566777799999999999999999888888888754  4443345554   23  224556666666544

>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=90.75  E-value=0.25  Score=32.92  Aligned_cols=65  Identities=3%  Similarity=0.002  Sum_probs=46.6

Q ss_pred             ceEEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          116 NKLRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKG-ATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       116 ~~v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~-~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      +..-|-+.+++++|.|.++|.+|...|+.+.+..+-+..+ ..-|.|.+... |   . .-..+..+|..+
T Consensus        15 ~ktSl~f~~~~~pGaL~~vL~~f~~~~INLt~IeSRP~~~~~~~Y~F~id~e-g---~-~~~~i~~~l~~L   80 (97)
T d1phza1          15 GAISLIFSLKEEVGALAKVLRLFEENDINLTHIESRPSRLNKDEYEFFTYLD-K---R-TKPVLGSIIKSL   80 (97)
T ss_dssp             CCEEEEEEEECCTTHHHHHHHHHHTTTCCTTSEEEEECSSCTTEEEEEECBC-G---G-GHHHHHHHHHHH
T ss_pred             CcEEEEEEeCCCCCHHHHHHHHHHHCCCCEEEEEeeccCCCCceEEEEEEcc-c---C-ChHHHHHHHHHH
Confidence            3455666677899999999999999999999999988543 33567888732 2   2 234566666544

>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=90.57  E-value=0.71  Score=29.45  Aligned_cols=47  Identities=17%  Similarity=0.148  Sum_probs=38.9

Q ss_pred             EEEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEE
Q 036599          118 LRINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGATLFSSVLE  164 (189)
Q Consensus       118 v~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~l~~~~vk  164 (189)
                      ..+-+.-.++||++.+|..+|-+.|+.|.+......++.-...+.++
T Consensus        12 ~rl~i~~~d~PGvla~I~~~l~~~~iNI~~~~~~~~~~~~~a~~~i~   58 (84)
T d1sc6a3          12 RRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIE   58 (84)
T ss_dssp             EEEEEEEESCTTHHHHHHHHHHHTTCEEEEEEEEECSSEEEEEEEEE
T ss_pred             eEEEEEeCCcCCHHHHHHHHHHHcCCCHHHhccccCCCCcEEEEEEE
Confidence            45666667899999999999999999999998888877665556666

>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=88.87  E-value=1.1  Score=28.42  Aligned_cols=56  Identities=9%  Similarity=0.214  Sum_probs=40.7

Q ss_pred             eCCCCChHHHHHHHHHhCCCeEEEEEEEeeCCeE-EEEEEEEeeeCCccccCHHHHHHHHHH
Q 036599          124 FGKKRGNFTKLVEAMNALGFVFGDTSVTTLKGAT-LFSSVLEGTHGGDRIIRVEETRELLLK  184 (189)
Q Consensus       124 c~~~~g~l~~il~aLe~l~L~V~~a~is~~~~~~-l~~~~vk~~~~~~~~~s~~~lk~~L~~  184 (189)
                      -.++||.|.++|..+...|+.+++..+-+..+.. -+.|.++.. +   ... +.++++|..
T Consensus         9 ~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~~-g---~~~-~~~~~~l~~   65 (80)
T d2qmwa2           9 MHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQAD-S---AIT-TDIKKVIAI   65 (80)
T ss_dssp             SSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEES-C---CSC-HHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEe-c---CCc-HHHHHHHHH
Confidence            3568999999999999999999999999876543 456777742 2   223 245555544

>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=87.11  E-value=2  Score=26.85  Aligned_cols=60  Identities=10%  Similarity=0.158  Sum_probs=41.4

Q ss_pred             EEEEEeCCCCChHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEEeeeCCccccCHHHHHHHHHHH
Q 036599          119 RINIIFGKKRGNFTKLVEAMNALGFVFGDTSVTTL--KGATLFSSVLEGTHGGDRIIRVEETRELLLKI  185 (189)
Q Consensus       119 ~I~i~c~~~~g~l~~il~aLe~l~L~V~~a~is~~--~~~~l~~~~vk~~~~~~~~~s~~~lk~~L~~~  185 (189)
                      .+-+.-.++||++.+|-.+|-+.|+.|....++..  ++..  .+.++.. +   .++ +++.++|.++
T Consensus         5 ~L~i~~~D~PGvi~~I~~~l~~~~iNI~~m~~~~~~~g~~a--~~vi~vD-~---~~~-~~vl~~I~~~   66 (78)
T d1ygya3           5 NLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGA--TILLRLD-Q---DVP-DDVRTAIAAA   66 (78)
T ss_dssp             EEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEECSSSSCE--EEEEEES-S---CCC-HHHHHHHHHH
T ss_pred             EEEEEeCCcCCHHHHHHHHHHhcCcChhhheeeecCCCCeE--EEEEEcC-C---Ccc-HHHHHHHHcC
Confidence            45556678999999999999999999999988774  4433  4455521 1   333 4555555543