Citrus Sinensis ID: 021208

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310------
Protein Sequence
MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEEEEEccEEEEEEEccccccHHHHHHHHHHccccEEEEEEEEEccccEEEEEEEEEEcccccccHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccHHccccccccccccccccHHHHccccccccccccccccccccccccHccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEccccccccccccccccccccEEEEEEEccEEEEEEEccccccHHHHHHHHHHHcccEEEEccEccccccEEEEEEEEEEcccccccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
meissikglpelgmedlsFMNQWHMmnsidefnllPIAAAFgenlqhsythpsfnnntgidrpqkqlktstwnssetgfnpnnvssinmnqmgilkpkqetgagypsdilpsqvsfgnnqnyvfkasqgakrispgagnrlsntqDHIIAERKRREKLSQRFIALSAIvpglkkmdkASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKtqlsdegdnpngafnealPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSvmtfgssvLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
Flexible Loop (DISEMBL)
meissikglpelgMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKASQgakrispgagnrlsntqDHIIAERKRREKLSQRFIALsaivpglkkmdKASVLGDAIKYLKQLQEKVKILeeqankktiesVVFVNktqlsdegdnpNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
Low Complexity Region (SEG)
MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
Disordered region (IsUnstruct)
**************EDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYT***********************************************************************YVF**********************************SQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNK*************FNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ***
Disordered Region (DISOPRED)
****SIKGLPELGMEDLSFMNQWHMMNSI*****************************************************************************************************************************REKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQ********************************************EARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQM*****MTVKDLVKNLHSAFQLFA
Disordered Region (DISEMBL)
MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
Disordered Region (DISPRO)
******KGLPELGMEDLSFMNQWHMMNSIDEFNLLP**AAF*****************************************NVS****NQMGI**************************************************QDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNK***************EALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVxxxxxxxxxxxxxxxxxxxxxxxxxxxxSVVFVNKTQLSDEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA
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	316	2.2.26 [Sep-21-2011]
Q9T072	328	Transcription factor bHLH	yes	no	0.943	0.908	0.421	2e-53
Q1PF17	305	Transcription factor bHLH	no	no	0.525	0.544	0.564	2e-42
Q1PF16	295	Transcription factor bHLH	no	no	0.582	0.623	0.463	1e-39
Q8S3F1	320	Transcription factor NAI1	no	no	0.639	0.631	0.4	2e-38
Q9ZPY8	566	Transcription factor ABA-	no	no	0.287	0.160	0.461	4e-16
Q9FIP9	592	Transcription factor ATR2	no	no	0.446	0.238	0.335	9e-16
Q39204	623	Transcription factor MYC2	no	no	0.471	0.239	0.341	5e-15
Q9LNJ5	590	Transcription factor bHLH	no	no	0.405	0.216	0.317	2e-14
O49687	589	Transcription factor MYC4	no	no	0.446	0.239	0.312	3e-14
O23487	467	Transcription factor bHLH	no	no	0.338	0.229	0.358	1e-13

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

 Score =  209 bits (532), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 145/344 (42%), Positives = 201/344 (58%), Gaps = 46/344 (13%)

Query: 1   MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHP-SF--NNN 57
           M I S +   E  +E+ S + Q+HM NSI            GE  +  Y  P SF  NN+
Sbjct: 1   MSILSTRWFSEQEIEENSIIQQFHM-NSI-----------VGEVQEAQYIFPHSFTTNND 48

Query: 58  TGID-----RPQKQLKTSTWNSSETGFNPNNVSS----------INMNQMGILKPKQETG 102
              D     +P K L+T T+ S  +   PN+             ++    G    + E  
Sbjct: 49  PSYDDLIEMKPPKILET-TYISPSSHLPPNSKPHHIHRHSSSRILSFEDYGSNDMEHEYS 107

Query: 103 AGYPSDI----LPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKL 158
             Y + I    L +QV      +   +  +G KR  P + N+ SN QDHIIAERKRREKL
Sbjct: 108 PTYLNSIFSPKLEAQVQPHQKSDEFNR--KGTKRAQPFSRNQ-SNAQDHIIAERKRREKL 164

Query: 159 SQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQL 218
           +QRF+ALSA+VPGLKKMDKASVLGDA+K++K LQE+V  LEEQ  ++ +ES+V V K++L
Sbjct: 165 TQRFVALSALVPGLKKMDKASVLGDALKHIKYLQERVGELEEQKKERRLESMVLVKKSKL 224

Query: 219 SDEGDN-------PNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLT 271
             + +N        +G  +  LPEIE RF D+ VLI++ CEK+KG   KI+AEIEKLH+ 
Sbjct: 225 ILDDNNQSFSSSCEDGFSDLDLPEIEVRFSDEDVLIKILCEKQKGHLAKIMAEIEKLHIL 284

Query: 272 VINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF 315
           + NSSV+ FG + LD+TIIA+ + +F+MT+ D+VK+L SA   F
Sbjct: 285 ITNSSVLNFGPT-LDITIIAKKESDFDMTLMDVVKSLRSALSNF 327

Arabidopsis thaliana (taxid: 3702)

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

 Score =  172 bits (437), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 100/177 (56%), Positives = 128/177 (72%), Gaps = 11/177 (6%)

Query: 142 SNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQ 201
           SN QDHI+AERKRREKL+QRF+ALSA++PGLKKMDKASVLGDAIK++K LQE VK  EEQ
Sbjct: 122 SNAQDHILAERKRREKLTQRFVALSALIPGLKKMDKASVLGDAIKHIKYLQESVKEYEEQ 181

Query: 202 ANKKTIESVVFVNKTQLS-DEGDNP---------NGAFNEALPEIEARFCDKSVLIRVHC 251
             +KT+ESVV V K+ L  DE   P           + +  LPEIE R   K VLI++ C
Sbjct: 182 KKEKTMESVVLVKKSSLVLDENHQPSSSSSSDGNRNSSSSNLPEIEVRVSGKDVLIKILC 241

Query: 252 EKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNL 308
           EK+KG   KI+ EIEKL L++ NS+V+ FG +  D++IIAQ +  F+M ++D+VKNL
Sbjct: 242 EKQKGNVIKIMGEIEKLGLSITNSNVLPFGPT-FDISIIAQKNNNFDMKIEDVVKNL 297

Arabidopsis thaliana (taxid: 3702)

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

 Score =  163 bits (413), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/194 (46%), Positives = 132/194 (68%), Gaps = 10/194 (5%)

Query: 128 QGAKRISPGAGNRLSN-TQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIK 186
           +G KR +   G R     ++H++AERKRREKLS++FIALSA++PGLKK DK ++L DAI 
Sbjct: 100 RGTKRKTCSHGTRSPVLAKEHVLAERKRREKLSEKFIALSALLPGLKKADKVTILDDAIS 159

Query: 187 YLKQLQEKVKIL-EEQANKKTIESVVFVNKTQL-SDEGDNPNGA------FNEALPEIEA 238
            +KQLQE+++ L EE+   + +ES++ V K+++  DE  N + +      F++ALPEIEA
Sbjct: 160 RMKQLQEQLRTLKEEKEATRQMESMILVKKSKVFFDEEPNLSCSPSVHIEFDQALPEIEA 219

Query: 239 RFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFN 298
           +     +LIR+ CEK KG    I+  IE   L + NS V+ FG S LD+T++AQMD +F+
Sbjct: 220 KISQNDILIRILCEKSKGCMINILNTIENFQLRIENSIVLPFGDSTLDITVLAQMDKDFS 279

Query: 299 MTV-KDLVKNLHSA 311
           M++ KDLV+NL  A
Sbjct: 280 MSILKDLVRNLRLA 293

Arabidopsis thaliana (taxid: 3702)

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

 Score =  159 bits (403), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 134/225 (59%), Gaps = 23/225 (10%)

Query: 111 PSQVSFGNNQNYVFKASQGAKR---ISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSA 167
           P + S   +         G+KR   ++ G        ++H++AERKRR+KL++R IALSA
Sbjct: 94  PVETSLNFSNQVSMDQKVGSKRKDCVNNGGRREPHLLKEHVLAERKRRQKLNERLIALSA 153

Query: 168 IVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQ--ANKKTIESVVFVNKTQL------- 218
           ++PGLKK DKA+VL DAIK+LKQLQE+VK LEE+    KK  +S++ V ++Q+       
Sbjct: 154 LLPGLKKTDKATVLEDAIKHLKQLQERVKKLEEERVVTKKMDQSIILVKRSQVYLDDDSS 213

Query: 219 -----------SDEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEK 267
                           +    F + +P IEAR  D+ +LIRVHCEK KG   KI++ +EK
Sbjct: 214 SYSSTCSAASPLSSSSDEVSIFKQTMPMIEARVSDRDLLIRVHCEKNKGCMIKILSSLEK 273

Query: 268 LHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAF 312
             L V+NS  + FG+S L +TI+ +MD +F+  V+++VKN+  A 
Sbjct: 274 FRLEVVNSFTLPFGNSTLVITILTKMDNKFSRPVEEVVKNIRVAL 318

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 85.9 bits (211), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 71/104 (68%), Gaps = 13/104 (12%)

Query: 146 DHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK 205
           +H+ AER+RREKL+QRF AL ++VP + KMDKAS+LGDAI Y+K+LQEKVKI+E++    
Sbjct: 395 NHVEAERQRREKLNQRFYALRSVVPNISKMDKASLLGDAISYIKELQEKVKIMEDER--- 451

Query: 206 TIESVVFVNKTQLSDEGDNPNGAFNEALPEIEARFCDKSVLIRV 249
                V  +K+ LS+     N    E  PE++ +  ++ V++RV
Sbjct: 452 -----VGTDKS-LSES----NTITVEESPEVDIQAMNEEVVVRV 485

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 84.7 bits (208), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/167 (33%), Positives = 93/167 (55%), Gaps = 26/167 (15%)

Query: 146 DHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK 205
           +H+ AER+RREKL+QRF +L A+VP + KMDKAS+LGDAI Y+ +L  K K+ + +++K+
Sbjct: 415 NHVEAERQRREKLNQRFYSLRAVVPNVSKMDKASLLGDAISYINEL--KSKLQQAESDKE 472

Query: 206 TIESVVFVNKTQLSDEGDNPNGAFNEALP---------------EIEARFCDKSVLIRVH 250
            I+  +      +S EG+N  G  + A                 EI+ +     V+IRV 
Sbjct: 473 EIQKKL----DGMSKEGNNGKGCGSRAKERKSSNQDSTASSIEMEIDVKIIGWDVMIRVQ 528

Query: 251 CEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEF 297
           C K+     + +  +++L L V ++S+     SV++  +I Q  V+ 
Sbjct: 529 CGKKDHPGARFMEALKELDLEVNHASL-----SVVNDLMIQQATVKM 570

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 = 82.0 bits (201), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 56/164 (34%), Positives = 93/164 (56%), Gaps = 15/164 (9%)

Query: 146 DHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK 205
           +H+ AER+RREKL+QRF AL A+VP + KMDKAS+LGDAI Y+ +L  K K+++ ++ K 
Sbjct: 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINEL--KSKVVKTESEKL 509

Query: 206 TIESVVFVNKTQL-----SDEGDNPNGAFNEALP---EIEARFCDKSVLIRVHCEKRKGV 257
            I++ +   K +L     S  G + + + +   P   EIE +      +IRV   KR   
Sbjct: 510 QIKNQLEEVKLELAGRKASASGGDMSSSCSSIKPVGMEIEVKIIGWDAMIRVESSKRNHP 569

Query: 258 FEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTV 301
             ++++ +  L L V ++S+     SV++  +I Q  V+    +
Sbjct: 570 AARLMSALMDLELEVNHASM-----SVVNDLMIQQATVKMGFRI 608

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|Q9LNJ5|BH013_ARATH Transcription factor bHLH13 OS=Arabidopsis thaliana GN=BHLH13 PE=2 SV=1

 Score = 80.1 bits (196), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 78/145 (53%), Gaps = 17/145 (11%)

Query: 146 DHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK 205
           +H+ AER+RREKL+QRF AL ++VP + KMDKAS+LGDA+ Y+ +L  K+K++E +  + 
Sbjct: 433 NHVEAERQRREKLNQRFYALRSVVPNISKMDKASLLGDAVSYINELHAKLKVMEAERERL 492

Query: 206 TIESVVFVNKTQLSDEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEI 265
              S              NP  + +    +I  +   + V +R++C        +I    
Sbjct: 493 GYSS--------------NPPISLDS---DINVQTSGEDVTVRINCPLESHPASRIFHAF 535

Query: 266 EKLHLTVINSSVMTFGSSVLDVTII 290
           E+  + VINS++     +VL   ++
Sbjct: 536 EESKVEVINSNLEVSQDTVLHTFVV 560

Arabidopsis thaliana (taxid: 3702)

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

 Score = 79.3 bits (194), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/163 (31%), Positives = 90/163 (55%), Gaps = 22/163 (13%)

Query: 146 DHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK 205
           +H+ AER+RREKL+QRF +L A+VP + KMDKAS+LGDAI Y+ +L  K K+ + +++K+
Sbjct: 416 NHVEAERQRREKLNQRFYSLRAVVPNVSKMDKASLLGDAISYISEL--KSKLQKAESDKE 473

Query: 206 TIESVVFVNKTQLSDEGDNPNGAFNEALP-----------EIEARFCDKSVLIRVHCEKR 254
            ++  + V    ++ E  N   +  +              E++ +      +IR+ C KR
Sbjct: 474 ELQKQIDV----MNKEAGNAKSSVKDRKCLNQESSVLIEMEVDVKIIGWDAMIRIQCSKR 529

Query: 255 KGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEF 297
                K +  +++L L V ++S+     SV++  +I Q  V+ 
Sbjct: 530 NHPGAKFMEALKELDLEVNHASL-----SVVNDLMIQQATVKM 567

Arabidopsis thaliana (taxid: 3702)

>sp|O23487|BH003_ARATH Transcription factor bHLH3 OS=Arabidopsis thaliana GN=BHLH3 PE=2 SV=1

 Score = 77.4 bits (189), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 42/117 (35%), Positives = 63/117 (53%), Gaps = 10/117 (8%)

Query: 95  LKPKQETGAGYPSDILPSQVSFGNNQNYVFKAS----------QGAKRISPGAGNRLSNT 144
             PK E   G+  +    Q   G+NQ Y ++            Q  ++      N     
Sbjct: 259 FSPKTEDDTGFSLESYEVQAIGGSNQVYGYEQGKDETLYLTDEQKPRKRGRKPANGREEA 318

Query: 145 QDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQ 201
            +H+ AER+RREKL+QRF AL A+VP + KMDKAS+L DAI Y+  +Q+K+++ E +
Sbjct: 319 LNHVEAERQRREKLNQRFYALRAVVPNISKMDKASLLADAITYITDMQKKIRVYETE 375

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	316
297736346	344	unnamed protein product [Vitis vinifera]	0.981	0.901	0.605	1e-103
224105829	324	predicted protein [Populus trichocarpa]	0.946	0.922	0.607	1e-100
359475553	331	PREDICTED: transcription factor bHLH25-l	0.939	0.897	0.604	4e-98
255554513	309	DNA binding protein, putative [Ricinus c	0.873	0.893	0.626	2e-91
449438279	340	PREDICTED: transcription factor bHLH25-l	0.946	0.879	0.555	1e-89
356521257	327	PREDICTED: transcription factor bHLH25-l	0.984	0.951	0.569	5e-89
358248228	347	transcription factor bHLH25-like [Glycin	0.981	0.893	0.571	1e-88
356549469	348	PREDICTED: transcription factor bHLH25-l	0.968	0.879	0.563	1e-87
357446133	338	Transcription factor bHLH25 [Medicago tr	0.939	0.878	0.522	4e-80
357476085	327	Transcription factor bHLH25 [Medicago tr	0.927	0.896	0.536	2e-78

>gi|297736346|emb|CBI25069.3| unnamed protein product [Vitis vinifera]

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 210/347 (60%), Positives = 252/347 (72%), Gaps = 37/347 (10%)

Query: 1   MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTH-------PS 53
           MEIS ++GL E+GMED +F++ W   N ++E  +LP+ AAFGE+L  +++H       PS
Sbjct: 1   MEISPLRGLSEVGMEDPTFIHPWQT-NFLEELTVLPMEAAFGEHLYQAFSHHQSFNLKPS 59

Query: 54  F--NNNTGIDRPQKQLKTSTWNSSETG----------FNPNNVSSIN---MNQMGILKPK 98
              N++ G+DRP K LK ++WN S T            +PN  S +N    NQ+ ++KPK
Sbjct: 60  MEINSHVGLDRPLKLLKPNSWNPSNTNDMDMPHPLVPSSPNVFSFVNSNYTNQVPVVKPK 119

Query: 99  QE-----TGAGYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERK 153
           +E     + A +PSD L SQ  F  NQNYVFKASQGAKRIS     R S TQDHIIAERK
Sbjct: 120 EEAVSSKSSATFPSDGLVSQGLF-ENQNYVFKASQGAKRISTTTA-RHSQTQDHIIAERK 177

Query: 154 RREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFV 213
           RREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQE+VK LEEQ  KKT ESVVFV
Sbjct: 178 RREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQERVKTLEEQTRKKTTESVVFV 237

Query: 214 NKTQLSDEGDNPNG-------AFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIE 266
            K+Q+  +GDN +          +E LPEIEARF DKSVLIR+HCEKRKGV EK+VAE+E
Sbjct: 238 KKSQVFLDGDNSSSDEDFSGSPLDEPLPEIEARFSDKSVLIRIHCEKRKGVVEKLVAEVE 297

Query: 267 KLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ 313
            LHLTVINSSVMTFG+S LDVTIIA+M+VEF+MTVKDLVK LH+  +
Sbjct: 298 GLHLTVINSSVMTFGNSALDVTIIAEMEVEFSMTVKDLVKKLHAGLK 344

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105829|ref|XP_002313947.1| predicted protein [Populus trichocarpa] gi|222850355|gb|EEE87902.1| predicted protein [Populus trichocarpa]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 198/326 (60%), Positives = 240/326 (73%), Gaps = 27/326 (8%)

Query: 14  MEDLSFMNQWHMMNSIDEFNLLPIAAA-FGENLQHSYTHPSFNNNTGID--------RPQ 64
           MED  F NQW+M NS+D+ +LLP+AAA FGEN+ H +++ +FN  T +D        RP 
Sbjct: 1   MEDPGFTNQWYM-NSLDDISLLPLAAAAFGENVHHPFSNQNFNLKTSMDSTPTSINVRPT 59

Query: 65  KQLKTSTWNSSETGFNPNNVSSIN---MNQMGILKPKQETGAG-----YPSDILPSQVSF 116
           KQ+KT   +  ++ F+PN +S +N    NQMG++KPK+E         +PSD++ SQ  F
Sbjct: 60  KQMKTFHLSDPQSAFSPNFLSFVNPNHANQMGLVKPKEEAVCSKSINNFPSDMVVSQDIF 119

Query: 117 GNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMD 176
           G+ QNYV K  QG +RIS     RLS +QDHIIAERKRREKLSQRFIALSA+VPGLKKMD
Sbjct: 120 GS-QNYVIKGCQGPERISTNTP-RLSQSQDHIIAERKRREKLSQRFIALSAVVPGLKKMD 177

Query: 177 KASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLS-DEGD------NPNGAF 229
           KASVLGDAIKYLKQLQEKVK LEEQ  +KT+ESVV V K+ +  DEGD         G  
Sbjct: 178 KASVLGDAIKYLKQLQEKVKTLEEQTKRKTMESVVIVKKSHIYVDEGDVNASSDESKGPI 237

Query: 230 NEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTI 289
           +E LPEIEARFCDK VLIR+HCEKRKGV EK VAEIEKLHL+VINSSV+ FG+S L VT 
Sbjct: 238 HETLPEIEARFCDKHVLIRIHCEKRKGVLEKTVAEIEKLHLSVINSSVLAFGTSALHVTF 297

Query: 290 IAQMDVEFNMTVKDLVKNLHSAFQLF 315
           IAQMD++FNM++KDLVK L SAF+ F
Sbjct: 298 IAQMDIDFNMSLKDLVKTLRSAFEFF 323

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359475553|ref|XP_002268443.2| PREDICTED: transcription factor bHLH25-like [Vitis vinifera] gi|147839680|emb|CAN75020.1| hypothetical protein VITISV_039940 [Vitis vinifera]

 Score =  363 bits (933), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 202/334 (60%), Positives = 241/334 (72%), Gaps = 37/334 (11%)

Query: 14  MEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTH-------PSF--NNNTGIDRPQ 64
           MED +F++ W   N ++E  +LP+ AAFGE+L  +++H       PS   N++ G+DRP 
Sbjct: 1   MEDPTFIHPWQT-NFLEELTVLPMEAAFGEHLYQAFSHHQSFNLKPSMEINSHVGLDRPL 59

Query: 65  KQLKTSTWNSSETG----------FNPNNVSSIN---MNQMGILKPKQE-----TGAGYP 106
           K LK ++WN S T            +PN  S +N    NQ+ ++KPK+E     + A +P
Sbjct: 60  KLLKPNSWNPSNTNDMDMPHPLVPSSPNVFSFVNSNYTNQVPVVKPKEEAVSSKSSATFP 119

Query: 107 SDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALS 166
           SD L SQ  F  NQNYVFKASQGAKRIS     R S TQDHIIAERKRREKLSQRFIALS
Sbjct: 120 SDGLVSQGLF-ENQNYVFKASQGAKRISTTTA-RHSQTQDHIIAERKRREKLSQRFIALS 177

Query: 167 AIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDNPN 226
           AIVPGLKKMDKASVLGDAIKYLKQLQE+VK LEEQ  KKT ESVVFV K+Q+  +GDN +
Sbjct: 178 AIVPGLKKMDKASVLGDAIKYLKQLQERVKTLEEQTRKKTTESVVFVKKSQVFLDGDNSS 237

Query: 227 G-------AFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT 279
                     +E LPEIEARF DKSVLIR+HCEKRKGV EK+VAE+E LHLTVINSSVMT
Sbjct: 238 SDEDFSGSPLDEPLPEIEARFSDKSVLIRIHCEKRKGVVEKLVAEVEGLHLTVINSSVMT 297

Query: 280 FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ 313
           FG+S LDVTIIA+M+VEF+MTVKDLVK LH+  +
Sbjct: 298 FGNSALDVTIIAEMEVEFSMTVKDLVKKLHAGLK 331

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554513|ref|XP_002518295.1| DNA binding protein, putative [Ricinus communis] gi|223542515|gb|EEF44055.1| DNA binding protein, putative [Ricinus communis]

 Score =  341 bits (875), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 193/308 (62%), Positives = 222/308 (72%), Gaps = 32/308 (10%)

Query: 39  AAFGENLQHSYTHPSFNNNTGID---------RPQKQLKTSTWNSSETGFNPNNVS---S 86
           AAFGEN+QHS +H +FN    ++         RP KQ      N   + F+PN +S   S
Sbjct: 2   AAFGENMQHSLSHQNFNLKASMETSPLSGINLRPTKQQLKPNENYLHSSFSPNILSFANS 61

Query: 87  INMNQ-MG-ILKPKQETGAGYPS-DILPSQ---VSFGN---NQNYVFKASQGAKRISPGA 137
            N N  MG ++KPK+E    Y S   LPS+   +S GN   N NYVF A QGAKRIS   
Sbjct: 62  ANTNHPMGLVVKPKEEAAVYYKSIHTLPSEHMLISQGNSLENHNYVFNACQGAKRISTNN 121

Query: 138 GN-RLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVK 196
            N R+S +QDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQE+VK
Sbjct: 122 NNGRISQSQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQERVK 181

Query: 197 ILEEQANKKTIESVVFVNKTQL---------SDEGDNPNGAFNEALPEIEARFCDKSVLI 247
            LEEQ  KKT+ESVV V K++L         SDE  +  G F+E LPEIEAR CDK VLI
Sbjct: 182 TLEEQTKKKTMESVVIVKKSRLVFGEEDTSSSDESFS-KGPFDEPLPEIEARICDKHVLI 240

Query: 248 RVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKN 307
           R+HCEKRKGV EK +AEIEKLHL+V NSSV+TFGSS LDVTIIAQMD EF+M+VKDLVK+
Sbjct: 241 RIHCEKRKGVLEKTIAEIEKLHLSVTNSSVLTFGSSALDVTIIAQMDNEFSMSVKDLVKD 300

Query: 308 LHSAFQLF 315
           LHSAF+LF
Sbjct: 301 LHSAFKLF 308

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438279|ref|XP_004136916.1| PREDICTED: transcription factor bHLH25-like [Cucumis sativus] gi|449511253|ref|XP_004163905.1| PREDICTED: transcription factor bHLH25-like [Cucumis sativus]

 Score =  335 bits (859), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 181/326 (55%), Positives = 232/326 (71%), Gaps = 27/326 (8%)

Query: 13  GMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGIDRPQ-------K 65
           GMED  F+NQWH  +S+D+  L P+AAAFGENLQHSY   + +    ++          K
Sbjct: 19  GMEDNGFVNQWHK-SSMDDLGLHPLAAAFGENLQHSYDQSNIDQKASLNHSHNAILGYMK 77

Query: 66  QLKTSTWNSSETGFN-PNN---------VSSIN-MNQMGILKPKQE-----TGAGYPSDI 109
           QLK+  W+S +T  + PN+         VS+ N MNQM   +PK+E     + +  PSD+
Sbjct: 78  QLKSDGWSSYQTTNHLPNSQVVAYPTVSVSASNYMNQMDFSRPKEEVVCPQSISNLPSDM 137

Query: 110 LPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIV 169
           L SQ S  + Q++  K+++G +  SP   +R+   QDHI+AER+RREKLSQRFIALSAIV
Sbjct: 138 LISQDSLAH-QSHTTKSNRGTR--SPSRNSRIPQAQDHILAERRRREKLSQRFIALSAIV 194

Query: 170 PGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDNPNGAF 229
           PGLKKMDKASVLGDAIKYLKQLQEKVKILEEQ  +K IESVVFV K+ +  +G++ +   
Sbjct: 195 PGLKKMDKASVLGDAIKYLKQLQEKVKILEEQTRRKDIESVVFVKKSHVFPDGNDTSKEE 254

Query: 230 NEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTI 289
           +E LPEIEAR CDK+VLIR+HCEK+K + EK +AEIE LHLT++NSSVM+FGS  LD+TI
Sbjct: 255 DEPLPEIEARICDKNVLIRIHCEKKKDIIEKTIAEIENLHLTIVNSSVMSFGSLALDITI 314

Query: 290 IAQMDVEFNMTVKDLVKNLHSAFQLF 315
           IAQMD EF +T+KDLVKNL S  + F
Sbjct: 315 IAQMDNEFCLTLKDLVKNLQSTLRSF 340

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521257|ref|XP_003529273.1| PREDICTED: transcription factor bHLH25-like [Glycine max]

 Score =  333 bits (855), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 188/330 (56%), Positives = 230/330 (69%), Gaps = 19/330 (5%)

Query: 1   MEISSIKGLPELG--MEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSY--THPSFNN 56
           MEISSI+GLP+    MED +F++QWH+ +SID+ NLLPIAAAFGE LQH    T+P+FN 
Sbjct: 1   MEISSIRGLPDDMEIMEDATFLHQWHL-SSIDDPNLLPIAAAFGETLQHHAFSTYPNFNP 59

Query: 57  NTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILK-PK-----QETGAGYPSDIL 110
            T ++      +  T +      NPN+ S+   ++   +  P             P D +
Sbjct: 60  KTSMETTLADDERGTKHHRNISLNPNSKSAQTSSETQFVSFPNLFSFVDSNHTTPPPDTI 119

Query: 111 PSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVP 170
            SQ + GN+ NYVFKA Q AK+   G   + S  QDHIIAERKRREKLSQRFIALSA+VP
Sbjct: 120 -SQGTLGNHNNYVFKACQEAKKT--GKRYKHSQPQDHIIAERKRREKLSQRFIALSALVP 176

Query: 171 GLKKMDKASVLGDAIKYLKQLQEKVKILEEQAN-KKTIESVVFVNKTQLSDEGDNP---- 225
           GL+K DKASVLGDAIKYLKQLQEKV  LEE+ N KK +ESVV V K QLS++ +N     
Sbjct: 177 GLQKTDKASVLGDAIKYLKQLQEKVNALEEEQNMKKNVESVVIVKKCQLSNDVNNSSSEH 236

Query: 226 NGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVL 285
           +G+F+EALPEIEARFC++SVLIRVHCEK KGV E  +  IEKLHL VINS+ MTFG   L
Sbjct: 237 DGSFDEALPEIEARFCERSVLIRVHCEKSKGVVENTIQGIEKLHLKVINSNTMTFGRCAL 296

Query: 286 DVTIIAQMDVEFNMTVKDLVKNLHSAFQLF 315
           D+T+IAQMD+EF M VKDLV+NL SAF  F
Sbjct: 297 DITVIAQMDMEFCMGVKDLVRNLRSAFTSF 326

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248228|ref|NP_001239843.1| transcription factor bHLH25-like [Glycine max] gi|3399777|gb|AAC32828.1| symbiotic ammonium transporter [Glycine max]

 Score =  332 bits (851), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 199/348 (57%), Positives = 248/348 (71%), Gaps = 38/348 (10%)

Query: 1   MEISSIKGLPELGM-EDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQ-HSYTHPS-FN-- 55
           MEISSI+GLPELG+ ED +F++QW + NSID  +L    AAFG+ LQ HS++  S FN  
Sbjct: 6   MEISSIRGLPELGIIEDPNFLHQWQL-NSIDTTSLK--GAAFGDILQKHSFSDNSNFNPK 62

Query: 56  -----NNTGIDRPQKQLKTSTWN-------SSETGFNP--NNVSSINMN---QMGILKPK 98
                + TGI+R  KQL  ++WN       + ET F    N +S +N N   ++G++KPK
Sbjct: 63  TSMETSQTGIERYAKQLGDNSWNHNKSQQQTPETQFASCSNLLSFVNTNYTSELGLVKPK 122

Query: 99  QETGA-----GYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERK 153
            E           +D+L SQ + GN QNY+FKASQ  K+I      +LS  QDHIIAERK
Sbjct: 123 VEMACPKIDNNALADMLISQGTLGN-QNYIFKASQETKKIKTRP--KLSQPQDHIIAERK 179

Query: 154 RREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK-TIESVVF 212
           RREKLSQRFIALSA+VPGLKKMDKASVLG+AIKYLKQ+QEKV  LEE+ N+K T+ESVV 
Sbjct: 180 RREKLSQRFIALSALVPGLKKMDKASVLGEAIKYLKQMQEKVSALEEEQNRKRTVESVVI 239

Query: 213 VNKTQLSDEGDN----PNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKL 268
           V K+QLS + ++      G F EALPEIEARF +++VLIR+HCEK KGV EK ++EIEKL
Sbjct: 240 VKKSQLSSDAEDSSSETGGTFVEALPEIEARFWERNVLIRIHCEKNKGVIEKTISEIEKL 299

Query: 269 HLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA 316
           HL VINSS +TFGS +LD+TIIAQMD+EF MTVKDLV++L SAF  F 
Sbjct: 300 HLKVINSSALTFGSFILDITIIAQMDMEFCMTVKDLVRSLRSAFSYFV 347

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356549469|ref|XP_003543116.1| PREDICTED: transcription factor bHLH25-like [Glycine max]

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 199/353 (56%), Positives = 249/353 (70%), Gaps = 47/353 (13%)

Query: 1   MEISSIKGLPELGM-EDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQ-HSYTHPS-FN-- 55
           MEISSI+GLPE+G+ ED +F++ W + NSID  +L    A FGE LQ HS++  S FN  
Sbjct: 6   MEISSIRGLPEMGIIEDPNFLHHWQL-NSIDTTSL--TGAPFGEILQKHSFSDNSNFNPK 62

Query: 56  -----NNTGIDRPQKQLKTSTWN-------SSETGFNP--NNVSSINMN---QMGILKPK 98
                + TGI+RP KQL+ ++WN       + ET F    N +S +N N   ++G++KPK
Sbjct: 63  TSMETSPTGIERPAKQLRNNSWNHNKSQQQTPETQFASCSNLLSFVNSNYTSELGLVKPK 122

Query: 99  QETGA-----GYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERK 153
            E           +D+L SQ + GN QNY+FKASQ AK+I      +LS  QDHIIAERK
Sbjct: 123 VEMVCPKINNNTLADMLISQGNLGN-QNYLFKASQEAKKIETRP--KLSQPQDHIIAERK 179

Query: 154 RREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKK-TIESVVF 212
           RREKLSQRFIALSA+VPGLKKMDKASVLG+AIKYLKQ+QEKV  LEE+ N+K T+ESVV 
Sbjct: 180 RREKLSQRFIALSALVPGLKKMDKASVLGEAIKYLKQMQEKVSALEEEQNRKRTVESVVI 239

Query: 213 VNKTQLSDE---------GDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVA 263
           V K++LS +         GD     F+EALPEIEARF +++VLIR+HCEK KGV EK ++
Sbjct: 240 VKKSRLSSDAEDSSSSETGD----TFDEALPEIEARFYERNVLIRIHCEKNKGVIEKTIS 295

Query: 264 EIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLFA 316
           EIEKLHL VINSS +TFGS +LD+TIIAQMD+EF MTVKDLV++L SAF  F 
Sbjct: 296 EIEKLHLKVINSSALTFGSFILDITIIAQMDMEFCMTVKDLVRSLRSAFSYFV 348

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446133|ref|XP_003593344.1| Transcription factor bHLH25 [Medicago truncatula] gi|355482392|gb|AES63595.1| Transcription factor bHLH25 [Medicago truncatula]

 Score =  304 bits (778), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 177/339 (52%), Positives = 229/339 (67%), Gaps = 42/339 (12%)

Query: 14  MEDLSFMNQWH-MMNSIDEFNLLPIAAAFGENLQHSY--THPSFNNNT-------GIDRP 63
           MED +F++ ++  ++SID  NL   A+AFG+ LQ      +P+FNN T       G +RP
Sbjct: 4   MEDPNFLHHFNNHLSSIDTNNL--TASAFGDALQKHILSNNPNFNNKTCMETSPTGNERP 61

Query: 64  QKQLKTSTWN------SSETGFNPNNVSSINM---------NQMGILKPKQET------G 102
            KQL+ ++WN      +S+T ++  N  S N+         NQ+G+LKPK E        
Sbjct: 62  AKQLRNNSWNYNNSPPTSDTQYD--NCCSNNLLSFADLNYTNQLGLLKPKSEMVCPKIDN 119

Query: 103 AGYPSDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRF 162
               +++L +Q +   NQN+VFKA Q AK I     N+LS   DHI+ ERKRREKLSQRF
Sbjct: 120 TSTLANMLITQGNLFGNQNHVFKAVQEAKDIE-NRPNKLSQAHDHIVTERKRREKLSQRF 178

Query: 163 IALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEE-QANKKTIESVVFVNKTQLS-- 219
           IALSA+VP LKKMDKASVLG+AI+YLKQ++EKV +LEE Q  KKT+ESVV V K+QLS  
Sbjct: 179 IALSALVPNLKKMDKASVLGEAIRYLKQMEEKVSVLEEEQKRKKTVESVVIVKKSQLSMN 238

Query: 220 ---DEGDNPNGAFNEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSS 276
              D  D  N  ++E LPEIEARFC++SVLIR+HC K +GV EKI++EIEKLHL VINSS
Sbjct: 239 EAEDRADTNNSTYDETLPEIEARFCERSVLIRLHCLKSQGVIEKIMSEIEKLHLKVINSS 298

Query: 277 VMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF 315
            +TFG+  LD+TIIAQMDV F MTVKDLV+ + SA+  F
Sbjct: 299 SLTFGNFTLDITIIAQMDVGFCMTVKDLVRKIRSAYSSF 337

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357476085|ref|XP_003608328.1| Transcription factor bHLH25 [Medicago truncatula] gi|355509383|gb|AES90525.1| Transcription factor bHLH25 [Medicago truncatula]

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 175/326 (53%), Positives = 226/326 (69%), Gaps = 33/326 (10%)

Query: 3   ISSIKGLPELGM-ED-LSFMNQWHMMNSIDEFNLLPIAAAFGENLQH-SYTHPSFNNNTG 59
           IS I+G P+  M ED L   +QWH+ +SI+E N LPI +AFG+  QH SY +P+FN  T 
Sbjct: 21  ISFIRGFPDQEMMEDPLLLHHQWHL-SSINESNSLPIGSAFGDTSQHHSYVYPNFNPRTS 79

Query: 60  IDRPQKQLKTSTWNSSETGF--NPNNVSSINMNQM---GILKPKQETGAGYPSDILPSQV 114
           ++  Q         + ET F   PN +S +++NQ+   G++KPK E        ++ SQ 
Sbjct: 80  METAQ---------TLETQFVSYPNLLSFVDLNQLNQLGLVKPKDE--------MIGSQN 122

Query: 115 SFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKK 174
           +   + + + + +   K+++     +LS  QDHIIAERKRREKLSQRFIALSA+VPGL+K
Sbjct: 123 NNATSSDMISQGTFETKKVATRP--KLSLPQDHIIAERKRREKLSQRFIALSALVPGLQK 180

Query: 175 MDKASVLGDAIKYLKQLQEKVKILEEQAN-KKTIESVVFVNKTQLSDEGDNPNG----AF 229
           MDK +VLGDAIKYLK+LQEKVK+LEE+ N KK +E VV V K QLS++ +N +      F
Sbjct: 181 MDKVTVLGDAIKYLKKLQEKVKVLEEEQNMKKNVEFVVVVKKYQLSNDVENSSAESGDPF 240

Query: 230 NEALPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTI 289
           +E LPEIEARFCD++VLIRVHCEK KGV EK + +IEKL+L V NSS MTFGS  LD+TI
Sbjct: 241 DEELPEIEARFCDRNVLIRVHCEKIKGVVEKTIHKIEKLNLKVTNSSFMTFGSCALDITI 300

Query: 290 IAQMDVEFNMTVKDLVKNLHSAFQLF 315
           IAQMDVEF MTVKDLV+NL S F  F
Sbjct: 301 IAQMDVEFCMTVKDLVRNLRSVFTSF 326

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	316
UNIPROTKB|Q75GI1	359	OSJNBa0013A09.16 "Putative tra	0.680	0.598	0.508	4.2e-53
TAIR|locus:2137574	328	AT4G37850 "AT4G37850" [Arabido	0.958	0.923	0.421	8.3e-51
TAIR|locus:2062235	320	NAI1 "AT2G22770" [Arabidopsis	0.674	0.665	0.340	1.4e-44
TAIR|locus:2062225	305	AT2G22750 "AT2G22750" [Arabido	0.803	0.832	0.439	2.4e-44
TAIR|locus:2062230	295	AT2G22760 "AT2G22760" [Arabido	0.582	0.623	0.469	5.5e-38
UNIPROTKB|Q2QLR0	338	LOC_Os12g43620 "Helix-loop-hel	0.740	0.692	0.364	1.3e-34
UNIPROTKB|Q8LSP3	451	OJ1203D03.3 "Helix-loop-helix	0.477	0.334	0.433	2.3e-30
UNIPROTKB|Q84R60	353	OSJNBb0113I20.8 "Putative ammo	0.689	0.617	0.354	4.9e-30
UNIPROTKB|Q84R79	301	OSJNBb0113I20.1 "Putative ammo	0.579	0.607	0.397	4.4e-29
UNIPROTKB|Q336P5	699	Os10g0575000 "Os10g0575000 pro	0.721	0.326	0.310	1.1e-19

UNIPROTKB|Q75GI1 OSJNBa0013A09.16 "Putative transcription factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 511 (184.9 bits), Expect = 4.2e-53, Sum P(2) = 4.2e-53
 Identities = 117/230 (50%), Positives = 159/230 (69%)

Query:    95 LKPKQET-GAGYP-SDILPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAER 152
             LKPKQE   A  P S   P + S+         A+  AK  +  A    S  Q+HI+AER
Sbjct:   133 LKPKQELDAAAAPFSQARPVKRSYD-----AMVAADVAKAPAAAASRPASQNQEHILAER 187

Query:   153 KRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVF 212
             KRREKLSQRFIALS IVPGLKKMDKASVLGDAIKY+KQLQ++VK LEE+A ++ +E+ V 
Sbjct:   188 KRREKLSQRFIALSKIVPGLKKMDKASVLGDAIKYVKQLQDQVKGLEEEARRRPVEAAVL 247

Query:   213 VNKTQLS---DEGDNPNGAFN--EA---LPEIEARFCDKSVLIRVHCEKRKGVFEKIVAE 264
             V K+QLS   D+G + +  F+  EA   LPEIEAR  +++VL+++HCE RKG     ++E
Sbjct:   248 VKKSQLSADDDDGSSCDENFDGGEATAGLPEIEARVSERTVLVKIHCENRKGALITALSE 307

Query:   265 IEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL 314
             +E + LT++N++V+ F SS LD+TI+A     F+++VKD+VK L+ AF+L
Sbjct:   308 VETIGLTIMNTNVLPFTSSSLDITIMATAGENFSLSVKDIVKKLNQAFKL 357

GO:0005634 "nucleus" evidence=IC

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

 Score = 528 (190.9 bits), Expect = 8.3e-51, P = 8.3e-51
 Identities = 143/339 (42%), Positives = 207/339 (61%)

Query:     1 MEISSIKGLPELGMEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYT---HPSFNNN 57
             M I S +   E  +E+ S + Q+HM + + E       A +     HS+T    PS+++ 
Sbjct:     1 MSILSTRWFSEQEIEENSIIQQFHMNSIVGEVQ----EAQY--IFPHSFTTNNDPSYDDL 54

Query:    58 TGIDRPQKQLKTSTWNSSETGFNPNNV-------SS---INMNQMGILKPKQETGAGYPS 107
               + +P K L+T T+ S  +   PN+        SS   ++    G    + E    Y +
Sbjct:    55 IEM-KPPKILET-TYISPSSHLPPNSKPHHIHRHSSSRILSFEDYGSNDMEHEYSPTYLN 112

Query:   108 DI----LPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFI 163
              I    L +QV   + ++  F   +G KR  P + N+ SN QDHIIAERKRREKL+QRF+
Sbjct:   113 SIFSPKLEAQVQ-PHQKSDEFNR-KGTKRAQPFSRNQ-SNAQDHIIAERKRREKLTQRFV 169

Query:   164 ALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGD 223
             ALSA+VPGLKKMDKASVLGDA+K++K LQE+V  LEEQ  ++ +ES+V V K++L  + +
Sbjct:   170 ALSALVPGLKKMDKASVLGDALKHIKYLQERVGELEEQKKERRLESMVLVKKSKLILDDN 229

Query:   224 NPN------GAFNEA-LPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSS 276
             N +        F++  LPEIE RF D+ VLI++ CEK+KG   KI+AEIEKLH+ + NSS
Sbjct:   230 NQSFSSSCEDGFSDLDLPEIEVRFSDEDVLIKILCEKQKGHLAKIMAEIEKLHILITNSS 289

Query:   277 VMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF 315
             V+ FG + LD+TIIA+ + +F+MT+ D+VK+L SA   F
Sbjct:   290 VLNFGPT-LDITIIAKKESDFDMTLMDVVKSLRSALSNF 327

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

 Score = 276 (102.2 bits), Expect = 1.4e-44, Sum P(2) = 1.4e-44
 Identities = 79/232 (34%), Positives = 126/232 (54%)

Query:    14 MEDLSFMNQWHMMNSIDEFNLLPIAAAFGENLQHSYTHPSFNNNTGI------DRPQKQL 67
             M+D SFM+   +M   DE+ +    + F      + T+P   + +G       +RP KQ+
Sbjct:     1 MDDSSFMD---LMIDTDEYLIDDWESDF-PICGETNTNPGSESGSGTGFELLAERPTKQM 56

Query:    68 KTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKAS 127
             KT+  N + T  +P++ SS       ++          P +   + ++F N  +   K  
Sbjct:    57 KTNN-NMNSTSSSPSSSSSSGSRTSQVISFGSPDTKTNPVE---TSLNFSNQVSMDQKVG 112

Query:   128 QGAKRISPGAGNRLSNT-QDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIK 186
                K      G R  +  ++H++AERKRR+KL++R IALSA++PGLKK DKA+VL DAIK
Sbjct:   113 SKRKDCVNNGGRREPHLLKEHVLAERKRRQKLNERLIALSALLPGLKKTDKATVLEDAIK 172

Query:   187 YLKQLQEKVKILEEQ--ANKKTIESVVFVNKTQ--LSDEGDNPNGAFNEALP 234
             +LKQLQE+VK LEE+    KK  +S++ V ++Q  L D+  + +   + A P
Sbjct:   173 HLKQLQERVKKLEEERVVTKKMDQSIILVKRSQVYLDDDSSSYSSTCSAASP 224

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0007029 "endoplasmic reticulum organization" evidence=IMP

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

 Score = 467 (169.5 bits), Expect = 2.4e-44, P = 2.4e-44
 Identities = 120/273 (43%), Positives = 166/273 (60%)

Query:    53 SFNNNTGIDRPQKQLKTSTWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPS 112
             S N +   +RP K LKT+  + +   F+ +N           +   ++TG    +   P+
Sbjct:    27 SCNKSLVEERPSKILKTTHISPNLHPFSSSNPPPPKHQPSSRILSFEKTGLHVMNHNSPN 86

Query:   113 QVSFGNNQNYVF----KAS---QGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIAL 165
              +    ++        KA    +G KR      ++ SN QDHI+AERKRREKL+QRF+AL
Sbjct:    87 LIFSPKDEEIGLPEHKKAELIIRGTKRAQSLTRSQ-SNAQDHILAERKRREKLTQRFVAL 145

Query:   166 SAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLS-DEGDN 224
             SA++PGLKKMDKASVLGDAIK++K LQE VK  EEQ  +KT+ESVV V K+ L  DE   
Sbjct:   146 SALIPGLKKMDKASVLGDAIKHIKYLQESVKEYEEQKKEKTMESVVLVKKSSLVLDENHQ 205

Query:   225 PN------GAFNEA---LPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINS 275
             P+      G  N +   LPEIE R   K VLI++ CEK+KG   KI+ EIEKL L++ NS
Sbjct:   206 PSSSSSSDGNRNSSSSNLPEIEVRVSGKDVLIKILCEKQKGNVIKIMGEIEKLGLSITNS 265

Query:   276 SVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNL 308
             +V+ FG +  D++IIAQ +  F+M ++D+VKNL
Sbjct:   266 NVLPFGPT-FDISIIAQKNNNFDMKIEDVVKNL 297

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:2062230 AT2G22760 "AT2G22760" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 91/194 (46%), Positives = 132/194 (68%)

Query:   128 QGAKRISPGAGNRLSN-TQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIK 186
             +G KR +   G R     ++H++AERKRREKLS++FIALSA++PGLKK DK ++L DAI 
Sbjct:   100 RGTKRKTCSHGTRSPVLAKEHVLAERKRREKLSEKFIALSALLPGLKKADKVTILDDAIS 159

Query:   187 YLKQLQEKVKIL-EEQANKKTIESVVFVNKTQLS-DEGDN----PNG--AFNEALPEIEA 238
              +KQLQE+++ L EE+   + +ES++ V K+++  DE  N    P+    F++ALPEIEA
Sbjct:   160 RMKQLQEQLRTLKEEKEATRQMESMILVKKSKVFFDEEPNLSCSPSVHIEFDQALPEIEA 219

Query:   239 RFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFN 298
             +     +LIR+ CEK KG    I+  IE   L + NS V+ FG S LD+T++AQMD +F+
Sbjct:   220 KISQNDILIRILCEKSKGCMINILNTIENFQLRIENSIVLPFGDSTLDITVLAQMDKDFS 279

Query:   299 MTV-KDLVKNLHSA 311
             M++ KDLV+NL  A
Sbjct:   280 MSILKDLVRNLRLA 293

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

 Score = 353 (129.3 bits), Expect = 1.3e-34, Sum P(2) = 1.3e-34
 Identities = 90/247 (36%), Positives = 138/247 (55%)

Query:    55 NNNTGIDRPQKQLKTST--WNSSETGFNPNNVSSINMN-QMGILKPKQE-TGAGYPSDIL 110
             N+ +  D P     T+   W+   TG        ++ N      +P  E +G G    ++
Sbjct:    71 NSWSSSDSPGGGAATAAAGWSPHVTGGGGRGHRPMSWNFSAASAQPTTEDSGGGGGGGVV 130

Query:   111 PSQV----SFGNNQNYVFKASQGAKRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALS 166
             P+ +    +    +  V K   G    S  A   +   QDHIIAER+RREK++QRFI LS
Sbjct:   131 PAPLQAMETTATARAAVKKGGGGGSSSSAAAPGYV---QDHIIAERRRREKINQRFIELS 187

Query:   167 AIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDNPN 226
              ++PGLKKMDKA++LGDA+KY+K+LQEKVK LEE+       ++V V K+  S       
Sbjct:   188 TVIPGLKKMDKATILGDAVKYVKELQEKVKTLEEEDGGGRPAAMV-VRKSSCSGRQSAAG 246

Query:   227 GAFNEA-LPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVL 285
                 E  +PEIE R  ++SVL+RV C   +G+  ++++E+E+L L + ++SVM F +S +
Sbjct:   247 DGDGEGRVPEIEVRVWERSVLVRVQCGNSRGLLVRLLSEVEELRLGITHTSVMPFPASTV 306

Query:   286 DVTIIAQ 292
              +TI A+
Sbjct:   307 IITITAK 313

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q8LSP3 OJ1203D03.3 "Helix-loop-helix DNA-binding domain containing protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 69/159 (43%), Positives = 110/159 (69%)

Query:   142 SNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQ 201
             +N Q+H+IAERKRREKL Q+F+AL+ IVPGLKK DK S+LG  I Y+KQL+EKVK LEE 
Sbjct:   283 ANAQEHVIAERKRREKLQQQFVALATIVPGLKKTDKISLLGSTIDYVKQLEEKVKALEEG 342

Query:   202 ANKKTIESVVFVNKTQLS---DEGDNPN-----GAFNEALPEIEARFCDKSVLIRVHCEK 253
             + +    +  F +K +++   D+G + +     G+ + + P +EA     +VL+++ C++
Sbjct:   343 SRRTAEPTTAFESKCRITVDDDDGGSASSGTDDGSSSSSSPTVEASIHGNTVLLKICCKE 402

Query:   254 RKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQ 292
             R+G+   I++E+EK  L++IN+SV+ F  S L++TI A+
Sbjct:   403 RRGLLVMILSELEKQGLSIINTSVVPFTDSCLNITITAK 441

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q84R60 OSJNBb0113I20.8 "Putative ammonium transporter" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 84/237 (35%), Positives = 131/237 (55%)

Query:    71 TWNSSETGFNPNNVSSINMNQMGILKPKQETGAGYPSDILPSQVSFGNNQNYVFKASQGA 130
             +WN S     P N  +   N     + +   G G     LP+ VS   +      +S+G 
Sbjct:   120 SWNFSSAMTQPCNDQATPSNPPTTTRARYG-GGGVR--YLPAAVSPSPSAQTRRASSKGN 176

Query:   131 KRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQ 190
                  G+ +     Q+HIIAERKRREK++QRFI LS ++PGLKKMDKA++L DA++Y+K+
Sbjct:   177 GGGGSGSSSAAPYAQEHIIAERKRREKINQRFIELSTVIPGLKKMDKATILSDAVRYVKE 236

Query:   191 LQEKVKILEEQANKKTIESVVFVNK----TQLSD----------EGDNPNGAFNEALPEI 236
             +QEK+  LE+  N   +ES + + K    T  SD           G + +G    +LPEI
Sbjct:   237 MQEKLSELEQHQNGG-VESAILLKKPCIATSSSDGGCPAASSAVAGSSSSGTARSSLPEI 295

Query:   237 EARFCDKSVLIRVHCEKR-KGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQ 292
             EA+    +V++R+H E   KG   +++A +E LHL + +++VM F +    +TI+A+
Sbjct:   296 EAKISHGNVMVRIHGENNGKGSLVRLLAAVEGLHLGITHTNVMPFSACTAIITIMAK 352

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q84R79 OSJNBb0113I20.1 "Putative ammonium transporter" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 83/209 (39%), Positives = 129/209 (61%)

Query:   111 PSQVSFGNN---QNYVFKASQGAKRISPGA--GNRLSNTQ-DHIIAERKRREKLSQRFIA 164
             PS     NN    ++ F A+  A +   GA  G   +  Q +H++AERKRREK++QRF+ 
Sbjct:    89 PSGGCGSNNLPLMSWDFSAASVAVQEDLGAHGGAAAAYAQLEHVVAERKRREKINQRFME 148

Query:   165 LSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVNKTQLSDEGDN 224
             LSA++P LKKMDKA++L DA  Y+++LQEK+K LEEQA  +  E+ +            +
Sbjct:   149 LSAVIPKLKKMDKATILSDAASYIRELQEKLKALEEQAAARVTEAAMAT---------PS 199

Query:   225 PNGAFNE--ALPEIEARFCDKS---VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT 279
             P  A N     PEIE R C  +   V++R+HCE  +GV  +I+AE+E++HL +IN++VM 
Sbjct:   200 PARAMNHLPVPPEIEVR-CSPTNNVVMVRIHCENGEGVIVRILAEVEEIHLRIINANVMP 258

Query:   280 F---GSSVLDVTIIAQMDVEFN-MTVKDL 304
             F   G++++ +TI A+  +  + + V+DL
Sbjct:   259 FLDQGATMI-ITIAAKAKINRSEVKVQDL 286

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q336P5 Os10g0575000 "Os10g0575000 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 244 (91.0 bits), Expect = 1.1e-19, P = 1.1e-19
 Identities = 77/248 (31%), Positives = 124/248 (50%)

Query:    46 QHSYTHPSFNNNTGIDRPQKQLKTSTWNSSETGFNPN---NVSSINMNQMGILKPKQETG 102
             QH+ T  +  N+   +  QK+   +T  +S T  +P    N   ++ +     +P   TG
Sbjct:   415 QHTPTLTAAANDAKSNN-QKRSMEATSRASNTNNHPAATANEGMLSFSSAPTTRPSTGTG 473

Query:   103 AGYPSDI----LPSQVSFGNNQNYVFKASQGAKRISPGAGNRLSNTQD----HIIAERKR 154
             A   S+     L + V    +   V    +  KR     G + +N ++    H+ AER+R
Sbjct:   474 APAKSESDHSDLEASVREVESSRVVAPPPEAEKRPRK-RGRKPANGREEPLNHVEAERQR 532

Query:   155 REKLSQRFIALSAIVPGLKKMDKASVLGDAIKYLKQLQEKVKILEEQANKKTIESVVFVN 214
             REKL+QRF AL A+VP + KMDKAS+LGDAI Y+ +L+ K+  LE   +K+T++S +   
Sbjct:   533 REKLNQRFYALRAVVPNVSKMDKASLLGDAISYINELRGKLTALE--TDKETLQSQMESL 590

Query:   215 KTQLSDEGDNPNGAFNEA-----LPEIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLH 269
             K +       P+G   +        EIEA+      +IRV C KR     +++  + +L 
Sbjct:   591 KKERDARPPAPSGGGGDGGARCHAVEIEAKILGLEAMIRVQCHKRNHPAARLMTALRELD 650

Query:   270 LTVINSSV 277
             L V ++SV
Sbjct:   651 LDVYHASV 658

GO:0005634 "nucleus" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9T072	BH025_ARATH	No assigned EC number	0.4215	0.9430	0.9085	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

Your Input: GSVIVG00038535001 SubName- Full=Chromosome chr3 scaffold_95, whole genome shotgun sequence; (309 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	316
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-12
smart00353	53	smart00353, HLH, helix loop helix domain	8e-12
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-10

>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 = 60.3 bits (147), Expect = 3e-12
 Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 3/53 (5%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVK 196
           H + ER+RRE+++  F  L +++P L   KK+ KA +L  A+ Y+K LQE ++
Sbjct: 8   HNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 59.2 bits (144), Expect = 8e-12
 Identities = 21/51 (41%), Positives = 35/51 (68%), Gaps = 3/51 (5%)

Query: 149 IAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVK 196
             ER+RR K+++ F  L +++P L   KK+ KA +L  AI+Y+K LQE+++
Sbjct: 2   ARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

Length = 53

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

 Score = 55.2 bits (134), Expect = 2e-10
 Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQ 192
           H   ER+RR++++  F  L  ++P    KK+ KA +L  AI+Y+K LQ
Sbjct: 5   HNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	316
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.38
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.35
smart00353	53	HLH helix loop helix domain.	99.31
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.89
KOG1318	411	consensus Helix loop helix transcription factor EB	98.85
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.35
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	98.34
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	98.34
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	98.33
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.24
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	98.21
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.18
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.18
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	98.12
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.99
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.82
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.66
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	97.47
KOG0561	373	consensus bHLH transcription factor [Transcription	97.46
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.41
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.41
PRK05007	884	PII uridylyl-transferase; Provisional	97.32
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	97.31
PLN03217	93	transcription factor ATBS1; Provisional	97.15
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	97.11
PRK00275	895	glnD PII uridylyl-transferase; Provisional	97.01
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	96.91
PRK01759	854	glnD PII uridylyl-transferase; Provisional	96.87
PRK04374	869	PII uridylyl-transferase; Provisional	96.84
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	96.82
PRK05092	931	PII uridylyl-transferase; Provisional	96.74
PRK03381	774	PII uridylyl-transferase; Provisional	96.59
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	96.54
PRK00194	90	hypothetical protein; Validated	96.41
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	96.41
PRK03059	856	PII uridylyl-transferase; Provisional	96.38
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	96.35
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	96.31
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	96.31
PRK03381	774	PII uridylyl-transferase; Provisional	96.3
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	96.14
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.12
PRK01759	854	glnD PII uridylyl-transferase; Provisional	96.08
PRK05007	884	PII uridylyl-transferase; Provisional	96.02
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	95.87
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	95.73
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	95.29
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.23
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	95.12
PRK03059	856	PII uridylyl-transferase; Provisional	95.09
PRK05092	931	PII uridylyl-transferase; Provisional	94.77
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.56
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	94.5
PRK04435	147	hypothetical protein; Provisional	94.45
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	94.44
cd02116	60	ACT ACT domains are commonly involved in specifica	94.44
PRK04374	869	PII uridylyl-transferase; Provisional	94.37
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	94.03
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	93.97
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	93.93
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	93.79
KOG3910	632	consensus Helix loop helix transcription factor [T	93.49
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	93.45
PRK08577	136	hypothetical protein; Provisional	93.38
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	93.26
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	92.59
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	92.57
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	92.37
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	92.36
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	91.74
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	91.72
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	91.3
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	91.14
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	91.11
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	90.62
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	90.27
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	90.2
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	89.85
PRK07334	403	threonine dehydratase; Provisional	89.59
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	89.35
PRK11589	190	gcvR glycine cleavage system transcriptional repre	88.27
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	87.49
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	87.41
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	87.12
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	86.94
cd04885	68	ACT_ThrD-I Tandem C-terminal ACT domains of threon	86.6
KOG3898	254	consensus Transcription factor NeuroD and related	86.43
COG4492	150	PheB ACT domain-containing protein [General functi	85.27
PRK11895	161	ilvH acetolactate synthase 3 regulatory subunit; R	84.98
KOG4395	285	consensus Transcription factor Atonal, contains HT	84.75
TIGR00119	157	acolac_sm acetolactate synthase, small subunit. ac	84.39
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	81.85
cd04930	115	ACT_TH ACT domain of the nonheme iron-dependent ar	81.18
COG0788	287	PurU Formyltetrahydrofolate hydrolase [Nucleotide	80.63

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

Probab=99.38  E-value=5.3e-13  Score=97.05  Aligned_cols=53  Identities=40%  Similarity=0.710  Sum_probs=50.3

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKV  195 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v  195 (316)
                      .+..|+..||+||++||..|..|+++||..   .|+||++||..||+||+.|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999988   89999999999999999999876

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

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

Probab=99.35  E-value=7.1e-13  Score=95.62  Aligned_cols=49  Identities=43%  Similarity=0.700  Sum_probs=46.5

Q ss_pred             cchhhHHHHHHHHHHHHHHHHHhcccCCC-----CCCCcchHHHHHHHHHHHHH
Q 021208          144 TQDHIIAERKRREKLSQRFIALSAIVPGL-----KKMDKASVLGDAIKYLKQLQ  192 (316)
Q Consensus       144 ~~~h~~~Er~RR~~in~~~~~LrslvP~~-----~k~dKasiL~~Ai~YIk~Lq  192 (316)
                      +..|+..||+||++||+.|..|+.+||..     .|++|++||..||+||++||
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            56899999999999999999999999976     78999999999999999997

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

>smart00353 HLH helix loop helix domain

Probab=99.31  E-value=3.1e-12  Score=91.17  Aligned_cols=49  Identities=41%  Similarity=0.645  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHHHHHHHHhcccCC---CCCCCcchHHHHHHHHHHHHHHHHH
Q 021208          148 IIAERKRREKLSQRFIALSAIVPG---LKKMDKASVLGDAIKYLKQLQEKVK  196 (316)
Q Consensus       148 ~~~Er~RR~~in~~~~~LrslvP~---~~k~dKasiL~~Ai~YIk~Lq~~v~  196 (316)
                      +..||+||++||+.|..|+++||.   ..|++|++||..||+||+.|+.+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999995   5799999999999999999999875

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.89  E-value=9.4e-10  Score=97.34  Aligned_cols=65  Identities=29%  Similarity=0.486  Sum_probs=57.2

Q ss_pred             CCCCcchhhHHHHHHHHHHHHHHHHHhcccCCC-------CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhh
Q 021208          140 RLSNTQDHIIAERKRREKLSQRFIALSAIVPGL-------KKMDKASVLGDAIKYLKQLQEKVKILEEQANK  204 (316)
Q Consensus       140 ~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-------~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~  204 (316)
                      +..++..|..+||+||+.||..+..|+.|||.+       .|..||.||..+|+||.+|..++..-+++...
T Consensus        59 k~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~  130 (229)
T KOG1319|consen   59 KDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVST  130 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345688999999999999999999999999965       36779999999999999999998888876654

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

Probab=98.85  E-value=3.6e-09  Score=104.23  Aligned_cols=59  Identities=27%  Similarity=0.528  Sum_probs=52.9

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQLQEKVKILEE  200 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~Lq~~v~~L~~  200 (316)
                      .+|..|+++|||||++||++|..|..|||.+    .+..|..||..+++||+.||+..++..+
T Consensus       232 ~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E  294 (411)
T KOG1318|consen  232 RKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRARE  294 (411)
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHH
Confidence            4788999999999999999999999999987    4667999999999999999998875443

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

Probab=98.35  E-value=5.1e-06  Score=63.64  Aligned_cols=67  Identities=16%  Similarity=0.327  Sum_probs=57.5

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      +|+|.+.+++|+|.+|.++|..+||+|..|.|++.|+++.+++.+ .-.++..++-.+..+.|+.+|.
T Consensus         3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV-~d~~g~kl~d~~~~~~l~~~L~   69 (72)
T cd04895           3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHV-TDQLGNKLTDDSLIAYIEKSLG   69 (72)
T ss_pred             EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEE-ECCCCCCCCCHHHHHHHHHHhc
Confidence            689999999999999999999999999999999999999997765 4445666666677778887774

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

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

Probab=98.34  E-value=5.3e-06  Score=64.03  Aligned_cols=67  Identities=12%  Similarity=0.259  Sum_probs=53.9

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      +|.|.|++++|||.+|..+|-.+|+.|.+|.|++.|+++.+.+.+ .-.++..++-++..+.|+++|.
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV-~d~~g~kl~~~~~~~~l~~~L~   69 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYI-RHKDGRTLSTEGERQRVIKCLE   69 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEE-EcCCCCccCCHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999997765 4445566654444444444443

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.

>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=98.34  E-value=4.1e-06  Score=64.31  Aligned_cols=71  Identities=23%  Similarity=0.337  Sum_probs=54.7

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCccc---CHHHHHHHHHHHHHhhC
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNM---TVKDLVKNLHSAFQLFA  316 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~l---s~~eL~~~L~~al~~~~  316 (316)
                      ++|+|.|+.++|+|.+|..+|..+||.|+.|.+.+ .++.+++.+++... ++...   ..++|.+.|+.+|.+-|
T Consensus         1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~-~~~~~~~~~~~~l~~~L~~~L~~~~   75 (76)
T cd04927           1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDA-RELLHTKKRREETYDYLRAVLGDSM   75 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCC-CCCCCCHHHHHHHHHHHHHHHchhc
Confidence            47899999999999999999999999999999996 89999997665332 22211   23446777777766544

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=98.33  E-value=5.6e-06  Score=63.91  Aligned_cols=66  Identities=15%  Similarity=0.255  Sum_probs=53.1

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEE--EeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVM--TFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs--~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      +|.|.|.+|+|+|.+|.++|..+|++|..|.|+  +.|+++.+++.+ .. ++..++-.+-.+.|+++|.
T Consensus         2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~-~g~kl~d~~~~~~L~~~L~   69 (75)
T cd04896           2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QS-DGKKIMDPKKQAALCARLR   69 (75)
T ss_pred             EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eC-CCCccCCHHHHHHHHHHHH
Confidence            689999999999999999999999999999999  999999998876 43 3434554444455555544

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.

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

Probab=98.24  E-value=5.9e-07  Score=84.06  Aligned_cols=56  Identities=25%  Similarity=0.416  Sum_probs=49.3

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC--------CCCCcchHHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL--------KKMDKASVLGDAIKYLKQLQEKVKI  197 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--------~k~dKasiL~~Ai~YIk~Lq~~v~~  197 (316)
                      .++..|-+.||+||++||+.+..|+.|||..        .|++||.||.-|++|++.||.....
T Consensus        31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            4677899999999999999999999999932        6788999999999999999976443

>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=98.21  E-value=2.6e-05  Score=58.99  Aligned_cols=69  Identities=14%  Similarity=0.281  Sum_probs=55.8

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe-CCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF-GSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~-g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      .|.|.|++++|+|.+|..+|..+||+|+.|.+.+. ++.+++++.+ .-.++..+...+..++|++.|.+.
T Consensus         3 ~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v-~~~~~~~~~~~~~~~~l~~~L~~~   72 (73)
T cd04900           3 EVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVV-LDPDGEPIGERERLARIREALEDA   72 (73)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEE-ECCCCCCCChHHHHHHHHHHHHhh
Confidence            57899999999999999999999999999999888 6889986654 444555555566667777777664

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.

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

Probab=98.18  E-value=6.3e-06  Score=76.29  Aligned_cols=64  Identities=25%  Similarity=0.366  Sum_probs=53.7

Q ss_pred             CCCCcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCC-cchHHHHHHHHHHHHHHHHHHHHHHHh
Q 021208          140 RLSNTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMD-KASVLGDAIKYLKQLQEKVKILEEQAN  203 (316)
Q Consensus       140 ~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~d-KasiL~~Ai~YIk~Lq~~v~~L~~~~~  203 (316)
                      ....+..|+.-||+||+.|++.|..|+.+||..  .+.. .++||..|+.||+.|+.+........+
T Consensus        56 ~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e  122 (232)
T KOG2483|consen   56 AASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIE  122 (232)
T ss_pred             CCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHH
Confidence            345788999999999999999999999999976  3333 689999999999999988777665443

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

Probab=98.18  E-value=1.5e-06  Score=92.09  Aligned_cols=52  Identities=29%  Similarity=0.469  Sum_probs=48.7

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQLQEK  194 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~Lq~~  194 (316)
                      .+.+|+.+|||||+++|..+.+|.+|||.+    -|+||.+||..||.+|+.+++.
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            478899999999999999999999999986    5999999999999999999885

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

Probab=98.12  E-value=3.8e-05  Score=58.50  Aligned_cols=69  Identities=13%  Similarity=0.211  Sum_probs=52.2

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +|.|.++.++|+|.+|..+|..+|+.|+.|.+.+.|+.+++++.+...+++..+...+-.++|+++|.+
T Consensus         2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~   70 (74)
T cd04925           2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGAPIDDPIRLASIEDRLDN   70 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHH
Confidence            688999999999999999999999999999999999999986654332213334444444555555544

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.

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.99  E-value=4.5e-06  Score=89.02  Aligned_cols=62  Identities=31%  Similarity=0.530  Sum_probs=57.2

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHh
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILEEQAN  203 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~  203 (316)
                      .+|.+||++|||.|-.||+++..|+.+||+. .|..|..+|..||+||++|+...+.|+.+.+
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~  337 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENA  337 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhh
Confidence            6799999999999999999999999999987 8999999999999999999998888876544

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

Probab=97.82  E-value=0.00032  Score=51.71  Aligned_cols=68  Identities=13%  Similarity=0.227  Sum_probs=55.2

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      .|.|.++.++|+|.+|+.+|.++|+.|+++.+.+.++.+++ +++++-.++.... .+..+.|+++|.+.
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~-~f~i~~~~~~~~~-~~~~~~i~~~l~~~   69 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAED-VFYVTDADGQPLD-PERQEALRAALGEA   69 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEE-EEEEECCCCCcCC-HHHHHHHHHHHHhh
Confidence            57899999999999999999999999999999998887775 4666655555544 35677788887654

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.

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

Probab=97.66  E-value=8.9e-05  Score=68.81  Aligned_cols=61  Identities=21%  Similarity=0.416  Sum_probs=51.8

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHH-hcccCCC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHh
Q 021208          143 NTQDHIIAERKRREKLSQRFIAL-SAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILEEQAN  203 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~L-rslvP~~-~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~  203 (316)
                      +|.+-.+.||+|=.|+|+.|.+| |.-.++. ...-|+.||..||+||..||.-++++.++..
T Consensus       118 RRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~  180 (284)
T KOG3960|consen  118 RRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEK  180 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccch
Confidence            56677899999999999999999 5556766 6778999999999999999998888876443

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

Probab=97.47  E-value=0.0014  Score=49.71  Aligned_cols=64  Identities=11%  Similarity=0.190  Sum_probs=50.4

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe-CCeEEEEEEEEEecCCcccCHHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF-GSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAF  312 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~-g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al  312 (316)
                      .|-|.|+.++|+|.+|..+|..+||.|+.|.+.+. ++.+++.+++...+.   =...+|-++|+.+|
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~~---~~~~~~~~~~~~~~   67 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWKR---GETAALGHALQKEI   67 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCCc---cchHHHHHHHHHhh
Confidence            46788999999999999999999999999999865 677887554433322   25667888888776

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.

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.46  E-value=8.9e-05  Score=70.42  Aligned_cols=57  Identities=26%  Similarity=0.411  Sum_probs=49.4

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKVKILE  199 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~v~~L~  199 (316)
                      +|.--|.-||+|-.-||..|..||+|+|.-  .|..||.||+.+.+||.+|+.+.-+|-
T Consensus        60 RReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll  118 (373)
T KOG0561|consen   60 RREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELL  118 (373)
T ss_pred             HHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccc
Confidence            345556779999999999999999999974  899999999999999999988765553

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

Probab=97.41  E-value=0.00015  Score=66.82  Aligned_cols=61  Identities=26%  Similarity=0.371  Sum_probs=52.8

Q ss_pred             CCCcchhhHHHHHHHHHHHHHHHHHhcccCC----CCCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q 021208          141 LSNTQDHIIAERKRREKLSQRFIALSAIVPG----LKKMDKASVLGDAIKYLKQLQEKVKILEEQ  201 (316)
Q Consensus       141 ~~~~~~h~~~Er~RR~~in~~~~~LrslvP~----~~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~  201 (316)
                      ...+..++..||+|=..+|..|..||.+||.    .+|..|..+|.-||.||..|+.-++.-+..
T Consensus       107 ~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  107 SAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            3567788888999999999999999999984    578899999999999999999876665543

>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=97.41  E-value=0.0021  Score=48.55  Aligned_cols=66  Identities=12%  Similarity=0.199  Sum_probs=51.9

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      .|.|.++.++|+|.+|..+|.++|+.|+++.+.+.++.+++ +|..+-.++.... .+..++|+++|.
T Consensus         3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d-~f~v~~~~~~~~~-~~~~~~l~~~l~   68 (72)
T cd04926           3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVN-VFYVTDANGNPVD-PKTIEAVRQEIG   68 (72)
T ss_pred             EEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEE-EEEEECCCCCcCC-HHHHHHHHHHhc
Confidence            56788999999999999999999999999999988887765 4555544444453 356677887775

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.

>PRK05007 PII uridylyl-transferase; Provisional

Probab=97.32  E-value=0.0012  Score=71.86  Aligned_cols=71  Identities=15%  Similarity=0.294  Sum_probs=57.1

Q ss_pred             CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          242 DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       242 ~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +.-.+|.|.+.+++|+|.+|.++|..+||+|.+|.|+|.|+++.+++++. -.++..++ .+..+.|+++|..
T Consensus       806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~-~~~g~~l~-~~~~~~l~~~L~~  876 (884)
T PRK05007        806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILA-TADRRALN-EELQQELRQRLTE  876 (884)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEE-cCCCCcCC-HHHHHHHHHHHHH
Confidence            44579999999999999999999999999999999999999999987664 34555666 4445555555543

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

Probab=97.31  E-value=0.0046  Score=44.99  Aligned_cols=68  Identities=16%  Similarity=0.236  Sum_probs=52.6

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      .|.|.|+.++|++.+|+.+|.++|+.|..+.+.+.++... ..+.+.-+++...+ ++-.+.|++.|...
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~-~~~~v~~~~~~~~~-~~~~~~l~~~l~~~   69 (70)
T cd04873           2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERAL-DVFYVTDSDGRPLD-PERIARLEEALEDA   69 (70)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEE-EEEEEECCCCCcCC-HHHHHHHHHHHHhh
Confidence            4778999999999999999999999999999988877554 45666655544433 36666777777653

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

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.15  E-value=0.001  Score=52.22  Aligned_cols=51  Identities=27%  Similarity=0.517  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHhcccCCC------CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          155 REKLSQRFIALSAIVPGL------KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       155 R~~in~~~~~LrslvP~~------~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      -+.|++.+..|++|+|..      .|..-+-||.|+..||+.|+.+|..|.+.+...
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~L   75 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL   75 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999964      233445589999999999999999999977654

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

Probab=97.11  E-value=0.0075  Score=45.97  Aligned_cols=66  Identities=12%  Similarity=0.226  Sum_probs=51.0

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      .++|.+.+++++|++..|..+|.++|..+++++..+.++.+. ..+.+..+.   -+.++|...|.....
T Consensus         2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~-~~~~v~~~~---~~~~~l~~~L~~l~~   67 (76)
T PF13740_consen    2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFT-LIMLVSIPE---DSLERLESALEELAE   67 (76)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEE-EEEEEEESH---HHHHHHHHHHHHHHH
T ss_pred             EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEE-EEEEEEeCc---ccHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999866 556677662   255666666666543

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=97.01  E-value=0.0062  Score=66.60  Aligned_cols=79  Identities=15%  Similarity=0.230  Sum_probs=59.7

Q ss_pred             CeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCH----HHHHHH
Q 021208          234 PEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTV----KDLVKN  307 (316)
Q Consensus       234 p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~----~eL~~~  307 (316)
                      |.|.+..  .++-..|.|.+..++|+|.+|..+|..+||+|+.|.|.|.|+++++++++ .-.++..++.    ++|.+.
T Consensus       802 ~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V-~d~~g~~l~~~~~~~~l~~~  880 (895)
T PRK00275        802 TQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFI-TDADNQPLSDPQLCSRLQDA  880 (895)
T ss_pred             CEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEE-ECCCCCCCCCHHHHHHHHHH
Confidence            4555443  23457899999999999999999999999999999999999999997655 4334444433    346666


Q ss_pred             HHHHHH
Q 021208          308 LHSAFQ  313 (316)
Q Consensus       308 L~~al~  313 (316)
                      |..+|.
T Consensus       881 L~~~L~  886 (895)
T PRK00275        881 ICEQLD  886 (895)
T ss_pred             HHHHHh
Confidence            666654

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

Probab=96.91  E-value=0.014  Score=44.56  Aligned_cols=66  Identities=12%  Similarity=0.258  Sum_probs=52.5

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +.|.+.|++++|++.+|-+.|.++|..++.++....++.++ ..++...+.   .+.++|.+.|......
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~-m~~~~~~~~---~~~~~l~~~l~~~~~~   67 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFA-LTMLVEGSW---DAIAKLEAALPGLARR   67 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEE-EEEEEEecc---ccHHHHHHHHHHHHHH
Confidence            57889999999999999999999999999999988888765 344555542   4677888777765433

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

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=96.87  E-value=0.0061  Score=66.36  Aligned_cols=71  Identities=17%  Similarity=0.315  Sum_probs=57.2

Q ss_pred             CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          242 DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       242 ~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +.-.+|.|.+.+++|+|.+|.++|.++|++|..|.|+|.|+++.+++++.. .++..++-++. +.|+++|..
T Consensus       781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~-~~g~~l~~~~~-~~l~~~L~~  851 (854)
T PRK01759        781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTN-QQGQALDEEER-KALKSRLLS  851 (854)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEEC-CCCCcCChHHH-HHHHHHHHH
Confidence            345799999999999999999999999999999999999999999876643 44455664444 666666554

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.84  E-value=0.011  Score=64.41  Aligned_cols=79  Identities=19%  Similarity=0.267  Sum_probs=58.8

Q ss_pred             CeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          234 PEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       234 p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      |.|.+..  .++-..|.|.+..++|+|.+|..+|..+|++|+.|.|.|.|+++.+++.+ +-.++..++..+. +.|+++
T Consensus       784 ~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V-~d~~g~~~~~~~~-~~l~~~  861 (869)
T PRK04374        784 PRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQI-TDEHDRPLSESAR-QALRDA  861 (869)
T ss_pred             CeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE-ECCCCCcCChHHH-HHHHHH
Confidence            4555543  23457899999999999999999999999999999999999999997655 4334444544443 555555


Q ss_pred             HHh
Q 021208          312 FQL  314 (316)
Q Consensus       312 l~~  314 (316)
                      |..
T Consensus       862 L~~  864 (869)
T PRK04374        862 LCA  864 (869)
T ss_pred             HHH
Confidence            543

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

Probab=96.82  E-value=0.011  Score=42.53  Aligned_cols=61  Identities=11%  Similarity=0.189  Sum_probs=46.1

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC--eEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS--SVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~--~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      .|.|.|++++|+|.+|...|-++|+.|..+.+.+.++  ..+.++  ...   .....+.+++.|+++
T Consensus         2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~--~~~---~~~~~~~~~~~l~~~   64 (66)
T PF01842_consen    2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIV--IVV---DEEDLEKLLEELEAL   64 (66)
T ss_dssp             EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEE--EEE---EGHGHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEE--EEC---CCCCHHHHHHHHHcc
Confidence            5789999999999999999999999999999998877  222221  122   123566777777764

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 ....

>PRK05092 PII uridylyl-transferase; Provisional

Probab=96.74  E-value=0.013  Score=64.34  Aligned_cols=79  Identities=16%  Similarity=0.317  Sum_probs=57.6

Q ss_pred             CeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          234 PEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       234 p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      |.|.+.-  .+....|.|.|.+++|+|.+|..+|..+|++|..|.|.+.|+++.+++. +.-.++..+...+..+.|+++
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 PRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFY-VTDLFGLKITNEARQAAIRRA  909 (931)
T ss_pred             CEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEE-EeCCCCCcCCCHHHHHHHHHH
Confidence            4454432  2345789999999999999999999999999999999999999998654 454445445433334444444


Q ss_pred             HH
Q 021208          312 FQ  313 (316)
Q Consensus       312 l~  313 (316)
                      |.
T Consensus       910 L~  911 (931)
T PRK05092        910 LL  911 (931)
T ss_pred             HH
Confidence            43

>PRK03381 PII uridylyl-transferase; Provisional

Probab=96.59  E-value=0.017  Score=62.33  Aligned_cols=68  Identities=18%  Similarity=0.265  Sum_probs=56.5

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      +-..|.|.+..++|+|.+|..+|..+|++|++|.|.+.|+.+++++. +.-.++..++- + .+.|+++|.
T Consensus       706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~-V~d~~g~~~~~-~-~~~l~~~L~  773 (774)
T PRK03381        706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFY-VTGAAGGPLAD-A-RAAVEQAVL  773 (774)
T ss_pred             CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEE-EECCCCCcCch-H-HHHHHHHhh
Confidence            34789999999999999999999999999999999999999999765 45455555553 3 778888774

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

Probab=96.54  E-value=0.017  Score=44.97  Aligned_cols=68  Identities=15%  Similarity=0.276  Sum_probs=53.2

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +.|.+.|++++|++.+|.+.|-.+|+.+++.+..+.++.+. ..+.+..+. ...++++|.+.|......
T Consensus         2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~-~~~~v~~~~-~~~~~~~L~~~l~~l~~~   69 (88)
T cd04872           2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFT-MIMIVDISE-SNLDFAELQEELEELGKE   69 (88)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccE-EEEEEEeCC-CCCCHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999887766543 455555542 246788888888775543

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

>PRK00194 hypothetical protein; Validated

Probab=96.41  E-value=0.024  Score=44.17  Aligned_cols=67  Identities=10%  Similarity=0.228  Sum_probs=51.9

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHH
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAF  312 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al  312 (316)
                      .+.|.|.|++++|++.+|...|-++|+.|++.+..+.++.+. +.+.+..+. ...+.++|.+.|...-
T Consensus         3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~-~~~~v~~~~-~~~~~~~l~~~l~~l~   69 (90)
T PRK00194          3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFT-MIMLVDISE-SKKDFAELKEELEELG   69 (90)
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeE-EEEEEEecC-CCCCHHHHHHHHHHHH
Confidence            568899999999999999999999999999999877666443 455555543 2356778887776643

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=96.41  E-value=0.022  Score=62.00  Aligned_cols=70  Identities=20%  Similarity=0.331  Sum_probs=57.4

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +-.+|.|.|.+++|+|.+|.++|..+|++|.++.+.+.|+++.+++ .++...+..++- +..+.|+++|..
T Consensus       778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F-~v~~~~g~~~~~-~~~~~l~~~L~~  847 (850)
T TIGR01693       778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVF-YVTDLFGLKLTD-EEEQRLLEVLAA  847 (850)
T ss_pred             CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEE-EEECCCCCCCCH-HHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999999999865 456556666664 555666666654

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.

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.38  E-value=0.022  Score=62.09  Aligned_cols=69  Identities=17%  Similarity=0.279  Sum_probs=53.0

Q ss_pred             CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          242 DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       242 ~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      ++-..|.|.+.+++|+|.+|..+|..+||+|+.|.|.|.|+.+.+++++ . +..  ....+-.++|+++|..
T Consensus       784 ~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V-~-~~~--~~~~~~~~~l~~~L~~  852 (856)
T PRK03059        784 GQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI-D-GSG--LSDNRLQIQLETELLD  852 (856)
T ss_pred             CCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE-c-CCC--CCCHHHHHHHHHHHHH
Confidence            3457899999999999999999999999999999999999999997765 2 222  2233444555555443

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

Probab=96.35  E-value=0.06  Score=40.68  Aligned_cols=66  Identities=11%  Similarity=0.228  Sum_probs=51.2

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC-----eEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS-----SVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~-----~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      |.|.|+.++|++.+|-+.|.++|+.|.+.+..+.+.     ..+...+.+.++.  ..+..+|...|...-..
T Consensus         2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p~--~~~~~~l~~~l~~l~~~   72 (81)
T cd04869           2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPA--GTDLDALREELEELCDD   72 (81)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecCC--CCCHHHHHHHHHHHHHH
Confidence            679999999999999999999999999999987761     2333455555553  45788888888775543

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

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

Probab=96.31  E-value=0.045  Score=41.05  Aligned_cols=67  Identities=10%  Similarity=0.203  Sum_probs=49.0

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCc-ccCHHHHHHHHHHHHHh
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEF-NMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~-~ls~~eL~~~L~~al~~  314 (316)
                      .|.|.|+.++|++.+|.+.|-++|+.++..+..+ .++..+..  .++++-.. ..+.++|.+.|...-..
T Consensus         1 ii~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~--~~~~~~~~~~~~~~~l~~~l~~l~~~   69 (74)
T cd04875           1 ILTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFM--RVEFELEGFDLSREALEAAFAPVAAE   69 (74)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEE--EEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999999999999998775 23333433  34443322 25788888888775544

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.

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=96.31  E-value=0.027  Score=61.26  Aligned_cols=79  Identities=18%  Similarity=0.157  Sum_probs=58.2

Q ss_pred             CCeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEE-EeCCeEEEEEEEEEecCCcccCHHH----HH
Q 021208          233 LPEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVM-TFGSSVLDVTIIAQMDVEFNMTVKD----LV  305 (316)
Q Consensus       233 ~p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs-~~g~~~l~~ti~aq~~~~~~ls~~e----L~  305 (316)
                      .|.|.+.-  .++...|.|.+.+++|+|.+|..+|..+||+|+.|.|. +.++.++++++ ++-.++..+...+    |.
T Consensus       655 ~~~v~~~~~~~~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~-V~~~~g~~~~~~~~~~~i~  733 (850)
T TIGR01693       655 GPLALIDGTRPSGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFV-VQDLFGSPPAAERVFQELL  733 (850)
T ss_pred             CCEEEEeccCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEE-EECCCCCCCCcHHHHHHHH
Confidence            45554422  24556899999999999999999999999999999998 77999998654 4545555554444    55


Q ss_pred             HHHHHHH
Q 021208          306 KNLHSAF  312 (316)
Q Consensus       306 ~~L~~al  312 (316)
                      +.|..+|
T Consensus       734 ~~L~~~L  740 (850)
T TIGR01693       734 QGLVDVL  740 (850)
T ss_pred             HHHHHHH
Confidence            5555555

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

>PRK03381 PII uridylyl-transferase; Provisional

Probab=96.30  E-value=0.039  Score=59.55  Aligned_cols=79  Identities=16%  Similarity=0.143  Sum_probs=60.8

Q ss_pred             CeeEEEEe-CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHH
Q 021208          234 PEIEARFC-DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAF  312 (316)
Q Consensus       234 p~Vev~v~-~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al  312 (316)
                      |.|.++.. .+.+.|.|.|.+++|+|.+|..+|..+|+.|++|.+.+.++.++++++ +.-.++.....++|.+.|..+|
T Consensus       588 ~~v~~~~~~~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~-V~~~~~~~~~~~~l~~~L~~~L  666 (774)
T PRK03381        588 VHVEIAPADPHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFV-VSPRFGSPPDAALLRQDLRRAL  666 (774)
T ss_pred             CEEEEeeCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEE-EECCCCCcchHHHHHHHHHHHH
Confidence            44544332 356789999999999999999999999999999999998888887554 4444444445677888888776


Q ss_pred             H
Q 021208          313 Q  313 (316)
Q Consensus       313 ~  313 (316)
                      .
T Consensus       667 ~  667 (774)
T PRK03381        667 D  667 (774)
T ss_pred             c
Confidence            4

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

Probab=96.14  E-value=0.033  Score=42.33  Aligned_cols=63  Identities=16%  Similarity=0.298  Sum_probs=45.0

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-CeEEEEEEEEEecCCcccCHHHHHHHH
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-SSVLDVTIIAQMDVEFNMTVKDLVKNL  308 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-~~~l~~ti~aq~~~~~~ls~~eL~~~L  308 (316)
                      .+.|+|.+.+++|+|.+|..+|-+.|+.|.+.++.... +....+++..++.+-  --+..|.++|
T Consensus         6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~--~~L~~ii~~L   69 (80)
T PF13291_consen    6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDL--EHLNQIIRKL   69 (80)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSH--HHHHHHHHHH
T ss_pred             EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCH--HHHHHHHHHH
Confidence            46788999999999999999999999999999998863 555556777777543  2333444444

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

Probab=96.12  E-value=0.063  Score=40.52  Aligned_cols=66  Identities=15%  Similarity=0.205  Sum_probs=52.4

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      +|.|.+.+++|++.+|.+.|-++|+.+.+.+..+.++.+. ..+.+.++.+  .+.++|...|......
T Consensus         1 ~vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~-~~~~v~~p~~--~~~~~l~~~l~~l~~~   66 (75)
T cd04870           1 LITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLS-LGILVQIPDS--ADSEALLKDLLFKAHE   66 (75)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeE-EEEEEEcCCC--CCHHHHHHHHHHHHHH
Confidence            4788999999999999999999999999999888876533 4555565544  5788888888776543

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.

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=96.08  E-value=0.049  Score=59.43  Aligned_cols=79  Identities=19%  Similarity=0.242  Sum_probs=58.1

Q ss_pred             CCeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCcccCHH---HHHH
Q 021208          233 LPEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNMTVK---DLVK  306 (316)
Q Consensus       233 ~p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~ls~~---eL~~  306 (316)
                      .|.|.++-  ..+...|.|.|++++|+|.+|..+|..+||+|+.|.|.+ .++.+++++++.. .++..++.+   .|.+
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d-~~g~~~~~~~~~~l~~  742 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTE-LNGKLLEFDRRRQLEQ  742 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeC-CCCCCCCHHHHHHHHH
Confidence            45555543  345578999999999999999999999999999999977 7999998765544 455555532   3444


Q ss_pred             HHHHHH
Q 021208          307 NLHSAF  312 (316)
Q Consensus       307 ~L~~al  312 (316)
                      .|..+|
T Consensus       743 ~L~~aL  748 (854)
T PRK01759        743 ALTKAL  748 (854)
T ss_pred             HHHHHH
Confidence            444444

>PRK05007 PII uridylyl-transferase; Provisional

Probab=96.02  E-value=0.056  Score=59.21  Aligned_cols=79  Identities=18%  Similarity=0.228  Sum_probs=57.7

Q ss_pred             CCeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC-eEEEEEEEEEecCCcccCH---HHHHH
Q 021208          233 LPEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS-SVLDVTIIAQMDVEFNMTV---KDLVK  306 (316)
Q Consensus       233 ~p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~-~~l~~ti~aq~~~~~~ls~---~eL~~  306 (316)
                      .|.|.++.  .++...|.|.|++++|+|.+|..+|..+||+|+.|.|.+.++ .+++++++.. .++..++.   +.|.+
T Consensus       688 ~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        688 KPLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLE-PDGSPLSQDRHQVIRK  766 (884)
T ss_pred             CCeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEEC-CCCCCCCHHHHHHHHH
Confidence            35555543  345679999999999999999999999999999999987755 8998665543 44444443   23555


Q ss_pred             HHHHHH
Q 021208          307 NLHSAF  312 (316)
Q Consensus       307 ~L~~al  312 (316)
                      .|..+|
T Consensus       767 ~L~~aL  772 (884)
T PRK05007        767 ALEQAL  772 (884)
T ss_pred             HHHHHH
Confidence            555555

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

Probab=95.87  E-value=0.037  Score=59.36  Aligned_cols=78  Identities=19%  Similarity=0.327  Sum_probs=59.7

Q ss_pred             CeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          234 PEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       234 p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      |.|...-  ..+--+|+|.+..++|+|..|..+|..++|++.+|.|+|+|.++-+.+++ +--.+..++. ++.+.|.++
T Consensus       779 p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~v-t~~~~~~l~~-~~~q~l~~~  856 (867)
T COG2844         779 PRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIV-TDADGQALNA-ELRQSLLQR  856 (867)
T ss_pred             CceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEE-eccccccCCH-HHHHHHHHH
Confidence            5555432  33456899999999999999999999999999999999999999997654 4445555544 555555555


Q ss_pred             HH
Q 021208          312 FQ  313 (316)
Q Consensus       312 l~  313 (316)
                      +.
T Consensus       857 ll  858 (867)
T COG2844         857 LL  858 (867)
T ss_pred             HH
Confidence            43

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

Probab=95.73  E-value=0.099  Score=38.71  Aligned_cols=62  Identities=13%  Similarity=0.199  Sum_probs=45.5

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      |+|.+..++|+|.+|+.+|.+.|..|.+.++.........+.+..++.+.  --+..|.++|+.
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~--~~l~~i~~~L~~   63 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSE--EHAETIVAAVRA   63 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCH--HHHHHHHHHHhc
Confidence            68899999999999999999999999998887765444444555555443  234455555543

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.

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

Probab=95.29  E-value=0.1  Score=39.05  Aligned_cols=66  Identities=18%  Similarity=0.178  Sum_probs=50.2

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      .|.|.|+.+.|+-.+|.+.+-+.||.|....+++-|.-.+-++-+..-.....+.-+-|+++|.++
T Consensus         2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv~~~~~~~~rW~lLK~RL~~~   67 (69)
T cd04894           2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVVPRPPSIKVRWDLLKNRLMSA   67 (69)
T ss_pred             EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEecCCCCCcccHHHHHHHHHhc
Confidence            588999999999999999999999999999999999876643333322223345566677777654

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.

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.23  E-value=0.19  Score=55.13  Aligned_cols=69  Identities=19%  Similarity=0.284  Sum_probs=51.7

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCccc-C----HHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNM-T----VKDLVKNLHSAF  312 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~l-s----~~eL~~~L~~al  312 (316)
                      +...|.|.|..++|+|.+|..+|..+||+|+.|.|.+ -++.+++.++ +.-.++..+ .    .+.|.+.|.++|
T Consensus       703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~-V~d~~g~~~~~~~~r~~~i~~~L~~~L  777 (895)
T PRK00275        703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYI-VLDDDGEPIGDNPARIEQIREGLTEAL  777 (895)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEE-EeCCCCCCccchHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999854 5678888654 444444432 2    334556666555

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

Probab=95.12  E-value=0.17  Score=36.33  Aligned_cols=62  Identities=18%  Similarity=0.243  Sum_probs=42.6

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC----CeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG----SSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g----~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +.|.++.++|.|.+|+..|.+.|+.|.+.......    .....+.+...+.+  .-.++++.+.|+.
T Consensus         1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~--~~~l~~l~~~l~~   66 (73)
T cd04886           1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRG--AEHIEEIIAALRE   66 (73)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCC--HHHHHHHHHHHHH
Confidence            46788999999999999999999999988776542    23333444445432  2234566666654

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

>PRK03059 PII uridylyl-transferase; Provisional

Probab=95.09  E-value=0.16  Score=55.45  Aligned_cols=77  Identities=16%  Similarity=0.254  Sum_probs=55.1

Q ss_pred             CeeEEEE--eCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCcccC----HHHHHH
Q 021208          234 PEIEARF--CDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNMT----VKDLVK  306 (316)
Q Consensus       234 p~Vev~v--~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~ls----~~eL~~  306 (316)
                      |-|-++.  ..+...|-|.|+.++|+|.+|..+|..+||+|+.|.|.+ -+|.+++.+++ .-.++. ..    .+.|.+
T Consensus       666 ~~v~~~~~~~~~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V-~~~~~~-~~~~~~~~~i~~  743 (856)
T PRK03059        666 PIVRARLSPAGEGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQV-LDPEED-VHYRDIINLVEH  743 (856)
T ss_pred             CeEEEEecCCCCeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEE-eCCCCC-CChHHHHHHHHH
Confidence            4444443  335678899999999999999999999999999999964 57888986544 433333 33    334555


Q ss_pred             HHHHHH
Q 021208          307 NLHSAF  312 (316)
Q Consensus       307 ~L~~al  312 (316)
                      .|.++|
T Consensus       744 ~l~~~l  749 (856)
T PRK03059        744 ELAERL  749 (856)
T ss_pred             HHHHHH
Confidence            555555

>PRK05092 PII uridylyl-transferase; Provisional

Probab=94.77  E-value=0.25  Score=54.51  Aligned_cols=78  Identities=17%  Similarity=0.204  Sum_probs=56.7

Q ss_pred             CeeEEEEe--CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCcccC----HHHHHH
Q 021208          234 PEIEARFC--DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNMT----VKDLVK  306 (316)
Q Consensus       234 p~Vev~v~--~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~ls----~~eL~~  306 (316)
                      +.|.++..  .+...|.|.|..++|+|.+|..+|..+|++|+.|.+.+ .++.+++++ .++-.++....    .+.|.+
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 LATEVRPDPARGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTF-WIQDAFGRDEDEPRRLARLAK  798 (931)
T ss_pred             cEEEEEecCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEE-EEECCCCCCCCCHHHHHHHHH
Confidence            45555443  35678999999999999999999999999999999987 577888744 44444443332    444666


Q ss_pred             HHHHHH
Q 021208          307 NLHSAF  312 (316)
Q Consensus       307 ~L~~al  312 (316)
                      .|..++
T Consensus       799 ~L~~~l  804 (931)
T PRK05092        799 AIEDAL  804 (931)
T ss_pred             HHHHHH
Confidence            666555

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.56  E-value=0.021  Score=49.63  Aligned_cols=52  Identities=31%  Similarity=0.451  Sum_probs=46.6

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEK  194 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~  194 (316)
                      ++.-|++.||+|=..||+.|.+||.++|..  .|..|.--|.-|..||..|-+-
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence            566799999999999999999999999975  7888988999999999988653

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

Probab=94.50  E-value=0.22  Score=36.81  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=43.6

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      .|.|.+..++|++.+|+..|.+.|+.|...+.....+...++.+.....+. ...+++|.++|++
T Consensus         2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~-~~~l~~l~~~L~~   65 (76)
T cd04888           2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTM-NGDIDELLEELRE   65 (76)
T ss_pred             EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCch-HHHHHHHHHHHhc
Confidence            477899999999999999999999999888765433333334444444332 1245566666653

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

>PRK04435 hypothetical protein; Provisional

Probab=94.45  E-value=0.3  Score=42.16  Aligned_cols=70  Identities=16%  Similarity=0.190  Sum_probs=51.2

Q ss_pred             EeCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          240 FCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       240 v~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      ..|+.+.|.+.+.+++|+|.+|+..|.+.|+.|...+.....+....++|.....+. ...+++|..+|++
T Consensus        65 ~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~-~~~L~~Li~~L~~  134 (147)
T PRK04435         65 VKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSM-EGDIDELLEKLRN  134 (147)
T ss_pred             CCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCCh-HHHHHHHHHHHHc
Confidence            468889999999999999999999999999999988765433333445555555332 2256677777654

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

Probab=94.44  E-value=0.35  Score=36.16  Aligned_cols=63  Identities=8%  Similarity=0.141  Sum_probs=44.4

Q ss_pred             EEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCC-cccCHHHHHHHHHH
Q 021208          248 RVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVE-FNMTVKDLVKNLHS  310 (316)
Q Consensus       248 ~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~-~~ls~~eL~~~L~~  310 (316)
                      -+..++++|.|.+||+.+..+|+.+.+-...+..+..-.+.|.+.++.. .....+++.+.|+.
T Consensus         3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~   66 (75)
T cd04880           3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKR   66 (75)
T ss_pred             EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence            3455778999999999999999999998777765533344455555443 23456667666655

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

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

Probab=94.44  E-value=0.29  Score=31.89  Aligned_cols=34  Identities=15%  Similarity=0.282  Sum_probs=30.0

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF  280 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~  280 (316)
                      |.|.|+.++|.+.+|+..|...|+.+........
T Consensus         1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~   34 (60)
T cd02116           1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTS   34 (60)
T ss_pred             CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEc
Confidence            4688899999999999999999999999887654

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

>PRK04374 PII uridylyl-transferase; Provisional

Probab=94.37  E-value=0.39  Score=52.70  Aligned_cols=71  Identities=17%  Similarity=0.275  Sum_probs=52.4

Q ss_pred             CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCcc-cCHHHHHHHHHHHHH
Q 021208          242 DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFN-MTVKDLVKNLHSAFQ  313 (316)
Q Consensus       242 ~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~-ls~~eL~~~L~~al~  313 (316)
                      .+...|-|.|..++|+|.+|..+|..+||+|+.|.|.+ -+|.+++.+++ .-.++.. -....|.+.|.++|.
T Consensus       688 ~~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V-~~~~~~~~~~~~~i~~~l~~~l~  760 (869)
T PRK04374        688 NDALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEV-LPQDTYADGDPQRLAAALRQVLA  760 (869)
T ss_pred             CCeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEE-eCCCCCChHHHHHHHHHHHHHHc
Confidence            35578899999999999999999999999999999987 57888986554 4333321 123345566655553

>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=94.03  E-value=0.27  Score=35.86  Aligned_cols=63  Identities=11%  Similarity=0.226  Sum_probs=42.8

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC-eEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS-SVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~-~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      ++|+|.+.+++|++.+|+..|.+.|+.+.+....+..+ ....+.+.....+  .-.++++..+|+
T Consensus         1 ~yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~~~~--~~~l~~~i~~L~   64 (79)
T cd04881           1 YYLRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTHETS--EAALNAALAEIE   64 (79)
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEccCC--HHHHHHHHHHHH
Confidence            36899999999999999999999999999888765532 3222333333222  233445555555

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.

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

Probab=93.97  E-value=0.44  Score=32.79  Aligned_cols=61  Identities=15%  Similarity=0.285  Sum_probs=41.2

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      |+|.+.+++|.+.+|+..|.++++.+.+..+...++....+.+.....+.  ..+..+.+.|+
T Consensus         1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~   61 (71)
T cd04876           1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRDL--EHLARIMRKLR   61 (71)
T ss_pred             CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECCH--HHHHHHHHHHh
Confidence            46889999999999999999999999998887655333323344443332  23444554443

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

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

Probab=93.93  E-value=0.56  Score=33.61  Aligned_cols=60  Identities=12%  Similarity=0.221  Sum_probs=41.9

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .|.|.+..++|.+.+|+..|.++++.|.+....+.++....+++  .+++.  -.+.++.+.|+
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i--~~~~~--~~~~~~~~~L~   61 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYM--ELEGV--GDIEELVEELR   61 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEE--EEecc--ccHHHHHHHHh
Confidence            47789999999999999999999999998877665333333333  33332  24556666554

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.

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

Probab=93.79  E-value=0.43  Score=35.40  Aligned_cols=63  Identities=13%  Similarity=0.157  Sum_probs=43.9

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe--CCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF--GSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~--g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      +.|.-+.++|.|.+++..|.++|..|++......  +.....+.|...++...  ..+.|.+.|+..
T Consensus         2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~e~~~--~~~~i~~~L~~~   66 (72)
T cd04884           2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTPMDRS--KENELIEELKAK   66 (72)
T ss_pred             EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEEecch--HHHHHHHHHhCc
Confidence            4677889999999999999999999998876654  33334445555542221  256677776544

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=93.49  E-value=0.044  Score=55.65  Aligned_cols=57  Identities=19%  Similarity=0.244  Sum_probs=46.7

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQLQEKVKIL  198 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~Lq~~v~~L  198 (316)
                      .+|...+..||-|=..||+.|.+|..+.---    +.-.|.-||..|+.-|-.|++||.+-
T Consensus       525 ERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  525 ERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            3678889999999889999999998765321    22357899999999999999999764

>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=93.45  E-value=0.87  Score=34.55  Aligned_cols=65  Identities=6%  Similarity=0.143  Sum_probs=44.4

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCc-ccCHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEF-NMTVKDLVKNLHS  310 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~-~ls~~eL~~~L~~  310 (316)
                      .|.+..+.++|.|.+|+..+.++|+.+++....+..+....+.+.+..+... .-.+.++...|+.
T Consensus         3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~   68 (80)
T cd04905           3 SIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKR   68 (80)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence            3455667889999999999999999999888777655444456666665431 2234445555544

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

>PRK08577 hypothetical protein; Provisional

Probab=93.38  E-value=0.95  Score=38.22  Aligned_cols=67  Identities=19%  Similarity=0.368  Sum_probs=49.7

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-CeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-SSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +.+.|.|.+.+++|+|.+|+..|.++++.+.+.++.+.. +....+.+...+.+. ...+.++.++|+.
T Consensus        55 ~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~~-~~~l~~l~~~L~~  122 (136)
T PRK08577         55 KLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSKS-DIDLEELEEELKK  122 (136)
T ss_pred             cEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCCc-hhhHHHHHHHHHc
Confidence            367899999999999999999999999999988876653 444445555666553 1345677777653

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

Probab=93.26  E-value=0.37  Score=36.10  Aligned_cols=58  Identities=9%  Similarity=0.186  Sum_probs=41.4

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .|+|.|.+++|++.+|+.++.+.+..+.+.++.+- +. ++++  .++.+-.  .++.|.++|+
T Consensus         2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~-i~l~--i~v~~~~--~L~~li~~L~   59 (74)
T cd04877           2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GR-IYLN--FPTIEFE--KLQTLMPEIR   59 (74)
T ss_pred             EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-Ce-EEEE--eEecCHH--HHHHHHHHHh
Confidence            47899999999999999999999999999998664 33 4443  3333321  2445555554

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

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=92.59  E-value=0.12  Score=53.23  Aligned_cols=39  Identities=31%  Similarity=0.564  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHH
Q 021208          151 ERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLK  189 (316)
Q Consensus       151 Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk  189 (316)
                      -||-|++||.-+..|.+|+|..    .|.||.|||.-++-|++
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            3567899999999999999963    89999999999999975

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

Probab=92.57  E-value=1.1  Score=31.92  Aligned_cols=61  Identities=20%  Similarity=0.300  Sum_probs=42.6

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe-CCeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF-GSSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~-g~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .|.|.+.+++|++.+|+..|.+.++.+.+...... ++....+.+.....  . -.+.++...|+
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~l~~~l~   63 (72)
T cd04878           2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEGD--D-DVIEQIVKQLN   63 (72)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEECC--H-HHHHHHHHHHh
Confidence            46788899999999999999999999998887654 34433344444432  2 34555665554

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

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

Probab=92.37  E-value=1.1  Score=35.68  Aligned_cols=68  Identities=9%  Similarity=0.161  Sum_probs=46.0

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAF  312 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al  312 (316)
                      ..|-+..++++|.|.++|..+...|+.+.+-..-+..+....|.|-..++....-.++.+...|++.|
T Consensus        15 tslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~~~   82 (90)
T cd04931          15 ISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDKKSAPALDPIIKSLRNDI   82 (90)
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCCCHHHHHHHHHHHHHh
Confidence            44556668889999999999999999999888877655544445555554432233445555555543

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.

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=92.36  E-value=0.68  Score=44.41  Aligned_cols=69  Identities=12%  Similarity=0.211  Sum_probs=49.6

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEE--E-eCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVM--T-FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs--~-~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      .+.|.|.|++++|++.+|-..|-++|+.+++.+-.  + .+.+++-+.+...  .....+.++|.+.|...-..
T Consensus         9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~--~~~~~~~~~l~~~l~~l~~~   80 (289)
T PRK13010          9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQ--SAEAASVDTFRQEFQPVAEK   80 (289)
T ss_pred             CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcC--CCCCCCHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999974  3 3344443222211  12246788888888765443

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=91.74  E-value=1.7  Score=41.59  Aligned_cols=70  Identities=9%  Similarity=0.119  Sum_probs=51.7

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      .+.|.|.|++++|++.+|.+.|-++|+.|.+.+..+ .++..+..  .+.+.-....+.++|.+.|...-..+
T Consensus         7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m--~~~~~~p~~~~~~~L~~~L~~l~~~l   77 (286)
T PRK13011          7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFM--RVEFHSEEGLDEDALRAGFAPIAARF   77 (286)
T ss_pred             eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEE--EEEEecCCCCCHHHHHHHHHHHHHHh
Confidence            467999999999999999999999999999998763 34444433  34443223357888888887765443

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=91.72  E-value=1.5  Score=41.87  Aligned_cols=70  Identities=7%  Similarity=0.161  Sum_probs=52.5

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE--eCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT--FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~--~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      ..+.|.+.|++++|++.+|.+.|-++|+.+.+++..+  .++. +...+.+..+ ....+.++|...|...-..
T Consensus         5 ~~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~-F~m~i~v~~~-~~~~~~~~L~~~L~~l~~~   76 (286)
T PRK06027          5 QRYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGR-FFMRVEFEGD-GLIFNLETLRADFAALAEE   76 (286)
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCe-EEEEEEEEeC-CCCCCHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999988  7773 3333444441 2234577888777765443

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=91.30  E-value=1.9  Score=41.23  Aligned_cols=63  Identities=21%  Similarity=0.346  Sum_probs=48.4

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe--CCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF--GSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~--g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      .|.|.|++++|++.+|-..|-++|+.+++++-...  ++.++ ..+.+..+ +...+.++|.+.|..
T Consensus         2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~-mr~~v~~~-~~~~~~~~l~~~l~~   66 (280)
T TIGR00655         2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFF-MRVEFQLE-GFRLEESSLLAAFKS   66 (280)
T ss_pred             EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEE-EEEEEEeC-CCCCCHHHHHHHHHH
Confidence            57899999999999999999999999999997763  34433 23344443 234678888888887

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.

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

Probab=91.14  E-value=1.7  Score=30.69  Aligned_cols=59  Identities=10%  Similarity=0.157  Sum_probs=42.4

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-CeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-SSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +.|.+..++|.+.+|+..|.+.|+.|.+..+...+ +....+++..  ++.   ...+|.+.|+.
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v--~~~---~~~~l~~~l~~   61 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV--DSP---VPEEVLEELKA   61 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc--CCC---CCHHHHHHHHc
Confidence            56789999999999999999999999998887654 2233234433  332   35677777764

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

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

Probab=91.11  E-value=1.2  Score=31.63  Aligned_cols=56  Identities=11%  Similarity=0.207  Sum_probs=39.4

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC--CeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG--SSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g--~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      |.|.-+.++|.|.+++..|.++|+.|.+.......  +...   +...+++     .+++.+.|+.
T Consensus         2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~---v~~~ve~-----~~~~~~~L~~   59 (65)
T cd04882           2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKAL---LIFRTED-----IEKAIEVLQE   59 (65)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEE---EEEEeCC-----HHHHHHHHHH
Confidence            67788899999999999999999999776654443  2222   3344443     5566666654

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.

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

Probab=90.62  E-value=1.4  Score=47.84  Aligned_cols=77  Identities=19%  Similarity=0.223  Sum_probs=57.2

Q ss_pred             eeEEEEeCCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE-eCCeEEEEEEEEEecCCcccCH---HHHHHHHHH
Q 021208          235 EIEARFCDKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT-FGSSVLDVTIIAQMDVEFNMTV---KDLVKNLHS  310 (316)
Q Consensus       235 ~Vev~v~~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~-~g~~~l~~ti~aq~~~~~~ls~---~eL~~~L~~  310 (316)
                      .+.++...+...|-|.|+.++.+|..|..++...|++|+.|.|.+ -+|++++.+ +++..++..+..   ..+.+.|.+
T Consensus       675 ~~~~r~~~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtf-iv~~~~g~~~~~dr~~~~~~~l~~  753 (867)
T COG2844         675 LISVRPHSGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTF-IVLEPDGFPVEEDRRAALRGELIE  753 (867)
T ss_pred             eeeecccCCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeE-EEecCCCCccchhHHHHHHHHHHH
Confidence            344555667788999999999999999999999999999999865 577899955 455556655552   124445555


Q ss_pred             HH
Q 021208          311 AF  312 (316)
Q Consensus       311 al  312 (316)
                      ++
T Consensus       754 ~l  755 (867)
T COG2844         754 AL  755 (867)
T ss_pred             HH
Confidence            44

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

Probab=90.27  E-value=2.5  Score=29.92  Aligned_cols=59  Identities=8%  Similarity=0.169  Sum_probs=41.1

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe-CCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF-GSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~-g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      |.+.+.+++|.+.+|+..|.++|+.+.+...... ++....+.  ..+++.   .+.++.+.|+.
T Consensus         2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~--i~v~~~---~~~~~i~~l~~   61 (71)
T cd04903           2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMV--IEVDQP---IDEEVIEEIKK   61 (71)
T ss_pred             EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEE--EEeCCC---CCHHHHHHHHc
Confidence            5788999999999999999999999988876653 22222222  333332   55677777654

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.

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

Probab=90.20  E-value=2.8  Score=30.45  Aligned_cols=37  Identities=11%  Similarity=0.201  Sum_probs=32.1

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS  282 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~  282 (316)
                      .|.|..++++|.|.+|++.|.+.|+.|.+.-+.+.++
T Consensus         3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~   39 (66)
T cd04908           3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSE   39 (66)
T ss_pred             EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCC
Confidence            4667889999999999999999999998887766655

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.

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

Probab=89.85  E-value=2.1  Score=31.04  Aligned_cols=35  Identities=11%  Similarity=0.261  Sum_probs=30.8

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF  280 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~  280 (316)
                      .+.|.+++++|.|.+|+..|.++|+.+......+.
T Consensus         3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            47788999999999999999999999988776554

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.

>PRK07334 threonine dehydratase; Provisional

Probab=89.59  E-value=1.9  Score=42.92  Aligned_cols=67  Identities=13%  Similarity=0.272  Sum_probs=49.4

Q ss_pred             CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe----CCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          242 DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF----GSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       242 ~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~----g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +-.+.|+|.+.+++|+|.+|+..|.+.++.|.+.++.+-    .+....+.+..++.+.  -.+.+|.++|++
T Consensus       324 ~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~--~~L~~vi~~Lr~  394 (403)
T PRK07334        324 GRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDA--AHLQEVIAALRA  394 (403)
T ss_pred             CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCH--HHHHHHHHHHHH
Confidence            345899999999999999999999999999999987654    3344444555555432  345567777765

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

Probab=89.35  E-value=1.5  Score=33.10  Aligned_cols=48  Identities=6%  Similarity=0.102  Sum_probs=36.8

Q ss_pred             EEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecC
Q 021208          248 RVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDV  295 (316)
Q Consensus       248 ~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~  295 (316)
                      -+..++++|.|.+||..+...|+.+.+-..-+..+....|.|...++.
T Consensus         4 ~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~   51 (74)
T cd04904           4 IFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEV   51 (74)
T ss_pred             EEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEc
Confidence            344577899999999999999999999888776665545555556554

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

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=88.27  E-value=1.4  Score=39.81  Aligned_cols=65  Identities=11%  Similarity=0.159  Sum_probs=49.3

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      ..++|.+.+++|+|++..|-++|.++|..+++++.+.+|+.+- ..+++...   ...+.+|...|...
T Consensus         7 ~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa-~i~lvs~~---~~~~~~le~~L~~l   71 (190)
T PRK11589          7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFT-FIMLLSGS---WNAITLIESTLPLK   71 (190)
T ss_pred             cEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceE-EEEEEeCC---hhHHHHHHHHHHhh
Confidence            4678999999999999999999999999999999999998654 22333322   22566666665443

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

Probab=87.49  E-value=0.4  Score=50.68  Aligned_cols=47  Identities=32%  Similarity=0.477  Sum_probs=40.1

Q ss_pred             cchhhHHHHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHH
Q 021208          144 TQDHIIAERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQ  190 (316)
Q Consensus       144 ~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~  190 (316)
                      +..-.-+-|-||.|-|+-|..|..+||-.    ...|||+|+.-||-|++-
T Consensus        47 kEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   47 KEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            44455677999999999999999999942    778999999999999873

>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=87.41  E-value=3.6  Score=31.33  Aligned_cols=61  Identities=13%  Similarity=0.206  Sum_probs=40.5

Q ss_pred             EEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          249 VHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       249 I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +..++++|.|.++|..++..|+.+.+-..-+..+..-.|.+-..++.... .++.+...|++
T Consensus         5 ~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e~~~~-~i~~~l~~l~~   65 (74)
T cd04929           5 FSLKNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCECDQR-RLDELVQLLKR   65 (74)
T ss_pred             EEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCHH-HHHHHHHHHHH
Confidence            34467899999999999999999998887776554444455555543322 34444444433

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.

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=87.12  E-value=0.58  Score=46.84  Aligned_cols=42  Identities=38%  Similarity=0.536  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHHH
Q 021208          150 AERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQL  191 (316)
Q Consensus       150 ~Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~L  191 (316)
                      +-|.||++-|.-|..|..++|-.    ...||++|+.-|..|||--
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            45889999999999999999953    6799999999999999853

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

Probab=86.94  E-value=6  Score=28.67  Aligned_cols=60  Identities=15%  Similarity=0.191  Sum_probs=40.0

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe-CCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF-GSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~-g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      .|.+..++++|.|.+++..|.+.|+.+.+...... +...-.+.|.....     ..+++.+.|+.
T Consensus         3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~-----~~~~~~~~L~~   63 (72)
T cd04883           3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTM-----NPRPIIEDLRR   63 (72)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecC-----CHHHHHHHHHH
Confidence            56788899999999999999999999987765433 12222233443321     23467666654

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.

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

Probab=86.60  E-value=4  Score=29.97  Aligned_cols=60  Identities=15%  Similarity=0.170  Sum_probs=40.8

Q ss_pred             EEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          248 RVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       248 ~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +|.-+.++|-|.++++.|.. |..|+....-..+.....+++..+..+.  -..++|.+.|+.
T Consensus         2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~~~~v~v~ie~~~~--~~~~~i~~~L~~   61 (68)
T cd04885           2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGDEARVLVGIQVPDR--EDLAELKERLEA   61 (68)
T ss_pred             EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCCceEEEEEEEeCCH--HHHHHHHHHHHH
Confidence            56778999999999999999 9999887766544333334455555442  245566666654

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.

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

Probab=86.43  E-value=0.4  Score=45.18  Aligned_cols=53  Identities=26%  Similarity=0.315  Sum_probs=45.9

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCC---CCCCCcchHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPG---LKKMDKASVLGDAIKYLKQLQEK  194 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~---~~k~dKasiL~~Ai~YIk~Lq~~  194 (316)
                      .++..=|..||+|--.+|+.|..||.++|.   ..|+.|+-.|.-|-+||..|++-
T Consensus        71 ~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   71 LRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            355667889999999999999999999994   37888999999999999988754

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

Probab=85.27  E-value=5.3  Score=34.36  Aligned_cols=67  Identities=13%  Similarity=0.336  Sum_probs=50.6

Q ss_pred             CCeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEE-EEeCCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          242 DKSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSV-MTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       242 ~~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asv-s~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      +..+.+.++.+.|.|.|+++|+++-..++.|+..+= .+..++.- +|+..... .-...+++|+.+|+.
T Consensus        70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~An-vtlsi~~s-sm~~~V~~ii~kl~k  137 (150)
T COG4492          70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGRAN-VTLSIDTS-SMEKDVDKIIEKLRK  137 (150)
T ss_pred             ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCceee-EEEEEEch-hhhhhHHHHHHHHhc
Confidence            456788899999999999999999999999988764 46777654 55544433 334578888888764

>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed

Probab=84.98  E-value=4.8  Score=35.44  Aligned_cols=61  Identities=16%  Similarity=0.269  Sum_probs=45.6

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-CeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-SSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .|.|..++++|.|.+|...|...|+.+.+..+.+.. .....++|++.-++   -.++.|++-|.
T Consensus         4 ~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~---~~i~qi~kQl~   65 (161)
T PRK11895          4 TLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDE---QVIEQITKQLN   65 (161)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCH---HHHHHHHHHHh
Confidence            577889999999999999999999999999888765 45566777766322   24445554443

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

Probab=84.75  E-value=1.4  Score=41.61  Aligned_cols=54  Identities=28%  Similarity=0.281  Sum_probs=46.3

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVK  196 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~  196 (316)
                      ++.+-+..||+|-..||..|..||..||..   .|..|-.-|..|-.||--|-....
T Consensus       174 rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  174 RRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             hhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            456778999999999999999999999975   667788889999999988876653

>TIGR00119 acolac_sm acetolactate synthase, small subunit

Probab=84.39  E-value=6.5  Score=34.47  Aligned_cols=61  Identities=16%  Similarity=0.302  Sum_probs=46.3

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-CeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-SSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .|.|..++++|.|.+|...|...|+.+.+..+.+.+ .....++|++.-+   .-.++.|.+-|.
T Consensus         3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~d---~~~i~qi~kQl~   64 (157)
T TIGR00119         3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVGD---DKVLEQITKQLN   64 (157)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEECC---HHHHHHHHHHHh
Confidence            577889999999999999999999999999888776 4566677776532   234555555544

acetohydroxyacid synthase is a synonym.

>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=81.85  E-value=7.4  Score=27.04  Aligned_cols=35  Identities=11%  Similarity=0.245  Sum_probs=30.0

Q ss_pred             EEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC
Q 021208          247 IRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG  281 (316)
Q Consensus       247 I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g  281 (316)
                      |.|..+.++|.+.++++.|.+.|+.|....+...+
T Consensus         1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~   35 (56)
T cd04889           1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETR   35 (56)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence            45788999999999999999999999887766544

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

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

Probab=81.18  E-value=6.4  Score=32.64  Aligned_cols=51  Identities=8%  Similarity=0.102  Sum_probs=36.7

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecC
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDV  295 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~  295 (316)
                      ..|-+..++++|.|.+||..+...|+.+.+-..-+..+....|.|...++.
T Consensus        42 tSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~~eY~FfIdieg   92 (115)
T cd04930          42 ATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEGGDLEVLVRCEV   92 (115)
T ss_pred             EEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCCceEEEEEEEEe
Confidence            344455577899999999999999999998887776544434444445443

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.

>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]

Probab=80.63  E-value=9.6  Score=36.45  Aligned_cols=68  Identities=10%  Similarity=0.215  Sum_probs=48.2

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE--eCCeEEEEEEEEEecCC-cccCHHHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT--FGSSVLDVTIIAQMDVE-FNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~--~g~~~l~~ti~aq~~~~-~~ls~~eL~~~L~~al~  313 (316)
                      ..+.+.|+|+.++|++..|-.-|-++|..|+.++-..  .+++++   ..+....+ ...+.+.|.+.+.....
T Consensus         6 ~~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf~D~~~g~FF---mR~~f~~~~~~~~~~~l~~~f~~~a~   76 (287)
T COG0788           6 DTFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQFDDPETGRFF---MRVEFEGEGGPLDREALRAAFAPLAE   76 (287)
T ss_pred             cceEEEEecCCCCCcHHHHHHHHHHcCCceeecccccccccCeEE---EEEEEecCCCcccHHHHHHHHHHHHH
Confidence            4568889999999999999999999999999988663  133332   22333333 33677777777666433

---

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	316
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	3e-15
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-13
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	6e-13
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-12
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	8e-10
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	2e-08
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	6e-05
4f3l_A	361	Mclock, circadian locomoter output cycles protein	6e-05
1a0a_A	63	BHLH, protein (phosphate system positive regulator	1e-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 = 68.9 bits (169), Expect = 3e-15
 Identities = 17/56 (30%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGLK-KMDKASVLGDAIKYLKQLQEKVKILEEQ 201
           H   E++ R  ++ + I L  +V G + K++K++VL  AI Y++ LQ   + L+++
Sbjct: 10  HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE 65

>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 = 64.7 bits (158), Expect = 1e-13
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQAN 203
           H + ER+RR +L + F AL   +P L   +K  K  +L  A  Y+  +Q + + L  + +
Sbjct: 10  HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEED 69

Query: 204 K 204
            
Sbjct: 70  L 70

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

 Score = 62.4 bits (152), Expect = 6e-13
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGLK--KMDKASVLGDAIKYLKQLQEKVKILEEQ 201
           H   ERKRR+ +   F +L   VP L+  K  +A +L  A +Y++ ++ K    ++ 
Sbjct: 16  HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 72

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGLK--KMDKASVLGDAIKYLKQLQEKVKILEEQANK 204
           H   ERKRR+ +   F +L   VP L+  K  +A +L  A +Y++ ++ K    ++  + 
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD 65

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

 Score = 53.1 bits (128), Expect = 8e-10
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 6/56 (10%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL------KKMDKASVLGDAIKYLKQLQEKVK 196
           H   ER+RR+K++   + LS I+P            K  +L  A  Y+++L++   
Sbjct: 9   HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGLKKMDKAS---VLGDAIKYLKQLQEKVKILEEQAN 203
           H   E+ RR  L      L  +VP      + +   +L  A  ++K+L++  +    Q +
Sbjct: 5   HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQID 64

Query: 204 K 204
           +
Sbjct: 65  Q 65

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

 Score = 43.5 bits (102), Expect = 6e-05
 Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 4/47 (8%)

Query: 150 AERKRREKLSQRFIALSAIVPGLK----KMDKASVLGDAIKYLKQLQ 192
            E++RR+K++     L+++VP       K+DK +VL  A++++K L+
Sbjct: 20  IEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66

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

 Score = 43.4 bits (102), Expect = 6e-05
 Identities = 16/45 (35%), Positives = 31/45 (68%), Gaps = 1/45 (2%)

Query: 150 AERKRREKLSQRFIALSAIVPGLK-KMDKASVLGDAIKYLKQLQE 193
           +E+KRR++ +     L +++PG   KMDK++VL  +I +L++ +E
Sbjct: 19  SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKE 63

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1 Length = 63

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 7/57 (12%)

Query: 147 HIIAERKRREKLSQRFIALSAIVP-------GLKKMDKASVLGDAIKYLKQLQEKVK 196
           H  AE+ RR +L+     L++++P             KA+ +  A +Y++ LQ+   
Sbjct: 6   HKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	316
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.63
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.53
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.52
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.52
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.51
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.51
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.5
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.48
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.45
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.42
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.36
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.13
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.13
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.88
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.72
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.59
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.47
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.06
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	97.09
1u8s_A	192	Glycine cleavage system transcriptional repressor,	96.41
2nyi_A	195	Unknown protein; protein structure initiative, PSI	96.08
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	95.87
2nyi_A	195	Unknown protein; protein structure initiative, PSI	95.38
1u8s_A	192	Glycine cleavage system transcriptional repressor,	95.29
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	92.77
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	92.36
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	91.9
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	91.54
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	90.14
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	90.0
2f1f_A	164	Acetolactate synthase isozyme III small subunit; f	88.58
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	88.51
3nrb_A	287	Formyltetrahydrofolate deformylase; N-terminal ACT	87.06
2pc6_A	165	Probable acetolactate synthase isozyme III (small;	85.61
2fgc_A	193	Acetolactate synthase, small subunit; regulatory s	83.96

>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=2.4e-16  Score=122.29  Aligned_cols=63  Identities=27%  Similarity=0.452  Sum_probs=59.3

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      ++..|+.+||+||++||+.|.+|+++||+. .|+||++||.+||+||++||.+++.|+++.+..
T Consensus         6 rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L   69 (82)
T 1am9_A            6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578899999999999999999999999997 899999999999999999999999999977654

>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=99.53  E-value=7.8e-15  Score=113.11  Aligned_cols=64  Identities=27%  Similarity=0.479  Sum_probs=59.4

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      .++..|+.+||+||..||+.|..|+++||..  .|++|++||..||+||+.|+.++++|+.+.+..
T Consensus        11 ~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           11 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999976  699999999999999999999999999987653

>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=99.52  E-value=9.8e-15  Score=113.19  Aligned_cols=62  Identities=27%  Similarity=0.487  Sum_probs=57.5

Q ss_pred             cchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          144 TQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       144 ~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      +..|+..||+||..||+.|..|+++||.+  .|++|++||..||+||+.|+.++++|+.+.+..
T Consensus         3 R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L   66 (83)
T 1nkp_B            3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999974  899999999999999999999999999876654

>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=99.52  E-value=3.5e-15  Score=110.63  Aligned_cols=54  Identities=28%  Similarity=0.517  Sum_probs=50.0

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCCC------CCCcchHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGLK------KMDKASVLGDAIKYLKQLQEKV  195 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~~------k~dKasiL~~Ai~YIk~Lq~~v  195 (316)
                      .++..|+.+||+||++||+.|..|++|||.+.      |++|++||.+||+||++||++.
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999874      7899999999999999999865

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

Probab=99.51  E-value=1.1e-14  Score=109.79  Aligned_cols=58  Identities=31%  Similarity=0.533  Sum_probs=53.3

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC-CCCCcchHHHHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILE  199 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dKasiL~~Ai~YIk~Lq~~v~~L~  199 (316)
                      .++.+|+.+||+||++||+.|..|++|||+. .|+||++||..||+||++||.++.=|+
T Consensus         7 ~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            7 AKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            4678999999999999999999999999975 799999999999999999999887554

>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=99.51  E-value=2.3e-15  Score=111.22  Aligned_cols=54  Identities=26%  Similarity=0.460  Sum_probs=48.7

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC-------CCCCcchHHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL-------KKMDKASVLGDAIKYLKQLQEKVK  196 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~-------~k~dKasiL~~Ai~YIk~Lq~~v~  196 (316)
                      ++.+|+.+||+||++||..|..|++|||++       .+.+||+||+.||+||++||++++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            468899999999999999999999999964       466799999999999999998753

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

Probab=99.50  E-value=2.4e-14  Score=118.18  Aligned_cols=61  Identities=21%  Similarity=0.505  Sum_probs=52.3

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCCC----CCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGLK----KMDKASVLGDAIKYLKQLQEKVKILEEQA  202 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~~----k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~  202 (316)
                      .++..|+.+||+||++||++|..|++|||++.    |++|++||.+||+||++||.+++.|+++.
T Consensus        26 ~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           26 QKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999873    67899999999999999999999998753

>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=99.48  E-value=3.4e-14  Score=111.59  Aligned_cols=62  Identities=29%  Similarity=0.475  Sum_probs=56.5

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhh
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQANK  204 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~  204 (316)
                      .+..|+..||+||++||+.|..|+++||..   .|++|++||.+||+||++|+.+.+.|..+.+.
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~   70 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL   70 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999975   69999999999999999999999988775543

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

Probab=99.45  E-value=1.6e-13  Score=105.93  Aligned_cols=62  Identities=23%  Similarity=0.247  Sum_probs=56.8

Q ss_pred             cchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          144 TQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       144 ~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      +..|+..||+||..||+.|..|+++||..   .|.+|++||..|++||++|+++.+.|..+.+..
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            56899999999999999999999999965   688899999999999999999999999876643

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

Probab=99.42  E-value=3.4e-14  Score=107.86  Aligned_cols=52  Identities=31%  Similarity=0.505  Sum_probs=48.5

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQLQE  193 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~Lq~  193 (316)
                      .++.+|+.+||+||++||+.|.+|++|||.+    .|+|||+||+.||+||+.|+.
T Consensus         8 ~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            8 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999975    799999999999999999974

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

Probab=99.36  E-value=2.3e-13  Score=104.08  Aligned_cols=58  Identities=24%  Similarity=0.350  Sum_probs=48.2

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCC---CCCC-CcchHHHHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPG---LKKM-DKASVLGDAIKYLKQLQEKVKILE  199 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~---~~k~-dKasiL~~Ai~YIk~Lq~~v~~L~  199 (316)
                      .++..|+..||+||..||+.|..|+.+||.   ..|. .|++||..||+||+.||+++++++
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            357889999999999999999999999995   3444 688899999999999999998865

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

Probab=99.13  E-value=3.6e-11  Score=87.79  Aligned_cols=54  Identities=26%  Similarity=0.318  Sum_probs=49.1

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVK  196 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~  196 (316)
                      ++..|+..||+|+..||+.|..||.+||..   .|.+|+.+|..||+||..|++.++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            367799999999999999999999999964   689999999999999999998753

>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=99.13  E-value=2.7e-11  Score=90.63  Aligned_cols=54  Identities=24%  Similarity=0.444  Sum_probs=49.7

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKV  195 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~v  195 (316)
                      .++..|+..||+|+..||+.|..||.+||..  .|++|+.||..||+||..|++.+
T Consensus        11 ~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999964  78999999999999999999764

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

Probab=98.88  E-value=1e-09  Score=105.09  Aligned_cols=54  Identities=28%  Similarity=0.526  Sum_probs=43.1

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccC-CCCCCCcchHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVP-GLKKMDKASVLGDAIKYLKQLQEKV  195 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP-~~~k~dKasiL~~Ai~YIk~Lq~~v  195 (316)
                      .++..|+.+||+||++||..|..|++||| ...|+||++||..||.||+.|+...
T Consensus        11 ~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A           11 AKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            46788999999999999999999999999 4589999999999999999998653

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

Probab=98.72  E-value=4.7e-09  Score=101.65  Aligned_cols=53  Identities=30%  Similarity=0.474  Sum_probs=49.2

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccC----CCCCCCcchHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVP----GLKKMDKASVLGDAIKYLKQLQEK  194 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP----~~~k~dKasiL~~Ai~YIk~Lq~~  194 (316)
                      .++.+|+.+||+||++||..|..|++|||    ...|+||++||..||.||+.|+..
T Consensus        12 ~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           12 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            46889999999999999999999999999    568999999999999999999853

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

Probab=98.59  E-value=9.2e-09  Score=76.45  Aligned_cols=45  Identities=20%  Similarity=0.417  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHH
Q 021208          149 IAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQE  193 (316)
Q Consensus       149 ~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~  193 (316)
                      ..||+|+..||+.|..||.+||..   +|++|..+|.-||+||..||.
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            347889999999999999999965   789999999999999999984

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

Probab=98.47  E-value=2.3e-07  Score=71.50  Aligned_cols=48  Identities=19%  Similarity=0.452  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHhcccCCC----CCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q 021208          155 REKLSQRFIALSAIVPGL----KKMDKASVLGDAIKYLKQLQEKVKILEEQA  202 (316)
Q Consensus       155 R~~in~~~~~LrslvP~~----~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~  202 (316)
                      |..||++|..|..|||.+    .|.+|++||..|++||++||+.++.+.++.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e   55 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   55 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999964    578999999999999999999998887643

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

Probab=98.06  E-value=5.2e-06  Score=65.82  Aligned_cols=48  Identities=23%  Similarity=0.373  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHHH
Q 021208          150 AERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKI  197 (316)
Q Consensus       150 ~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~~  197 (316)
                      .||.|-..||+.|..||.+||..   +|..|..+|.-||+||..|++-++.
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            35788889999999999999964   6899999999999999999987543

>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=97.09  E-value=0.01  Score=44.74  Aligned_cols=68  Identities=15%  Similarity=0.203  Sum_probs=54.3

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      .+.|.|.|++++|++.+|...|-+.|..|++.+....++. +.+.+...+.+  ...+++|.+.|+..-..
T Consensus         5 ~~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~-~~~~i~v~~~~--~~~l~~l~~~L~~~~~~   72 (91)
T 1zpv_A            5 KAIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEY-FTMMAVVSSDE--KQDFTYLRNEFEAFGQT   72 (91)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTE-EEEEEEEEESS--CCCHHHHHHHHHHHHHH
T ss_pred             eEEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCE-EEEEEEEEeCC--CCCHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999998877654 33555666654  34788999998875443

>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=96.41  E-value=0.02  Score=49.40  Aligned_cols=66  Identities=15%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      .+.|.|.|++++|++.+|...|.++|+.|+.++....++.+. .++++..+.   ...++|.+.|..++.
T Consensus         6 ~~~itv~~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~-~~~~v~~~~---~~~~~l~~~L~~~~~   71 (192)
T 1u8s_A            6 HLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFT-LLMLISGSP---SNITRVETTLPLLGQ   71 (192)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEE-EEEEEEECH---HHHHHHHHHHHHHHH
T ss_pred             EEEEEEEcCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceE-EEEEEecCC---CCHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999988777655 355555432   245667777666543

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

Probab=96.08  E-value=0.034  Score=48.39  Aligned_cols=50  Identities=14%  Similarity=0.333  Sum_probs=41.9

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEec
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMD  294 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~  294 (316)
                      .+.|.|.|+.++|++..|...|.++|+.|+.+...+..+.++ .++.+..+
T Consensus         5 ~~~ltv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~-m~~~v~~~   54 (195)
T 2nyi_A            5 SFVVSVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFA-MIVLVSLN   54 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEE-EEEEEEES
T ss_pred             EEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEE-EEEEEEec
Confidence            478999999999999999999999999999999988776654 24555544

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

Probab=95.87  E-value=0.033  Score=41.21  Aligned_cols=63  Identities=14%  Similarity=0.227  Sum_probs=46.4

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .+.|+|.+.+++|+|.+|...|.+.|+.|.+..+...++ ...+.+...+.+.  -.++++.+.|+
T Consensus         5 ~~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~-~~~~~i~v~~~~~--~~l~~l~~~L~   67 (88)
T 2ko1_A            5 LAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDG-IFTCNLMIFVKNT--DKLTTLMDKLR   67 (88)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSS-EEEEEEEEEESSH--HHHHHHHHHHT
T ss_pred             EEEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCC-EEEEEEEEEECCH--HHHHHHHHHHh
Confidence            457889999999999999999999999999999887776 4445555555432  23444554443

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

Probab=95.38  E-value=0.1  Score=45.26  Aligned_cols=69  Identities=13%  Similarity=0.190  Sum_probs=51.7

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-----CeEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-----SSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-----~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      .+.|.|.|+.++|++..|-..|-++|+.|..+...+.+     ...+.+.+.....+  ... ++|.+.|......|
T Consensus        93 ~~iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~~~--~~~-~~l~~~l~~~a~~l  166 (195)
T 2nyi_A           93 EYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAFPF--PLY-QEVVTALSRVEEEF  166 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEEEG--GGH-HHHHHHHHHHHHHH
T ss_pred             EEEEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEcCC--Ccc-HHHHHHHHHHHHHc
Confidence            47899999999999999999999999999999998775     22333444444442  334 77777777665543

>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=95.29  E-value=0.19  Score=43.09  Aligned_cols=71  Identities=15%  Similarity=0.247  Sum_probs=53.8

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-------CeEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-------SSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-------~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      ....|.|.|+.++|++.+|.+.|.++|+.|..+...+.+       ...+.+.+.....+  ....++|.+.|......|
T Consensus        92 ~~~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~~~~~--~~~~~~l~~~l~~~~~~~  169 (192)
T 1u8s_A           92 YTVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVDS--GCNLMQLQEEFDALCTAL  169 (192)
T ss_dssp             EEEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEECT--TSCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEEeCCC--CCCHHHHHHHHHHHHHHh
Confidence            346889999999999999999999999999999988765       22443444444433  457888888888766554

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

Probab=92.77  E-value=0.41  Score=45.67  Aligned_cols=69  Identities=14%  Similarity=0.217  Sum_probs=52.9

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      ..++|.|.|+.++|++..|...|-++|..|+.++-...++.++ ..+.+.+++. ..+.++|.+.|...-.
T Consensus        11 ~~~~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~-~~~~~~~~~~-~~~~~~l~~~l~~~~~   79 (415)
T 3p96_A           11 VSVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLT-LGVLVCCPAD-VADGPALRHDVEAAIR   79 (415)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEE-EEEEEEECHH-HHTSHHHHHHHHHHHH
T ss_pred             CeEEEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeE-EEEEEEecCC-cCCHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999888887655 3445555332 2355777777765443

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

Probab=92.36  E-value=0.83  Score=42.35  Aligned_cols=69  Identities=6%  Similarity=0.098  Sum_probs=51.2

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE--eCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT--FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~--~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      ..+.|.|.|++++|++..|...|-++|+.|+.++-..  ..+.++ ..+.+..++  ..+.++|.+.|...-..
T Consensus         7 ~~~vLtv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff-mr~~~~~~~--~~~~~~L~~~f~~la~~   77 (286)
T 3n0v_A            7 DTWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFF-IRVEFRQPD--DFDEAGFRAGLAERSEA   77 (286)
T ss_dssp             CCEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEE-EEEEEECCS--SCCHHHHHHHHHHHHGG
T ss_pred             CcEEEEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeE-EEEEEecCC--CCCHHHHHHHHHHHHHH
Confidence            3478999999999999999999999999999988763  344333 234444433  46788888888654433

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

Probab=91.90  E-value=1.4  Score=41.20  Aligned_cols=70  Identities=9%  Similarity=0.145  Sum_probs=50.9

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe--CCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF--GSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~--g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      ..+.|.|.|++++|++..|...|-++|+.|+.++-...  ++.++ ..+.+..++ ...+.++|.+.|...-..
T Consensus        21 ~~~iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~Ff-Mr~~~~~~~-~~~~~~~L~~~l~~la~~   92 (302)
T 3o1l_A           21 RTFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFF-MRHEIRADT-LPFDLDGFREAFTPIAEE   92 (302)
T ss_dssp             CEEEEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEE-EEEEEEGGG-SSSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEE-EEEEEecCC-CCCCHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999999987754  34333 223333322 246788888888654443

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

Probab=91.54  E-value=1.7  Score=40.25  Aligned_cols=70  Identities=6%  Similarity=0.177  Sum_probs=51.4

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE--eCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHHh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT--FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~--~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~  314 (316)
                      ..+.|.|.|++++|++..|...|-++|+.|+.++...  ..+.++ ..+.+.+++. ..+.++|.+.|...-..
T Consensus         5 ~~~iLtv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff-mr~~~~~~~~-~~~~~~L~~~f~~la~~   76 (288)
T 3obi_A            5 HQYVLTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFF-MRVVFNAAAK-VIPLASLRTGFGVIAAK   76 (288)
T ss_dssp             CEEEEEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEE-EEEEEEESSC-CCCHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceE-EEEEEEcCCC-CCCHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999988752  334333 2344455432 46788888888655443

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

Probab=90.14  E-value=1.9  Score=39.95  Aligned_cols=71  Identities=11%  Similarity=0.220  Sum_probs=49.7

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE--eCCeEEEEEEEEEecC-CcccCHHHHHHHHHHHHHh
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT--FGSSVLDVTIIAQMDV-EFNMTVKDLVKNLHSAFQL  314 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~--~g~~~l~~ti~aq~~~-~~~ls~~eL~~~L~~al~~  314 (316)
                      ..+.|.|.|++++|++.+|...|-++|+.|+.++-..  ..+.++ ..+....+. +...+.++|.+.|...-..
T Consensus         9 ~~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff-mr~~~~~~~~~~~~~~~~L~~~f~~la~~   82 (292)
T 3lou_A            9 HQFVLTLSCPSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFF-VRCVFHATDDADALRVDALRREFEPIAER   82 (292)
T ss_dssp             CEEEEEEEEESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEE-EEEEEEECC----CCHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceE-EEEEEEccCcccCCCHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999988773  344333 223333330 1236788888887654433

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

Probab=90.00  E-value=0.71  Score=37.89  Aligned_cols=36  Identities=17%  Similarity=0.333  Sum_probs=32.8

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG  281 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g  281 (316)
                      -|+|.|.+|.|++.+|+.+|-+.++.+...++.+-|
T Consensus         2 ~~~v~~~dr~g~l~~i~~~l~~~~~ni~~~~~~~~g   37 (190)
T 2jhe_A            2 RLEVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPIG   37 (190)
T ss_dssp             EEEEEECSCTTHHHHHHHHHHHTTCCEEEEEEETTT
T ss_pred             EEEEEEecCCcHHHHHHHHHHHcCCCeEEEEEecCC
Confidence            478999999999999999999999999999987653

>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=88.58  E-value=2.3  Score=36.25  Aligned_cols=62  Identities=15%  Similarity=0.254  Sum_probs=45.6

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC-eEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS-SVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~-~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      ..|.|..++++|+|.+|...|...|+.+.+.++.+..+ ....++|.+. ++  .-.++.|.+.|+
T Consensus         4 ~~IsV~v~NrpGvLarIt~lfs~rg~NI~Sl~v~~t~d~~~sriti~V~-~d--~~~leqI~kqL~   66 (164)
T 2f1f_A            4 RILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTV-GD--EKVLEQIEKQLH   66 (164)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEEEE-SC--HHHHHHHHHHHH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHHCCCCeeeceeeecCCCCEEEEEEEEe-cc--HHHHHHHHHHHc
Confidence            46788999999999999999999999999988876653 4555666665 33  223444555544

>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=88.51  E-value=1.4  Score=39.58  Aligned_cols=62  Identities=10%  Similarity=0.143  Sum_probs=45.1

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC----CeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG----SSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g----~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      .+.|.|.+.+++|+|.+|+..|-+.+..|.+.+...-.    +..-.  +..++++.   .+++|.++|++
T Consensus         4 ~VtL~I~a~DRpGLLsDIt~vLAe~kiNIltIn~~~~~kG~~ng~A~--I~IEV~d~---~Le~LL~kLrk   69 (223)
T 1y7p_A            4 LRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKAL--IYFEIEGG---DFEKILERVKT   69 (223)
T ss_dssp             CEEEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEE--EEEEECSS---CHHHHHHHHHT
T ss_pred             eEEEEEEEcCCCCHHHHHHHHHHHcCCCceEEEEEccccCCcCCEEE--EEEEECCC---CHHHHHHHHhC
Confidence            46788999999999999999999999999999987754    33332  33566544   88888888864

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

Probab=87.06  E-value=3.1  Score=38.47  Aligned_cols=65  Identities=9%  Similarity=0.252  Sum_probs=44.4

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEE--eCCeEEEEEEEEEecCCcccCHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMT--FGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSA  311 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~--~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~a  311 (316)
                      ..+.|.|.|++++|++..|...|-++|+.|+.++...  .++.++ ..+....+.   ....+|.+.|...
T Consensus         6 ~~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff-mr~~~~~~~---~~~~~L~~~f~~l   72 (287)
T 3nrb_A            6 NQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFF-MRVSVEIPV---AGVNDFNSAFGKV   72 (287)
T ss_dssp             TEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEE-EEEEEECCC------CHHHHHHHHH
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHCCCCEEeeeeeecCCCCeEE-EEEEEEcCC---CCHHHHHHHHHHH
Confidence            4578999999999999999999999999999998752  344333 223333322   2344666666543

>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=85.61  E-value=3.2  Score=35.40  Aligned_cols=62  Identities=15%  Similarity=0.256  Sum_probs=45.2

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC-eEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS-SVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~-~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      -.|.|..++++|+|.+|...|...|+.|.+.++.+..+ ....++|++. ++  .-.++.|.+.|+
T Consensus         5 ~~IsV~veNrpGvL~rI~~lfs~rg~NI~Sl~v~~t~d~g~sritivV~-~d--~~~leql~kQL~   67 (165)
T 2pc6_A            5 HIISLLMENEAGALSRVAGLFSARGYNIESLSVAPTEDPTLSRMTLVTN-GP--DEIVEQITKQLN   67 (165)
T ss_dssp             EEEEEEEECSTTHHHHHHHHHHHHTCCCCEEEEEECSSTTEEEEEEEEE-EC--HHHHHHHHHHHH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHHCCCcEEEEEEEecCCCCEEEEEEEEe-cc--HHHHHHHHHHhc
Confidence            46788999999999999999999999999998876553 4555666665 22  223444444444

>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=83.96  E-value=6.2  Score=34.56  Aligned_cols=62  Identities=15%  Similarity=0.250  Sum_probs=46.4

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCC-eEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGS-SVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~-~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      -.|.|..++++|.|.+|...|...|+.|.+-.+.+..+ .+..+||++.-+   .-.++.|.+.|.
T Consensus        30 ~~LsVlVeN~pGvLaRItglfsrRG~NI~SLtV~~ted~gisRitIvV~g~---e~~ieqL~kQL~   92 (193)
T 2fgc_A           30 HLVSMLVHNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVKGD---DKTIEQIEKQAY   92 (193)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEEEC---TTHHHHHHHHHT
T ss_pred             EEEEEEECCCChHHHHHHHHHHHCCceEEEEEeeccCCCCEEEEEEEEECC---HHHHHHHHHHhc
Confidence            46778889999999999999999999999988876544 455667776533   234555555543

---

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	316
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-13
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	5e-13
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	6e-13
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-12
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-12
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-12
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	4e-12
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	5e-12

>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 = 63.3 bits (154), Expect = 1e-13
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKVKILEEQANK 204
           H   ERKRR+ +   F +L   VP L  +K  +A +L  A +Y++ ++ K    ++  + 
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD 65

>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 = 60.9 bits (148), Expect = 5e-13
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 155 REKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILEEQ 201
           R  ++ + I L  +V G   KM K+ VL  AI Y+K LQ+    L ++
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE 48

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

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

 Score = 61.1 bits (148), Expect = 6e-13
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQAN 203
           H   E+ RR  L      L  +VP      +    S+L  A  ++K+L++  +    Q +
Sbjct: 5   HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQID 64

Query: 204 K 204
           +
Sbjct: 65  Q 65

>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 = 60.3 bits (146), Expect = 1e-12
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 140 RLSNTQDHIIAERKRREKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKIL 198
           R      H   E++ R  ++ + I L  +V G   K++K++VL  AI Y++ LQ   + L
Sbjct: 3   RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL 62

Query: 199 EEQANK 204
           +++   
Sbjct: 63  KQENLS 68

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQAN 203
           H + ER+RR +L + F AL   +P L   +K  K  +L  A  Y+  +Q + + L  + +
Sbjct: 10  HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEED 69

Query: 204 K 204
            
Sbjct: 70  L 70

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

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

 Score = 59.5 bits (144), Expect = 2e-12
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 131 KRISPGAGNRLSNTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYL 188
           KR +  A  R +      + ER+R  K+++ F  L         +++ K  +L +AI+Y+
Sbjct: 4   KRKTTNADRRKA----ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYI 59

Query: 189 KQLQEKVK 196
           + LQ  ++
Sbjct: 60  EGLQALLR 67

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

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

 Score = 58.3 bits (141), Expect = 4e-12
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 7/57 (12%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL-------KKMDKASVLGDAIKYLKQLQEKVK 196
           H  AE+ RR +L+     L++++P             KA+ +  A +Y++ LQ+   
Sbjct: 6   HKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

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

 Score = 58.2 bits (141), Expect = 5e-12
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 6/56 (10%)

Query: 147 HIIAERKRREKLSQRFIALSAIVPGL------KKMDKASVLGDAIKYLKQLQEKVK 196
           H   ER+RR+K++   + LS I+P            K  +L  A  Y+++L++   
Sbjct: 9   HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	316
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.51
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.48
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.47
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.46
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.39
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.36
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	97.31
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.99
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	96.51
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	95.24
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	90.62
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	88.75
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	87.74
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	86.74
d1phza1	97	Phenylalanine hydroxylase N-terminal domain {Rat (	85.4
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	81.97

>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=99.55  E-value=2.3e-15  Score=114.28  Aligned_cols=64  Identities=27%  Similarity=0.446  Sum_probs=58.8

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      .++..|+.+||+||++||+.|..|++|||+. .|++|++||..||+||+.|+.+++.|+++....
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~l   69 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3577899999999999999999999999986 799999999999999999999999999876643

>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=99.53  E-value=7.7e-15  Score=110.88  Aligned_cols=62  Identities=23%  Similarity=0.247  Sum_probs=56.8

Q ss_pred             cchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          144 TQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       144 ~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      +..|+.+||+||++||+.|..|+++||+.   .|++|++||..||+||+.|+.+++.|..+.+..
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L   66 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999975   589999999999999999999999998876543

>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=99.51  E-value=3.5e-15  Score=108.33  Aligned_cols=53  Identities=26%  Similarity=0.473  Sum_probs=48.9

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCC-------CCCCCcchHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPG-------LKKMDKASVLGDAIKYLKQLQEKV  195 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~-------~~k~dKasiL~~Ai~YIk~Lq~~v  195 (316)
                      ++..|+.+||+||++||+.|..|++|||+       ..|++|++||..||+||++||+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999994       478999999999999999999865

>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=99.48  E-value=1.4e-14  Score=110.44  Aligned_cols=63  Identities=27%  Similarity=0.484  Sum_probs=57.4

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      ++..|+.+||+||++||+.|..|+++||+.  .|++|++||..||+||+.|+.+++.|..+.+..
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   66 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            367899999999999999999999999964  789999999999999999999999999876543

>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=99.47  E-value=1.9e-14  Score=110.81  Aligned_cols=62  Identities=29%  Similarity=0.475  Sum_probs=56.8

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC---CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhh
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL---KKMDKASVLGDAIKYLKQLQEKVKILEEQANK  204 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~  204 (316)
                      ++..|+.+||+||++||+.|..|+++||+.   .|++|++||..||+||+.|+.+++.|..+.+.
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   70 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL   70 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999964   67999999999999999999999999886654

>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=99.46  E-value=9e-15  Score=107.76  Aligned_cols=55  Identities=24%  Similarity=0.453  Sum_probs=50.6

Q ss_pred             CCcchhhHHHHHHHHHHHHHHHHHhcccCCC--CCCCcchHHHHHHHHHHHHHHHHH
Q 021208          142 SNTQDHIIAERKRREKLSQRFIALSAIVPGL--KKMDKASVLGDAIKYLKQLQEKVK  196 (316)
Q Consensus       142 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dKasiL~~Ai~YIk~Lq~~v~  196 (316)
                      .++..|+..||+||.+||+.|..|+++||.+  .|++|++||..||+||++||+.++
T Consensus        11 ~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            4578899999999999999999999999985  688999999999999999998764

>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=99.39  E-value=6.2e-14  Score=102.21  Aligned_cols=53  Identities=28%  Similarity=0.526  Sum_probs=48.4

Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHhcccCCC------CCCCcchHHHHHHHHHHHHHHHH
Q 021208          143 NTQDHIIAERKRREKLSQRFIALSAIVPGL------KKMDKASVLGDAIKYLKQLQEKV  195 (316)
Q Consensus       143 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~------~k~dKasiL~~Ai~YIk~Lq~~v  195 (316)
                      ++..|+.+||+||++||+.|..|+++||..      .|++|++||..||+||++||++.
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            467899999999999999999999999964      48999999999999999999753

>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=99.36  E-value=1.6e-13  Score=98.86  Aligned_cols=51  Identities=33%  Similarity=0.477  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHhcccCCC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 021208          155 REKLSQRFIALSAIVPGL-KKMDKASVLGDAIKYLKQLQEKVKILEEQANKK  205 (316)
Q Consensus       155 R~~in~~~~~LrslvP~~-~k~dKasiL~~Ai~YIk~Lq~~v~~L~~~~~~~  205 (316)
                      |++||++|.+|+++||++ +|+|||+||.+||+||+.||.++++|+++....
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L   52 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVL   52 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999987 699999999999999999999999999987654

>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=97.31  E-value=0.0022  Score=46.72  Aligned_cols=66  Identities=15%  Similarity=0.199  Sum_probs=53.6

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQ  313 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~  313 (316)
                      ++|.|.|++++|++.+|...|-++|..|.+++-.+.++.+. ..+.+.++.  ..+.++|.+.|...-.
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~-~~~~v~~~~--~~~~~~l~~~l~~la~   68 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFT-MMAVVSSDE--KQDFTYLRNEFEAFGQ   68 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEE-EEEEEEESS--CCCHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEE-EEEEEEEec--CCCHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999888887654 445556654  4568888888876544

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

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

Probab=96.99  E-value=0.0029  Score=46.53  Aligned_cols=66  Identities=14%  Similarity=0.249  Sum_probs=52.6

Q ss_pred             CeEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHHHHH
Q 021208          243 KSVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLHSAF  312 (316)
Q Consensus       243 ~~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~al  312 (316)
                      ..++|.+.|++++|++.+|...|-+.|..|++++...+++.+. +.+.+.++..   ++++|...|...-
T Consensus         4 ~~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~-~~~~v~~~~~---~~~~l~~~L~~l~   69 (86)
T d1u8sa1           4 QHLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFT-LLMLISGSPS---NITRVETTLPLLG   69 (86)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEE-EEEEEEECHH---HHHHHHHHHHHHH
T ss_pred             cEEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeE-EEEEEEcCcc---cHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999999776 4455555432   4666766666543

>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=96.51  E-value=0.023  Score=42.01  Aligned_cols=70  Identities=16%  Similarity=0.253  Sum_probs=52.4

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC----C---eEEEEEEEEEecCCcccCHHHHHHHHHHHHHhh
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG----S---SVLDVTIIAQMDVEFNMTVKDLVKNLHSAFQLF  315 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g----~---~~l~~ti~aq~~~~~~ls~~eL~~~L~~al~~~  315 (316)
                      .+.|.|.|++|+|++.+|...|-++|+.|.+.+..+..    +   ..+...+.+.++.+  .++++|.+.|...-..|
T Consensus         6 tv~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~p~~--~~~~~l~~~l~~l~~~l   82 (93)
T d1u8sa2           6 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVDSG--CNLMQLQEEFDALCTAL   82 (93)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEECTT--SCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEcCcc--ccHHHHHHHHHHHHHHc
Confidence            46788999999999999999999999999888765532    1   23444455666654  67888888887765443

>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=95.24  E-value=0.0085  Score=43.25  Aligned_cols=63  Identities=11%  Similarity=0.175  Sum_probs=41.5

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEe--CCeEEEEEEEEEecCCcccCHHHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTF--GSSVLDVTIIAQMDVEFNMTVKDLVKNLHS  310 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~--g~~~l~~ti~aq~~~~~~ls~~eL~~~L~~  310 (316)
                      .-|+|.|.+++|+|.+|...+-+.|..|.+.+....  |.....++|-.+..+   ..++.|.++|+.
T Consensus         2 ~~i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~~~---~~l~~ll~kL~~   66 (77)
T d1y7pa2           2 RGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEG---GDFEKILERVKT   66 (77)
T ss_dssp             EEEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEECS---SCHHHHHHHHHT
T ss_pred             eeEEEEEecCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEcCc---ccHHHHHHHHHc
Confidence            358999999999999999999999999988886642  223333344333322   357888888764

>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=90.62  E-value=1.1  Score=30.91  Aligned_cols=40  Identities=8%  Similarity=0.157  Sum_probs=35.2

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEE
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVL  285 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l  285 (316)
                      +|.|..++++|.|.++++.|.+.|+.|....+...+++.+
T Consensus         1 ViaV~v~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~   40 (71)
T d2f06a1           1 VVGISCPNVPGALAKVLGFLSAEGVFIEYMYSFANNNVAN   40 (71)
T ss_dssp             EEEEEEESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEE
T ss_pred             CEEEEecCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEE
Confidence            4678889999999999999999999999988877777654

>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=88.75  E-value=0.98  Score=31.36  Aligned_cols=40  Identities=8%  Similarity=0.176  Sum_probs=36.0

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEE
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVL  285 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l  285 (316)
                      .|.|..++++|.|.+|...|...|+.+...++....+..+
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i   44 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGI   44 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCE
Confidence            4778999999999999999999999999999888777655

>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=87.74  E-value=1.1  Score=31.72  Aligned_cols=47  Identities=6%  Similarity=0.123  Sum_probs=36.9

Q ss_pred             EEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecC
Q 021208          249 VHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDV  295 (316)
Q Consensus       249 I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~  295 (316)
                      +.-.+++|.|.++|..+.++|+.+.+-..-+..+...+|.|...++.
T Consensus         7 ~~~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~~g   53 (80)
T d2qmwa2           7 TPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQADS   53 (80)
T ss_dssp             EESSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEESC
T ss_pred             EeCCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEec
Confidence            34467899999999999999999998888887766555556666654

>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=86.74  E-value=1.2  Score=31.62  Aligned_cols=60  Identities=12%  Similarity=0.109  Sum_probs=41.6

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecCCcccCHHHHHHHHH
Q 021208          246 LIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDVEFNMTVKDLVKNLH  309 (316)
Q Consensus       246 ~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~~~~ls~~eL~~~L~  309 (316)
                      .|-|.-.+++|++.+|...|-+.|+.|.+......++.... .+...+++.   ..++++++|+
T Consensus        13 rl~i~~~d~PGvla~I~~~l~~~~iNI~~~~~~~~~~~~~a-~~~i~~D~~---~~~~v~~~i~   72 (84)
T d1sc6a3          13 RLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYV-VIDIEADED---VAEKALQAMK   72 (84)
T ss_dssp             EEEEEEESCTTHHHHHHHHHHHTTCEEEEEEEEECSSEEEE-EEEEECCHH---HHHHHHHHHH
T ss_pred             EEEEEeCCcCCHHHHHHHHHHHcCCCHHHhccccCCCCcEE-EEEEECCCC---CHHHHHHHHH
Confidence            33345578999999999999999999999888877765443 233444322   2455655554

>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=85.40  E-value=0.4  Score=35.60  Aligned_cols=52  Identities=8%  Similarity=0.115  Sum_probs=38.0

Q ss_pred             eEEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeCCeEEEEEEEEEecC
Q 021208          244 SVLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFGSSVLDVTIIAQMDV  295 (316)
Q Consensus       244 ~v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g~~~l~~ti~aq~~~  295 (316)
                      ..-|-+.+.+++|.|.++|..+..+|+.+..-..-+..+..-.|.|-+.++.
T Consensus        16 ktSl~f~~~~~pGaL~~vL~~f~~~~INLt~IeSRP~~~~~~~Y~F~id~eg   67 (97)
T d1phza1          16 AISLIFSLKEEVGALAKVLRLFEENDINLTHIESRPSRLNKDEYEFFTYLDK   67 (97)
T ss_dssp             CEEEEEEEECCTTHHHHHHHHHHTTTCCTTSEEEEECSSCTTEEEEEECBCG
T ss_pred             cEEEEEEeCCCCCHHHHHHHHHHHCCCCEEEEEeeccCCCCceEEEEEEccc
Confidence            3555567788999999999999999988876666665554444555566643

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

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

Probab=81.97  E-value=5.6  Score=28.00  Aligned_cols=61  Identities=15%  Similarity=0.247  Sum_probs=46.5

Q ss_pred             EEEEEEecCCCCHHHHHHHHHHhCCCeEEEEEEEEeC-CeEEEEEEEEEecCCcccCHHHHHHHH
Q 021208          245 VLIRVHCEKRKGVFEKIVAEIEKLHLTVINSSVMTFG-SSVLDVTIIAQMDVEFNMTVKDLVKNL  308 (316)
Q Consensus       245 v~I~I~c~k~~gll~~Il~~Le~lgL~Vv~asvs~~g-~~~l~~ti~aq~~~~~~ls~~eL~~~L  308 (316)
                      ..|.+..++++|+|.+|...+...|..+-+-++.+.. ..+..+||++.-++.   .++.|.+-|
T Consensus         4 ~tisvlv~n~pGvL~Ri~~lF~rRg~NI~SL~v~~te~~~iSR~tivv~g~~~---~i~qi~kQl   65 (78)
T d2fgca2           4 HLVSMLVHNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVKGDDK---TIEQIEKQA   65 (78)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEEECTT---HHHHHHHHH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHhhCCcceEEEEEeecCCCCeEEEEEEEEcCHH---HHHHHHHHH
Confidence            4678889999999999999999999999888887654 346667888775443   345554443