Citrus Sinensis ID: 018897

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------35
Protein Sequence
MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL
Secondary Structure (PSIPRED)
ccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEEcccEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEEEcccEEEEEEEEcccccccccHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccEEEEEcccccccccEEEcccccHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEEEEEcccEEEEEEccccccHHHHHHHHHHHccccEEEEEEEEccccEEEEEHHHHHcccccccHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MEFSEHGFLEELLALRRDaytwdtsipaemnqifsdgnwiydcfdenpaafspnsfsapihqqdhfnynnffneaaycpygddqlsapqltdsssmntldshthtppsfpiqeeaplsmmeldgeepnnllADEFQNLEMLQncfkvepvhespetlpvfnmgtdclerksrnkklggqpsknlMAERRRRKRLNDRLSMLRSIVpkiskmdrTSILADTIDYMKELLDKISSLQQEIQAGsnnletgifkdvkpneivvrnspkfdvertnMDTRVEIccagkpglllSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRnagyggkcl
Flexible Loop (DISEMBL)
MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLErksrnkklggqpsknlmaerrrrkrlndrlsmlrsivpkiskmdrtsILADTIDYMKELLDKISSLQQEIQAGsnnletgifkdvkpneivvrnspkfdvertnMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQAlfrnagyggkcl
Low Complexity Region (SEG)
MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHfnynnffnEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGGQPSKNLMAErrrrkrLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL
Disordered region (IsUnstruct)
******GFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHFNYNNFFNEAAYCPYG****************************************************EFQNLEMLQNCFKVEPV******LPVFNM*****************************************IVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGY*****
Disordered Region (DISOPRED)
*EFSEHGFLEELLALRR********************************************************************************************************************************************************************************LNDRLSMLRSIVPKISKMDRTSILADTIDYMKELL***************************************VERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQ**TLSCEDIKQALFRNAGYGG*C*
Disordered Region (DISEMBL)
MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL
Disordered Region (DISPRO)
******GFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSR*****GQPSK*LMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQA********************RNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSIxxxxxxxxxxxxxxxxxxxxxxxxxxxxLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL
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	349	2.2.26 [Sep-21-2011]
Q9LSL1	351	Transcription factor bHLH	yes	no	0.515	0.512	0.725	7e-67
Q9LXA9	315	Transcription factor bHLH	no	no	0.504	0.558	0.666	3e-57
Q9LSE2	494	Transcription factor ICE1	no	no	0.478	0.338	0.441	6e-35
Q9LPW3	450	Transcription factor SCRE	no	no	0.478	0.371	0.445	3e-34
Q9ZVX2	571	Transcription factor ABOR	no	no	0.349	0.213	0.380	1e-17
Q9FT81	518	Transcription factor TT8	no	no	0.575	0.388	0.263	7e-14
Q700E3	263	Transcription factor bHLH	no	no	0.169	0.224	0.542	2e-12
Q9ZPY8	566	Transcription factor ABA-	no	no	0.303	0.187	0.365	2e-12
O49687	589	Transcription factor MYC4	no	no	0.418	0.247	0.337	7e-12
Q9FIP9	592	Transcription factor ATR2	no	no	0.461	0.271	0.295	8e-11

>sp|Q9LSL1|BH093_ARATH Transcription factor bHLH93 OS=Arabidopsis thaliana GN=BHLH93 PE=1 SV=1

 Score =  254 bits (649), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 135/186 (72%), Positives = 154/186 (82%), Gaps = 6/186 (3%)

Query: 170 KSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLD 229
           K ++KKL GQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSIL D IDYMKELLD
Sbjct: 166 KKKSKKLEGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDAIDYMKELLD 225

Query: 230 KISSLQQEIQ--AGSNNLET----GIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAG 283
           KI+ LQ E Q    SNN       G  KD+  NE +VRNSPKF+++R + DTRV+ICC+ 
Sbjct: 226 KINKLQDEEQELGNSNNSHHSKLFGDLKDLNANEPLVRNSPKFEIDRRDEDTRVDICCSP 285

Query: 284 KPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAG 343
           KPGLLLSTV +LE LGLEI+QCVISCF+DF++QASCSEG EQR+ ++ EDIKQALFRNAG
Sbjct: 286 KPGLLLSTVNTLETLGLEIEQCVISCFSDFSLQASCSEGAEQRDFITSEDIKQALFRNAG 345

Query: 344 YGGKCL 349
           YGG CL
Sbjct: 346 YGGSCL 351

Transcription factor. May be involved in the differentiation of stomatal guard cells.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXA9|BH061_ARATH Transcription factor bHLH61 OS=Arabidopsis thaliana GN=BHLH61 PE=2 SV=1

 Score =  222 bits (566), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 122/183 (66%), Positives = 148/183 (80%), Gaps = 7/183 (3%)

Query: 169 RKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELL 228
           +K  NKKL GQPSKNLMAERRRRKRLNDRLS+LRSIVPKI+KMDRTSIL D IDYMKELL
Sbjct: 138 KKRSNKKLEGQPSKNLMAERRRRKRLNDRLSLLRSIVPKITKMDRTSILGDAIDYMKELL 197

Query: 229 DKISSLQQ-EIQAGSN-NLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPG 286
           DKI+ LQ+ E + GSN +L T I      NE +VRNS KF+V++  ++T ++ICC  KPG
Sbjct: 198 DKINKLQEDEQELGSNSHLSTLI-----TNESMVRNSLKFEVDQREVNTHIDICCPTKPG 252

Query: 287 LLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGG 346
           L++STV++LE LGLEI+QCVISCF+DF++QASC E  EQR  ++ E  KQAL RNAGYGG
Sbjct: 253 LVVSTVSTLETLGLEIEQCVISCFSDFSLQASCFEVGEQRYMVTSEATKQALIRNAGYGG 312

Query: 347 KCL 349
           +CL
Sbjct: 313 RCL 315

Arabidopsis thaliana (taxid: 3702)

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

 Score =  148 bits (373), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 83/188 (44%), Positives = 112/188 (59%), Gaps = 21/188 (11%)

Query: 180 PSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239
           P+KNLMAERRRRK+LNDRL MLRS+VPKISKMDR SIL D IDY+KELL +I+ L  E++
Sbjct: 305 PAKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDLHNELE 364

Query: 240 A---GSNNLETGIFKDVKPNEIVVR------------NSPKFDVERTNMDTR------VE 278
           +   GS    +  F  + P    +              SPK    R  +  R      + 
Sbjct: 365 STPPGSLPPTSSSFHPLTPTPQTLSCRVKEELCPSSLPSPKGQQARVEVRLREGRAVNIH 424

Query: 279 ICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQAL 338
           + C  +PGLLL+T+ +L+ LGL++QQ VISCFN FA+    +E  ++ + +  + IK  L
Sbjct: 425 MFCGRRPGLLLATMKALDNLGLDVQQAVISCFNGFALDVFRAEQCQEGQEILPDQIKAVL 484

Query: 339 FRNAGYGG 346
           F  AGY G
Sbjct: 485 FDTAGYAG 492

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  145 bits (367), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 82/184 (44%), Positives = 108/184 (58%), Gaps = 17/184 (9%)

Query: 180 PSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239
           P+KNLMAERRRRK+LNDRL MLRS+VPKISKMDR SIL D IDY+KELL +I+ L  E++
Sbjct: 265 PAKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDLHTELE 324

Query: 240 AGSNNLETGIFKDVKPNEIVVR-----------NSPKFDVERTNMDTR------VEICCA 282
           +   +  +       P  +  R            SPK    R  +  R      + + C 
Sbjct: 325 STPPSSSSLHPLTPTPQTLSYRVKEELCPSSSLPSPKGQQPRVEVRLREGKAVNIHMFCG 384

Query: 283 GKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342
            +PGLLLST+ +L+ LGL++QQ VISCFN FA+    +E  ++   +  E IK  L   A
Sbjct: 385 RRPGLLLSTMRALDNLGLDVQQAVISCFNGFALDVFRAEQCQEDHDVLPEQIKAVLLDTA 444

Query: 343 GYGG 346
           GY G
Sbjct: 445 GYAG 448

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 90.9 bits (224), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 83/155 (53%), Gaps = 33/155 (21%)

Query: 181 SKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
           +KNLMAERRRRK+LNDRL  LRS+VP+I+K+DR SIL D I+Y+KEL ++   LQ E++ 
Sbjct: 313 AKNLMAERRRRKKLNDRLYALRSLVPRITKLDRASILGDAINYVKELQNEAKELQDELEE 372

Query: 241 ------GSN----------NLETGIFKDVKPNEIVVRNSPKFDVERTN------------ 272
                 GSN           + TG    +  N  V       D+E +N            
Sbjct: 373 NSETEDGSNRPQGGMSLNGTVVTGFHPGLSCNSNVPSVKQDVDLENSNDKGQEMEPQVDV 432

Query: 273 --MDTR---VEICCAGKPGLLLSTVTSLEALGLEI 302
             +D R   V++ C  KPG     + +L++LGLE+
Sbjct: 433 AQLDGREFFVKVICEYKPGGFTRLMEALDSLGLEV 467

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FT81|TT8_ARATH Transcription factor TT8 OS=Arabidopsis thaliana GN=TT8 PE=1 SV=2

 Score = 78.6 bits (192), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 107/228 (46%), Gaps = 27/228 (11%)

Query: 127 PNNLLADEFQNLEMLQNCFKVEPV-----HESPETLP---------VFNMGTDCLERKSR 172
           P +LL+D       +Q+ F    V     H+  +T P         +F +    L   ++
Sbjct: 296 PTSLLSDSVSTSSYIQSSFATWRVENGKEHQQVKTAPSSQWVLKQMIFRV--PFLHDNTK 353

Query: 173 NKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKIS 232
           +K+L  +   +++AERRRR++LN++   LRS+VP ++KMD+ SIL DTI Y+  L  ++ 
Sbjct: 354 DKRLPREDLSHVVAERRRREKLNEKFITLRSMVPFVTKMDKVSILGDTIAYVNHLRKRVH 413

Query: 233 SLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTV 292
            L+       +          +      + S + +V     D  +E+ C  + GLLL  +
Sbjct: 414 ELENTHHEQQHK---------RTRTCKRKTSEEVEVSIIENDVLLEMRCEYRDGLLLDIL 464

Query: 293 TSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFR 340
             L  LG+E    V +  ND   +A     V  ++  S  ++K+A+ +
Sbjct: 465 QVLHELGIET-TAVHTSVNDHDFEAEIRAKVRGKKA-SIAEVKRAIHQ 510

Transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2. Involved in the control of flavonoid pigmentation. Plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). Not required for leucoanthocyanidin dioxygenase (LDOX) expression.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 73.9 bits (180), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 49/59 (83%)

Query: 181 SKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239
           SKN+++ER RR++LN RL  LRS+VP ISK+D+ S++ D+IDYM+EL+D+  +L+ EI+
Sbjct: 53  SKNVVSERNRRQKLNQRLFALRSVVPNISKLDKASVIKDSIDYMQELIDQEKTLEAEIR 111

Arabidopsis thaliana (taxid: 3702)

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

 Score = 73.9 bits (180), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 42/115 (36%), Positives = 63/115 (54%), Gaps = 9/115 (7%)

Query: 169 RKSRNKKLGG--QPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKE 226
           RK   K   G  +P  ++ AER+RR++LN R   LRS+VP ISKMD+ S+L D I Y+KE
Sbjct: 380 RKRGRKPANGREEPLNHVEAERQRREKLNQRFYALRSVVPNISKMDKASLLGDAISYIKE 439

Query: 227 LLDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICC 281
           L +K+  ++ E      +L        + N I V  SP+ D++  N +  V +  
Sbjct: 440 LQEKVKIMEDERVGTDKSLS-------ESNTITVEESPEVDIQAMNEEVVVRVIS 487

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 72.0 bits (175), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 85/163 (52%), Gaps = 17/163 (10%)

Query: 169 RKSRNKKLGG--QPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKE 226
           RK   K   G  +P  ++ AER+RR++LN R   LR++VP +SKMD+ S+L D I Y+ E
Sbjct: 401 RKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVVPNVSKMDKASLLGDAISYISE 460

Query: 227 L---LDKISSLQQEIQAGSN--NLETGIFK-DVKPNEIVVRNSP-----KFDVERTNMDT 275
           L   L K  S ++E+Q   +  N E G  K  VK  + + + S      + DV+    D 
Sbjct: 461 LKSKLQKAESDKEELQKQIDVMNKEAGNAKSSVKDRKCLNQESSVLIEMEVDVKIIGWDA 520

Query: 276 RVEICCAGK--PGLLLSTVTSLEALGLEIQQCVISCFNDFAMQ 316
            + I C+ +  PG     + +L+ L LE+    +S  ND  +Q
Sbjct: 521 MIRIQCSKRNHPGAKF--MEALKELDLEVNHASLSVVNDLMIQ 561

Arabidopsis thaliana (taxid: 3702)

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

 Score = 68.2 bits (165), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 90/196 (45%), Gaps = 35/196 (17%)

Query: 140 MLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGG--QPSKNLMAERRRRKRLNDR 197
           +++    VEP    PE  P          RK   K   G  +P  ++ AER+RR++LN R
Sbjct: 385 VVKEAIVVEP----PEKKP----------RKRGRKPANGREEPLNHVEAERQRREKLNQR 430

Query: 198 LSMLRSIVPKISKMDRTSILADTIDYMKELLDKIS---SLQQEIQ------AGSNNLETG 248
              LR++VP +SKMD+ S+L D I Y+ EL  K+    S ++EIQ      +   N   G
Sbjct: 431 FYSLRAVVPNVSKMDKASLLGDAISYINELKSKLQQAESDKEEIQKKLDGMSKEGNNGKG 490

Query: 249 IFKDVKPNEIVVRNSP------KFDVERTNMDTRVEICCAGK--PGLLLSTVTSLEALGL 300
                K  +   ++S       + DV+    D  + + C  K  PG     + +L+ L L
Sbjct: 491 CGSRAKERKSSNQDSTASSIEMEIDVKIIGWDVMIRVQCGKKDHPGARF--MEALKELDL 548

Query: 301 EIQQCVISCFNDFAMQ 316
           E+    +S  ND  +Q
Sbjct: 549 EVNHASLSVVNDLMIQ 564

Involved in tryptophan and other stress-responsive gene regulation.

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	349
356552989	336	PREDICTED: transcription factor bHLH93-l	0.951	0.988	0.634	1e-110
224067096	347	predicted protein [Populus trichocarpa]	0.948	0.953	0.613	1e-106
225459000	334	PREDICTED: transcription factor bHLH93 [	0.939	0.982	0.625	1e-102
384157481	334	transcription factor bHLH [Vitis amurens	0.939	0.982	0.625	1e-102
356500787	333	PREDICTED: transcription factor bHLH93-l	0.936	0.981	0.605	1e-102
404551200	334	transcription factor bHLH [Vitis vinifer	0.939	0.982	0.622	1e-101
255572814	349	DNA binding protein, putative [Ricinus c	0.936	0.936	0.618	1e-101
357466829	337	Transcription factor bHLH93 [Medicago tr	0.951	0.985	0.621	1e-98
356515677	331	PREDICTED: transcription factor bHLH93-l	0.945	0.996	0.617	2e-98
363814500	330	uncharacterized protein LOC100784380 [Gl	0.942	0.996	0.622	7e-97

>gi|356552989|ref|XP_003544841.1| PREDICTED: transcription factor bHLH93-like [Glycine max]

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 224/353 (63%), Positives = 266/353 (75%), Gaps = 21/353 (5%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDEN-PAAFSPNSFS-- 57
           ME  +H FLEEL++LRR+  TWDT+  ++ NQ+FS+G W +DCFD+N   AF PNSFS  
Sbjct: 1   MELHDHDFLEELMSLRRE--TWDTNPCSQENQLFSNG-WSFDCFDQNYHQAFPPNSFSCQ 57

Query: 58  -APIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAP 116
             P      + YN  ++   +      + SAPQ+ DSSS NTLDS  H  P F  QE+ P
Sbjct: 58  QVPQSYNHDYTYNEIYSSLLH------EFSAPQVIDSSSYNTLDSTPHNTPPFLAQEDYP 111

Query: 117 LSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKL 176
           LSMME   EE    L +E Q L++   C K+E  H SPE +P+FN  + C+ERK+R KKL
Sbjct: 112 LSMME---EEDPGFLGEELQCLDLQTTC-KMESSH-SPE-MPIFNTTSSCVERKNRAKKL 165

Query: 177 GGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQ 236
            GQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRT+IL DTIDYMKELL+KI++L+Q
Sbjct: 166 QGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTAILGDTIDYMKELLEKINNLKQ 225

Query: 237 EIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLE 296
           EI+  SN     IFKDVKPNEI+VRNSPKFDVER N+ TRVEICCAGKPGLLLSTV +LE
Sbjct: 226 EIEVDSN--MASIFKDVKPNEIIVRNSPKFDVERRNVTTRVEICCAGKPGLLLSTVNTLE 283

Query: 297 ALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
            LGLEIQQCVISCFNDF +QASCSE ++Q+  LS EDIKQALFR+AGYGG+CL
Sbjct: 284 TLGLEIQQCVISCFNDFTVQASCSEELQQKTILSSEDIKQALFRSAGYGGRCL 336

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067096|ref|XP_002302353.1| predicted protein [Populus trichocarpa] gi|118482108|gb|ABK92985.1| unknown [Populus trichocarpa] gi|222844079|gb|EEE81626.1| predicted protein [Populus trichocarpa]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 224/365 (61%), Positives = 272/365 (74%), Gaps = 34/365 (9%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSF---- 56
           ME + H FLEEL+AL R+++    + P+EMN++FS G++ + CF+E PA     SF    
Sbjct: 1   MEINGHDFLEELIALSRESWQPTPNYPSEMNELFS-GSFNHGCFEEIPATLPQTSFCPEG 59

Query: 57  --SAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDS---------SSMNTLDSHTHT 105
             S+P+ Q    ++NN++    +CP+GD + SAPQ TD          SS NTLD    T
Sbjct: 60  LISSPLKQ----DFNNYYFNEVFCPFGD-EFSAPQFTDEFSSAPQFTDSSYNTLD----T 110

Query: 106 PPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTD 165
           PP FP+Q++ P+SMME   +E   LLA++ QNL+M   C KVEP+ +SPE +  FN G  
Sbjct: 111 PP-FPVQDDTPMSMME---DEELGLLANDQQNLQMQGTC-KVEPI-QSPE-VSAFNAGI- 162

Query: 166 CLERKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMK 225
           C ERK R KK+ GQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSIL DTIDYMK
Sbjct: 163 CPERKIRGKKMEGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDTIDYMK 222

Query: 226 ELLDKISSLQQEIQAGSNNLE-TGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGK 284
           ELL++I+SLQQEI+ GS  L+   IFKD KPNEIVVRNSPKF+VER N DTR++ICCA K
Sbjct: 223 ELLERINSLQQEIEVGSEELKMISIFKDTKPNEIVVRNSPKFEVERRNEDTRIDICCATK 282

Query: 285 PGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGY 344
           PGLLLS+VT+LE LGLEIQQCVISCFNDF MQASCSE +EQR  +S E IKQALF+NAGY
Sbjct: 283 PGLLLSSVTTLETLGLEIQQCVISCFNDFTMQASCSEELEQRTLISSEHIKQALFKNAGY 342

Query: 345 GGKCL 349
           GG+CL
Sbjct: 343 GGRCL 347

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225459000|ref|XP_002285595.1| PREDICTED: transcription factor bHLH93 [Vitis vinifera]

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 222/355 (62%), Positives = 260/355 (73%), Gaps = 27/355 (7%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDC-FDENPAAFSPNS---- 55
           ME +EHGFLEELLALR D   W+T IP  MN+ FS G W +D  FDENP  F PNS    
Sbjct: 1   MEVNEHGFLEELLALRGDP--WET-IPTGMNEFFSHG-WGFDYRFDENPVTFLPNSSFEA 56

Query: 56  FSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEA 115
           FS PI  +  F Y+  FNE  Y P+GD + S PQ+TDSS      +   TPP FP QE+ 
Sbjct: 57  FSGPI--EPGFGYS--FNEM-YSPFGD-EFSTPQVTDSSY-----TKQDTPP-FPTQEDY 104

Query: 116 PLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKK 175
           P  MME   EEP      +  N+ +   C KVEP+  +    PVFN+G     +  R KK
Sbjct: 105 PFPMME--EEEPAVHPGVDLHNMGLQATC-KVEPIQST--EFPVFNVGVCNEVKNKRTKK 159

Query: 176 LGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQ 235
           + GQPSKNLMAERRRRKRLNDRLSMLRS+VPKISKMDRTSIL DTIDYMKELL++I++LQ
Sbjct: 160 VEGQPSKNLMAERRRRKRLNDRLSMLRSVVPKISKMDRTSILGDTIDYMKELLERINNLQ 219

Query: 236 QEIQAGSNNLET-GIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTS 294
           +E +  S+ L   GIFKD+KPNEI+VRNSPKFDVER NMDTR+EICCAGKPGLLLSTV +
Sbjct: 220 EENEVDSSQLNLLGIFKDLKPNEIMVRNSPKFDVERRNMDTRIEICCAGKPGLLLSTVNT 279

Query: 295 LEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           LEALGLEIQQCVISCFNDF+MQASCSE +E+R  +S E++KQ LFRNAGYGG+CL
Sbjct: 280 LEALGLEIQQCVISCFNDFSMQASCSEELEKRTMVSSEELKQTLFRNAGYGGRCL 334

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|384157481|gb|AFH68208.1| transcription factor bHLH [Vitis amurensis] gi|384157483|gb|AFH68209.1| transcription factor bHLH [Vitis amurensis]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 222/355 (62%), Positives = 260/355 (73%), Gaps = 27/355 (7%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDC-FDENPAAFSPNS---- 55
           ME +E GFLEELLALR D   W+T IP  MN+ FS G W +D  FDENP  F PNS    
Sbjct: 1   MEVNERGFLEELLALRGDP--WET-IPTGMNEFFSHG-WGFDYRFDENPVTFLPNSSFEA 56

Query: 56  FSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEA 115
           FS PI  +  F Y+  FNE  Y P+GD + S PQ+TDSS      +   TPP FP QE+ 
Sbjct: 57  FSGPI--EPGFGYS--FNEM-YSPFGD-EFSTPQVTDSSY-----TKQDTPP-FPTQEDY 104

Query: 116 PLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKK 175
           P  MME   EEP      +  N+ +   C KVEP+  +    PVFN+G     +  R KK
Sbjct: 105 PFPMME--EEEPAVHPGVDLHNMGLQATC-KVEPIQST--EFPVFNVGVCNEVKNKRTKK 159

Query: 176 LGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQ 235
           + GQPSKNLMAERRRRKRLNDRLSMLRS+VPKISKMDRTSIL DTIDYMKELL++I++LQ
Sbjct: 160 VEGQPSKNLMAERRRRKRLNDRLSMLRSVVPKISKMDRTSILGDTIDYMKELLERINNLQ 219

Query: 236 QEIQAGSNNLET-GIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTS 294
           +E +  S+ L   GIFKD+KPNEI+VRNSPKFDVER NMDTR+EICCAGKPGLLLSTV +
Sbjct: 220 EENEVDSSQLNLLGIFKDLKPNEIMVRNSPKFDVERRNMDTRIEICCAGKPGLLLSTVNT 279

Query: 295 LEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           LEALGLEIQQCVISCFNDF+MQASCSE +E+R  +S E++KQALFRNAGYGG+CL
Sbjct: 280 LEALGLEIQQCVISCFNDFSMQASCSEELEKRTMVSSEELKQALFRNAGYGGRCL 334

Source: Vitis amurensis

Species: Vitis amurensis

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500787|ref|XP_003519212.1| PREDICTED: transcription factor bHLH93-like [Glycine max]

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 215/355 (60%), Positives = 262/355 (73%), Gaps = 28/355 (7%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDEN--PAAFSPNSFSA 58
           ME  +H FLEEL++LRR+  TWDT+  ++ NQ+FS+G W +DCF++     AF PNSFS 
Sbjct: 1   MELQDHDFLEELMSLRRE--TWDTNPCSQENQLFSNG-WSFDCFEDQNYHQAFPPNSFSC 57

Query: 59  PIHQQDH----FNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEE 114
               Q +    +NYN  ++   +      + SAPQ+ DSSS NTLD    T P F  QE+
Sbjct: 58  QQVPQSYNNKGYNYNEIYSSLLH------EFSAPQVIDSSSYNTLD----TSP-FLAQED 106

Query: 115 APLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNK 174
            PLSMME   EE    L +E   L++   C K+EP H +   +P+FN  +  +ERK+R K
Sbjct: 107 YPLSMME---EEDPGFLGEELHCLDLQTTC-KMEPSHST--EMPIFNTTSSFVERKNRAK 160

Query: 175 KLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSL 234
           KL GQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRT+IL DTI YMKELL+KI++L
Sbjct: 161 KLQGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTAILGDTIGYMKELLEKINNL 220

Query: 235 QQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTS 294
           +QEI+  SN    GIFKDVKPNEI+VRNSPKFDVER N++TRVEICCAGKPGLLL+TV +
Sbjct: 221 KQEIEVDSN--MAGIFKDVKPNEIIVRNSPKFDVERRNVNTRVEICCAGKPGLLLATVNT 278

Query: 295 LEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           LE LG+EIQQCVISCFNDF +QASCSE + Q+  LS EDIKQALFR+AGYGG+ L
Sbjct: 279 LETLGVEIQQCVISCFNDFTVQASCSEELLQKTILSSEDIKQALFRSAGYGGRYL 333

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|404551200|gb|AFR78197.1| transcription factor bHLH [Vitis vinifera] gi|404551202|gb|AFR78198.1| transcription factor bHLH [Vitis vinifera]

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 221/355 (62%), Positives = 260/355 (73%), Gaps = 27/355 (7%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDC-FDENPAAFSPNS---- 55
           ME +E GFLEELLALR D   W+T IP  MN+ FS G W +D  FDENP  F PNS    
Sbjct: 1   MEVNERGFLEELLALRGDP--WET-IPTGMNEFFSHG-WGFDYRFDENPVTFLPNSSFEG 56

Query: 56  FSAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEA 115
           FS PI  +  F Y+  FNE  Y P+G+ + S PQ+TDSS      +   TPP FP QE+ 
Sbjct: 57  FSGPI--EPGFGYS--FNEM-YSPFGE-EFSTPQVTDSSY-----TKQDTPP-FPTQEDY 104

Query: 116 PLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKK 175
           P  MME   EEP      +  N+ +   C KVEP+  +    PVFN+G     +  R KK
Sbjct: 105 PFPMME--EEEPAVHPGVDLHNMGLQATC-KVEPIQST--EFPVFNVGVCNEVKNKRTKK 159

Query: 176 LGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQ 235
           + GQPSKNLMAERRRRKRLNDRLSMLRS+VPKISKMDRTSIL DTIDYMKELL++I++LQ
Sbjct: 160 VEGQPSKNLMAERRRRKRLNDRLSMLRSVVPKISKMDRTSILGDTIDYMKELLERINNLQ 219

Query: 236 QEIQAGSNNLET-GIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTS 294
           +E +  S+ L   GIFKD+KPNEI+VRNSPKFDVER NMDTR+EICCAGKPGLLLSTV +
Sbjct: 220 EENEVDSSQLNLLGIFKDLKPNEIMVRNSPKFDVERRNMDTRIEICCAGKPGLLLSTVNT 279

Query: 295 LEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           LEALGLEIQQCVISCFNDF+MQASCSE +E+R  +S E++KQALFRNAGYGG+CL
Sbjct: 280 LEALGLEIQQCVISCFNDFSMQASCSEELEKRTMVSSEELKQALFRNAGYGGRCL 334

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255572814|ref|XP_002527339.1| DNA binding protein, putative [Ricinus communis] gi|223533258|gb|EEF35011.1| DNA binding protein, putative [Ricinus communis]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 224/362 (61%), Positives = 267/362 (73%), Gaps = 35/362 (9%)

Query: 5   EHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDE----NPAA---FSPNSF- 56
           + GFLEE L+LRRD      S P+E+ ++FS+G W + CFDE    N  A   F+PNSF 
Sbjct: 6   QQGFLEEFLSLRRDNLETIPSFPSEIGEMFSNG-WNFSCFDEFDGINSVASTLFAPNSFY 64

Query: 57  ----SAPIHQQDHFNYNNFFNEAAYCPYGD----DQLSAPQLTDSSSMNTLDSHTHTPPS 108
               S+P+  QD  +Y  +FNE + CP+GD    D  SAPQ TDSS  N LD    TPP 
Sbjct: 65  QEFSSSPLEHQDFSHY--YFNEVS-CPFGDPPFTDDFSAPQFTDSS-YNNLD----TPP- 115

Query: 109 FPIQE-EAPLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCL 167
           FP+QE   P+S+ME D E    LL +  Q  EM   C K EP  +SPE +PVF++G  C 
Sbjct: 116 FPVQEGHTPMSLMENDQE--TGLLPNHVQISEMQAAC-KFEP-SQSPE-VPVFSIGA-CP 169

Query: 168 ERKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKEL 227
           ERK R+KKL GQPSKNLMAERRRRKRLNDRL+MLRSIVPKISKMDRTSIL DTIDY+KEL
Sbjct: 170 ERKIRSKKLEGQPSKNLMAERRRRKRLNDRLAMLRSIVPKISKMDRTSILGDTIDYVKEL 229

Query: 228 LDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGL 287
           L++I+SLQQE++ GSN L   I KD K +E +VRNSPKF VER N DT++EICCA KPGL
Sbjct: 230 LERINSLQQELEMGSNQL--NILKDTKASEFIVRNSPKFHVERRNEDTQIEICCASKPGL 287

Query: 288 LLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGK 347
           LLSTVT+LEALGLEIQQCVISCFNDF++QASCSE +EQR+  + EDIKQALFR+AGYGG+
Sbjct: 288 LLSTVTALEALGLEIQQCVISCFNDFSIQASCSEELEQRKMTNSEDIKQALFRSAGYGGR 347

Query: 348 CL 349
           CL
Sbjct: 348 CL 349

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357466829|ref|XP_003603699.1| Transcription factor bHLH93 [Medicago truncatula] gi|355492747|gb|AES73950.1| Transcription factor bHLH93 [Medicago truncatula]

 Score =  366 bits (939), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 220/354 (62%), Positives = 261/354 (73%), Gaps = 22/354 (6%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSD-GNWIYD-CFDENPAAFSPNSF-- 56
           MEF +  F+EEL+ALRR+ Y   T+   E NQ FS   N  +D CF++N   + PNS   
Sbjct: 1   MEFYDGDFMEELMALRRETYEI-TNPSQEENQFFSSTSNLSFDNCFEQNSLPYLPNSSCT 59

Query: 57  -SAPIHQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEA 115
              P    ++ +Y+N FNE  Y    D+  + PQ+ DS   N++D    TP  F  QE+ 
Sbjct: 60  QQVPQSYNNNDHYSNTFNEI-YGSLLDESSTPPQILDSYYNNSID----TP--FISQEDF 112

Query: 116 PLSMMELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKK 175
            LSMM   GEE   LL DE QNLE+   C K+EP+ +SPE   VFN G + +ERK+R+KK
Sbjct: 113 SLSMM---GEEDQGLLDDELQNLELQTTC-KMEPI-QSPEMPVVFNTG-NGMERKNRSKK 166

Query: 176 LGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQ 235
           L GQPSKNLMAERRRRKRLNDRLSMLR+IVPKISKMDRT+IL DTIDYMKELL+KI +LQ
Sbjct: 167 LQGQPSKNLMAERRRRKRLNDRLSMLRAIVPKISKMDRTAILGDTIDYMKELLEKIKNLQ 226

Query: 236 QEIQAGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSL 295
           QEI+  SN   T I KDVKPNEI++RNSPKF+VER+  DTRVEICCAGKPGLLLSTV +L
Sbjct: 227 QEIELDSN--MTSIVKDVKPNEILIRNSPKFEVERS-ADTRVEICCAGKPGLLLSTVNTL 283

Query: 296 EALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           EALGLEIQQCVISCFNDF MQASCSE +E+RE LS EDIKQALFR+AGYGG+CL
Sbjct: 284 EALGLEIQQCVISCFNDFTMQASCSEELEKREMLSSEDIKQALFRSAGYGGRCL 337

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356515677|ref|XP_003526525.1| PREDICTED: transcription factor bHLH93-like [Glycine max]

 Score =  365 bits (937), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 216/350 (61%), Positives = 254/350 (72%), Gaps = 20/350 (5%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPI 60
           MEF +  FLEEL+ LRR+  TWDT+   E NQ FS+  W +DCFD+N   + PNS     
Sbjct: 1   MEFYDQDFLEELMTLRRE--TWDTNPSTEENQFFSNA-WSFDCFDQNSLPYLPNSSCG-- 55

Query: 61  HQQDHFNYNNFFN-EAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAPLSM 119
            Q+   +YNN +     Y    D+  S+PQ+ DS    TLD      P F  QE+ PLSM
Sbjct: 56  -QEVPQSYNNDYPFSEIYGSLLDE--SSPQIMDSY-YGTLDITPLNTPPFLGQEDYPLSM 111

Query: 120 MELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGGQ 179
           ME   EE    L +E +NLE+   C KVE    S   +P FNMGT    + +R+KKL GQ
Sbjct: 112 ME---EEDPGFLGEELKNLELQTTC-KVEKTQSS--EMPAFNMGTGLERKNNRSKKLQGQ 165

Query: 180 PSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239
           PSKNLMAERRRRKRLNDRLSMLR+IVPKISKMDRTSIL DTIDYMKELL+KI++LQQ ++
Sbjct: 166 PSKNLMAERRRRKRLNDRLSMLRAIVPKISKMDRTSILGDTIDYMKELLEKINNLQQ-VE 224

Query: 240 AGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALG 299
             S+    GIFKDVKPNEI+VRNSPKF+VER+ +DTRVEICCAGKPGLLLSTV ++EALG
Sbjct: 225 VDSSM--AGIFKDVKPNEIIVRNSPKFEVERS-VDTRVEICCAGKPGLLLSTVNTVEALG 281

Query: 300 LEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           LEIQQCVISCFNDF MQASCSE +EQR  LS EDIKQALFR+AGYGG+CL
Sbjct: 282 LEIQQCVISCFNDFTMQASCSEELEQRAMLSSEDIKQALFRSAGYGGRCL 331

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363814500|ref|NP_001242885.1| uncharacterized protein LOC100784380 [Glycine max] gi|255641815|gb|ACU21176.1| unknown [Glycine max]

 Score =  360 bits (923), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 218/350 (62%), Positives = 258/350 (73%), Gaps = 21/350 (6%)

Query: 1   MEFSEHGFLEELLALRRDAYTWDTSIPAEMNQIFSDGNWIYDCFDENPAAFSPNSFSAPI 60
           MEF +  FLEEL+ LRR+  TWDT+   E NQ F  G+  +DCFD+N   + PNS S   
Sbjct: 1   MEFYDQDFLEELMTLRRE--TWDTNPRTEENQFFDGGS--FDCFDQNSLPYLPNS-SCGQ 55

Query: 61  HQQDHFNYNNFFNEAAYCPYGDDQLSAPQLTDSSSMNTLDSHTHTPPSFPIQEEAP-LSM 119
                +N +  F+E   C   +   S+PQ+ DS   +TLD+  +TPP F  QE+ P LSM
Sbjct: 56  EVPQTYNNDYPFSEIYGCLLDE---SSPQIMDSF-YSTLDTPLNTPP-FLGQEDYPILSM 110

Query: 120 MELDGEEPNNLLADEFQNLEMLQNCFKVEPVHESPETLPVFNMGTDCLERKSRNKKLGGQ 179
           ME + +          +NLE+   C K+EP   S   +PVFNMGT  LERK+R+KKL GQ
Sbjct: 111 MEEEEQGLLGEEL---KNLELQTTC-KMEPTQSS--EMPVFNMGTG-LERKNRSKKLQGQ 163

Query: 180 PSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239
           PSKNLMAERRRRKRLNDRLSMLR+IVPKISKMDRTSIL DTIDYMKELL+KI++LQQE++
Sbjct: 164 PSKNLMAERRRRKRLNDRLSMLRAIVPKISKMDRTSILGDTIDYMKELLEKINNLQQEVE 223

Query: 240 AGSNNLETGIFKDVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALG 299
             SN    GIFKDVKPNEI+VRNSPKF+VER+ +DTRVEICCAGKPGL+LSTV +LEALG
Sbjct: 224 VDSNM--AGIFKDVKPNEILVRNSPKFEVERS-VDTRVEICCAGKPGLILSTVNTLEALG 280

Query: 300 LEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
           LEIQQCVISCFNDF MQASCSE  EQR  LS EDIKQALFR+ GYGG+CL
Sbjct: 281 LEIQQCVISCFNDFTMQASCSEESEQRTMLSSEDIKQALFRSVGYGGRCL 330

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	349
TAIR|locus:2155725	351	bHLH093 "AT5G65640" [Arabidops	0.573	0.569	0.649	1.4e-62
UNIPROTKB|Q8H8E4	430	OJ1006F06.1 "Putative bHLH tra	0.495	0.402	0.606	2.4e-57
TAIR|locus:2142419	315	AT5G10570 "AT5G10570" [Arabido	0.739	0.819	0.489	1.4e-55
UNIPROTKB|Q336V8	380	Os10g0544200 "Os10g0544200 pro	0.492	0.452	0.558	1e-43
UNIPROTKB|Q2R3F6	524	Os11g0523700 "Helix-loop-helix	0.189	0.125	0.636	3.4e-14
TAIR|locus:2090847	494	ICE1 "AT3G26744" [Arabidopsis	0.189	0.133	0.621	8.8e-14
TAIR|locus:2039445	571	AMS "AT2G16910" [Arabidopsis t	0.243	0.148	0.451	5.2e-12
UNIPROTKB|Q5Z988	213	P0548E04.5 "Os06g0724800 prote	0.123	0.201	0.651	5.8e-11
TAIR|locus:2141055	589	MYC4 "AT4G17880" [Arabidopsis	0.487	0.288	0.303	6.4e-09
TAIR|locus:2118524	518	TT8 "AT4G09820" [Arabidopsis t	0.667	0.449	0.253	8.7e-09

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

 Score = 639 (230.0 bits), Expect = 1.4e-62, P = 1.4e-62
 Identities = 135/208 (64%), Positives = 159/208 (76%)

Query:   149 PVHESPETLPVFNMGTDCLE-RKSRNKKLGGQPSKNLMAEXXXXXXLNDRLSMLRSIVPK 207
             P+ ES ++   F++G    E  K ++KKL GQPSKNLMAE      LNDRLSMLRSIVPK
Sbjct:   145 PLMESDQSKS-FSVGYCGGETNKKKSKKLEGQPSKNLMAERRRRKRLNDRLSMLRSIVPK 203

Query:   208 ISKMDRTSILADTIDYMKELLDKISSLQQEIQ--AGSNNLET----GIFKDVKPNEIVVR 261
             ISKMDRTSIL D IDYMKELLDKI+ LQ E Q    SNN       G  KD+  NE +VR
Sbjct:   204 ISKMDRTSILGDAIDYMKELLDKINKLQDEEQELGNSNNSHHSKLFGDLKDLNANEPLVR 263

Query:   262 NSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSE 321
             NSPKF+++R + DTRV+ICC+ KPGLLLSTV +LE LGLEI+QCVISCF+DF++QASCSE
Sbjct:   264 NSPKFEIDRRDEDTRVDICCSPKPGLLLSTVNTLETLGLEIEQCVISCFSDFSLQASCSE 323

Query:   322 GVEQRETLSCEDIKQALFRNAGYGGKCL 349
             G EQR+ ++ EDIKQALFRNAGYGG CL
Sbjct:   324 GAEQRDFITSEDIKQALFRNAGYGGSCL 351

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 522 (188.8 bits), Expect = 2.4e-57, Sum P(3) = 2.4e-57
 Identities = 108/178 (60%), Positives = 134/178 (75%)

Query:   175 KLGGQPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSL 234
             KL G PSKNLMAE      LNDRLSMLRSIVPKISKMDRTSIL DTIDY+KEL ++I +L
Sbjct:   175 KLHGTPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDTIDYVKELTERIKTL 234

Query:   235 QQEIQAGSNNLET-GIFKDVKP---NEIVVRNSPKFDVE-RTNMDTRVEICCAGKPGLLL 289
             ++EI      L+     KD      NE++VRNS KFDVE R + +TR+EICC   PG+LL
Sbjct:   235 EEEIGVTPEELDLLNTMKDSSSGNNNEMLVRNSTKFDVENRGSGNTRIEICCPANPGVLL 294

Query:   290 STVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGK 347
             STV++LE LGLEI+QCV+SCF+DF MQASC +   +R+ +S ++IKQ LFR+AGYGG+
Sbjct:   295 STVSALEVLGLEIEQCVVSCFSDFGMQASCLQEDGKRQVVSTDEIKQTLFRSAGYGGR 352

GO:0005634 "nucleus" evidence=IC

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

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 136/278 (48%), Positives = 178/278 (64%)

Query:    82 DDQLSAPQLTDSSSMNTLDSHT---HTPP--SFPIQEEAPLSMMELDGEEPNNLLADEFQ 136
             DD +  P  + SS MN +       H PP  S P+ +  PLS    D     +++   + 
Sbjct:    48 DDNIDHP--SSSSLMNLISQPPPLLHQPPQPSSPLYDSPPLSSA-FDYPFLEDIIHSSYS 104

Query:   137 NLEMLQNCFKVEPVHESP---ETLPVFNMGTDCLERKSRNKKLGGQPSKNLMAEXXXXXX 193
                ++    +    + SP   E+    ++G     +K  NKKL GQPSKNLMAE      
Sbjct:   105 PPPLILPASQENTNNYSPLMEESKSFISIGET--NKKRSNKKLEGQPSKNLMAERRRRKR 162

Query:   194 LNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQA-GSNN-LETGIFK 251
             LNDRLS+LRSIVPKI+KMDRTSIL D IDYMKELLDKI+ LQ++ Q  GSN+ L T I  
Sbjct:   163 LNDRLSLLRSIVPKITKMDRTSILGDAIDYMKELLDKINKLQEDEQELGSNSHLSTLI-- 220

Query:   252 DVKPNEIVVRNSPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311
                 NE +VRNS KF+V++  ++T ++ICC  KPGL++STV++LE LGLEI+QCVISCF+
Sbjct:   221 ---TNESMVRNSLKFEVDQREVNTHIDICCPTKPGLVVSTVSTLETLGLEIEQCVISCFS 277

Query:   312 DFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349
             DF++QASC E  EQR  ++ E  KQAL RNAGYGG+CL
Sbjct:   278 DFSLQASCFEVGEQRYMVTSEATKQALIRNAGYGGRCL 315

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|Q336V8 Os10g0544200 "Os10g0544200 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 461 (167.3 bits), Expect = 1.0e-43, P = 1.0e-43
 Identities = 105/188 (55%), Positives = 129/188 (68%)

Query:   178 GQPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQE 237
             G PSKNLMAE      LNDRLSMLRS+VP+ISKMDRTSIL DTI Y+KEL+D+I +LQ E
Sbjct:   192 GAPSKNLMAERRRRKRLNDRLSMLRSVVPRISKMDRTSILGDTIGYVKELMDRIKNLQVE 251

Query:   238 IQAGSN------NLETGIFKDVKP-------NEI-VVRNSPKFDVERT-NMDTRVEICCA 282
                G +      NL       +KP        E  ++RNS +F+VER  N  TR+E+ CA
Sbjct:   252 AATGDSSSSSTENLSMLKLNTLKPPPSSSSGEETPLIRNSTRFEVERRENGSTRIEMACA 311

Query:   283 GKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRE-TLSCEDIKQALFRN 341
               P LL ST+ +LEALG+EI+QCVISCF+DFAMQASC +  ++RE T   E+IKQ LFR+
Sbjct:   312 AIPELLPSTLAALEALGVEIEQCVISCFDDFAMQASCLQDDKKREMTRDTEEIKQTLFRS 371

Query:   342 AGYGGKCL 349
             AGYG  CL
Sbjct:   372 AGYGDGCL 379

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q2R3F6 Os11g0523700 "Helix-loop-helix DNA-binding domain containing protein, expressed" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 207 (77.9 bits), Expect = 3.4e-14, P = 3.4e-14
 Identities = 42/66 (63%), Positives = 50/66 (75%)

Query:   175 KLGGQPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSL 234
             K  G P+KNLMAE      LNDRL MLRS+VPKISKMDR SIL D I+Y+KELL KI+ L
Sbjct:   329 KKKGMPAKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIEYLKELLQKINDL 388

Query:   235 QQEIQA 240
             Q E+++
Sbjct:   389 QNELES 394

GO:0005634 "nucleus" evidence=IC

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

 Score = 203 (76.5 bits), Expect = 8.8e-14, P = 8.8e-14
 Identities = 41/66 (62%), Positives = 49/66 (74%)

Query:   175 KLGGQPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSL 234
             K  G P+KNLMAE      LNDRL MLRS+VPKISKMDR SIL D IDY+KELL +I+ L
Sbjct:   300 KKKGMPAKNLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDL 359

Query:   235 QQEIQA 240
               E+++
Sbjct:   360 HNELES 365

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009409 "response to cold" evidence=IEP

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

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

GO:0010440 "stomatal lineage progression" evidence=IMP

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

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

GO:0009640 "photomorphogenesis" evidence=RCA

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

GO:0009845 "seed germination" evidence=RCA

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

GO:0009933 "meristem structural organization" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

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

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

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

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

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

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

 Score = 174 (66.3 bits), Expect = 5.2e-12, Sum P(2) = 5.2e-12
 Identities = 42/93 (45%), Positives = 56/93 (60%)

Query:   163 GTDCLER------KSRNKKLG-GQPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDRTS 215
             G+DC ++          KK G G  +KNLMAE      LNDRL  LRS+VP+I+K+DR S
Sbjct:   288 GSDCSDQIDDEDDPKYKKKSGKGSQAKNLMAERRRRKKLNDRLYALRSLVPRITKLDRAS 347

Query:   216 ILADTIDYMKELLDKISSLQQEIQAGSNNLETG 248
             IL D I+Y+KEL ++   LQ E++  S   E G
Sbjct:   348 ILGDAINYVKELQNEAKELQDELEENSET-EDG 379

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009555 "pollen development" evidence=IMP

GO:0048658 "tapetal layer development" evidence=IMP

UNIPROTKB|Q5Z988 P0548E04.5 "Os06g0724800 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 134 (52.2 bits), Expect = 5.8e-11, Sum P(2) = 5.8e-11
 Identities = 28/43 (65%), Positives = 33/43 (76%)

Query:   171 SRNKKLGGQPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDR 213
             S+ K++ G PSKNLMAE      LNDRLSMLRS+VPKISK+ R
Sbjct:   144 SKKKRVEGMPSKNLMAERRRRKRLNDRLSMLRSVVPKISKVYR 186

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2141055 MYC4 "AT4G17880" [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 6.4e-09, P = 6.4e-09
 Identities = 58/191 (30%), Positives = 90/191 (47%)

Query:   169 RKSRNKKLGG--QPSKNLMAEXXXXXXLNDRLSMLRSIVPKISKMDRTSILADTIDYMKE 226
             RK   K   G  +P  ++ AE      LN R   LR++VP +SKMD+ S+L D I Y+ E
Sbjct:   401 RKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVVPNVSKMDKASLLGDAISYISE 460

Query:   227 L---LDKISSLQQEIQAGSN--NLETGIFKD-VKPNEIVVRNSP-----KFDVERTNMDT 275
             L   L K  S ++E+Q   +  N E G  K  VK  + + + S      + DV+    D 
Sbjct:   461 LKSKLQKAESDKEELQKQIDVMNKEAGNAKSSVKDRKCLNQESSVLIEMEVDVKIIGWDA 520

Query:   276 RVEICCAGK--PGLLLSTVTSLEALGLEIQQCVISCFNDFAMQ-ASCSEGVEQRETLSCE 332
              + I C+ +  PG     + +L+ L LE+    +S  ND  +Q A+   G    +  + +
Sbjct:   521 MIRIQCSKRNHPGAKF--MEALKELDLEVNHASLSVVNDLMIQQATVKMG---NQFFTQD 575

Query:   333 DIKQALFRNAG 343
              +K AL    G
Sbjct:   576 QLKVALTEKVG 586

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

GO:0006952 "defense response" evidence=IMP

GO:0043425 "bHLH transcription factor binding" evidence=IPI

TAIR|locus:2118524 TT8 "AT4G09820" [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 8.7e-09, P = 8.7e-09
 Identities = 65/256 (25%), Positives = 111/256 (43%)

Query:    95 SMNTLDSHTHTPPSFPIQEEAPLSMMELDGEEPNNLLADEFQNLEMLQNCF---KVE--P 149
             S +TLD+H               ++  L    P +LL+D       +Q+ F   +VE   
Sbjct:   264 STHTLDTHMDMMNLMEEGGNYSQTVTTLLMSHPTSLLSDSVSTSSYIQSSFATWRVENGK 323

Query:   150 VHESPETLP----VFNM---GTDCLERKSRNKKLGGQPSKNLMAEXXXXXXLNDRLSMLR 202
              H+  +T P    V          L   +++K+L  +   +++AE      LN++   LR
Sbjct:   324 EHQQVKTAPSSQWVLKQMIFRVPFLHDNTKDKRLPREDLSHVVAERRRREKLNEKFITLR 383

Query:   203 SIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQAGSNNLETGIFKDVKPNEIVVRN 262
             S+VP ++KMD+ SIL DTI Y+  L  ++  L+       +   T   K         + 
Sbjct:   384 SMVPFVTKMDKVSILGDTIAYVNHLRKRVHELENTHHEQQHK-RTRTCKR--------KT 434

Query:   263 SPKFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEG 322
             S + +V     D  +E+ C  + GLLL  +  L  LG+E    V +  ND   +A     
Sbjct:   435 SEEVEVSIIENDVLLEMRCEYRDGLLLDILQVLHELGIETT-AVHTSVNDHDFEAEIRAK 493

Query:   323 VEQRETLSCEDIKQAL 338
             V  ++  S  ++K+A+
Sbjct:   494 VRGKKA-SIAEVKRAI 508

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009962 "regulation of flavonoid biosynthetic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

GO:2000029 "regulation of proanthocyanidin biosynthetic process" evidence=IEP

GO:0010026 "trichome differentiation" evidence=IMP

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

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010224 "response to UV-B" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LSL1	BH093_ARATH	No assigned EC number	0.7258	0.5157	0.5128	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: estExt_fgenesh4_pg.C_LG_II0987 SubName- Full=Putative uncharacterized protein; (348 aa) (Populus trichocarpa)

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	349
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	4e-11
smart00353	53	smart00353, HLH, helix loop helix domain	3e-10
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	3e-09
cd04873	70	cd04873, ACT_UUR-ACR-like, ACT domains of the bact	0.004

>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 = 57.6 bits (140), Expect = 4e-11
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP---KISKMDRTSILADTIDYMKELLDKIS 232
           + ERRRR+R+ND    LRS++P      K+ +  IL   +DY+K L + + 
Sbjct: 10  LRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 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 = 54.9 bits (133), Expect = 3e-10
 Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 3/48 (6%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP---KISKMDRTSILADTIDYMKELLD 229
             ERRRR+++N+    LRS++P   K  K+ +  IL   I+Y+K L +
Sbjct: 2   ARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQE 49

Length = 53

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

 Score = 51.7 bits (125), Expect = 3e-09
 Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 8/48 (16%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP-----KISKMDRTSILADTIDYMKEL 227
             ERRRR R+ND    LR ++P     K+SK +   IL   I+Y+K L
Sbjct: 7   ERERRRRDRINDAFEELRELLPTPPNKKLSKAE---ILRLAIEYIKHL 51

Length = 52

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 15/42 (35%), Positives = 19/42 (45%)

Query: 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQ 316
           T VE+    +PGLL      L  LGL I    IS   + A+ 
Sbjct: 1   TVVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALD 42

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	349
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.33
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.28
smart00353	53	HLH helix loop helix domain.	99.27
KOG1318	411	consensus Helix loop helix transcription factor EB	98.83
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	98.61
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.58
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.45
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	98.42
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	98.41
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.31
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.23
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	98.22
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	98.04
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.94
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.91
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	97.84
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.79
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	97.75
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.65
PRK05007	884	PII uridylyl-transferase; Provisional	97.44
PLN03217	93	transcription factor ATBS1; Provisional	97.35
KOG0561	373	consensus bHLH transcription factor [Transcription	97.26
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.24
PRK00275	895	glnD PII uridylyl-transferase; Provisional	97.18
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	97.17
PRK04374	869	PII uridylyl-transferase; Provisional	97.07
PRK05092	931	PII uridylyl-transferase; Provisional	97.06
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.02
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.99
PRK03059	856	PII uridylyl-transferase; Provisional	96.88
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	96.59
PRK03381	774	PII uridylyl-transferase; Provisional	96.57
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	96.44
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	96.43
PRK01759	854	glnD PII uridylyl-transferase; Provisional	96.41
PRK03381	774	PII uridylyl-transferase; Provisional	96.41
PRK05007	884	PII uridylyl-transferase; Provisional	96.41
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	96.4
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.33
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	95.86
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	95.81
PRK03059	856	PII uridylyl-transferase; Provisional	95.79
PRK05092	931	PII uridylyl-transferase; Provisional	95.75
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.69
PRK00194	90	hypothetical protein; Validated	95.67
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	95.57
PRK04374	869	PII uridylyl-transferase; Provisional	95.31
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	94.99
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	94.75
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	94.59
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	93.24
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	92.82
cd02116	60	ACT ACT domains are commonly involved in specifica	91.76
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	91.69
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	91.51
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	91.28
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	91.24
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	90.79
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	90.58
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	90.27
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	89.59
KOG3910	632	consensus Helix loop helix transcription factor [T	89.54
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	89.46
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	89.38
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	89.33
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	89.32
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	88.94
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	88.43
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	88.27
PRK04435	147	hypothetical protein; Provisional	87.97
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	87.7
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	87.29
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	86.9
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	86.34
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	86.33
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	85.53
PRK08577	136	hypothetical protein; Provisional	85.27
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	84.5
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	84.22
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	84.12
PRK07334	403	threonine dehydratase; Provisional	83.11
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	81.06
KOG3898	254	consensus Transcription factor NeuroD and related	80.53
PRK11589	190	gcvR glycine cleavage system transcriptional repre	80.21

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

Probab=99.33  E-value=1.5e-12  Score=96.40  Aligned_cols=53  Identities=36%  Similarity=0.706  Sum_probs=50.0

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKI  231 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v  231 (349)
                      .+..|+.+||+||.+||+.|..|+++||..   .|++|++||..||+||+.|+.++
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            457899999999999999999999999987   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=99.28  E-value=2.7e-12  Score=94.53  Aligned_cols=49  Identities=43%  Similarity=0.697  Sum_probs=46.1

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC-----CCCCchhhHHHHHHHHHHHH
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI-----SKMDRTSILADTIDYMKELL  228 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~-----~K~dKaSIL~~AI~YIk~Lq  228 (349)
                      +..|+.+||+||.+||+.|..|+.+||..     .|++|++||..||+||++||
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            46899999999999999999999999975     68999999999999999997

; 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=99.27  E-value=8e-12  Score=90.76  Aligned_cols=49  Identities=35%  Similarity=0.659  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHHHHHHHHhHhcCCC---CCCCCchhhHHHHHHHHHHHHHHHH
Q 018897          184 LMAERRRRKRLNDRLSMLRSIVPK---ISKMDRTSILADTIDYMKELLDKIS  232 (349)
Q Consensus       184 ~~aER~RR~kin~~~~~LrslvP~---~~K~dKaSIL~~AI~YIk~Lq~~v~  232 (349)
                      +.+||+||.+||+.|..|+++||.   ..|++|++||..||+||+.|+++++
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            368999999999999999999994   6789999999999999999999875

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

Probab=98.83  E-value=3e-09  Score=107.16  Aligned_cols=57  Identities=32%  Similarity=0.580  Sum_probs=52.0

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDKISSLQ  235 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~v~~L~  235 (349)
                      +|..|+++|||||++||++|..|..|||++    .|..|..||..+++||++||+..++..
T Consensus       233 Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~  293 (411)
T KOG1318|consen  233 KRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR  293 (411)
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999986    477899999999999999999877544

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

Probab=98.61  E-value=4.2e-07  Score=72.03  Aligned_cols=69  Identities=19%  Similarity=0.223  Sum_probs=58.7

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCH---HHHHHHHHHHhh
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSC---EDIKQALFRNAG  343 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~---edIkqaL~~~~g  343 (349)
                      ..|+|.|.+|||||.+|..+|-.+|++|.+|.|+|.++.+.++|......+....+.   +.|+++|..+++
T Consensus         2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~kl~~~~~~~~l~~~L~~al~   73 (75)
T cd04897           2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGRTLSTEGERQRVIKCLEAAIE   73 (75)
T ss_pred             EEEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCCccCCHHHHHHHHHHHHHHHh
Confidence            368999999999999999999999999999999999999999999887655444443   567777777664

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.

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.58  E-value=4.1e-08  Score=89.61  Aligned_cols=63  Identities=25%  Similarity=0.426  Sum_probs=55.2

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC-------CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI-------SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~-------~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      +|..|.-+||+||+.||..+..|+.|||.+       .|+.||.||..+|+||..|++++.+.+++...+
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L  131 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL  131 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999953       378899999999999999999988877765443

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

Probab=98.45  E-value=1.7e-06  Score=68.03  Aligned_cols=52  Identities=31%  Similarity=0.323  Sum_probs=47.7

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCC
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQR  326 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~  326 (349)
                      ..|+|.+.+|||||.+|.++|..+||+|..|.|+|.++.+.++|......+.
T Consensus         2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~   53 (72)
T cd04895           2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGN   53 (72)
T ss_pred             EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCC
Confidence            4689999999999999999999999999999999999999999998875333

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.

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

Probab=98.42  E-value=2.3e-06  Score=67.88  Aligned_cols=67  Identities=12%  Similarity=0.129  Sum_probs=56.2

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe--eeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHhh
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS--CFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNAG  343 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS--t~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~g  343 (349)
                      .|+|.|.+|||||.+|.++|..+||+|..|.|+  |.|+.++++|.. ...+....+   .+.|+++|.+++-
T Consensus         2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~~g~kl~d~~~~~~L~~~L~~~l~   73 (75)
T cd04896           2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QSDGKKIMDPKKQAALCARLREEMV   73 (75)
T ss_pred             EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eCCCCccCCHHHHHHHHHHHHHHhc
Confidence            589999999999999999999999999999999  999999999999 433444223   3677888877653

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.

>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=98.41  E-value=2e-06  Score=67.47  Aligned_cols=68  Identities=18%  Similarity=0.192  Sum_probs=55.7

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccC---CHHHHHHHHHHHhh
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETL---SCEDIKQALFRNAG  343 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~i---s~edIkqaL~~~~g  343 (349)
                      +.++|.|.+++|||.+|..+|..+||+|+.|.|++ .++.+++++......+. ..   ..+.|+++|.+++|
T Consensus         1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~~~-~~~~~~~~~l~~~L~~~L~   72 (76)
T cd04927           1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDAREL-LHTKKRREETYDYLRAVLG   72 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCCCC-CCCHHHHHHHHHHHHHHHc
Confidence            46899999999999999999999999999999997 89999999988654222 22   23557777777776

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.

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.31  E-value=1.9e-06  Score=93.85  Aligned_cols=62  Identities=26%  Similarity=0.497  Sum_probs=56.2

Q ss_pred             CCCccchHHHHHHHHHHHHHHHHhHhcCCC-CCCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 018897          178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPK-ISKMDRTSILADTIDYMKELLDKISSLQQEIQ  239 (349)
Q Consensus       178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~-~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e  239 (349)
                      .+|..|++.|||.|..||+++..|+.+||+ ..|+.|..+|..||+||++|+...+.++.+.+
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            578999999999999999999999999997 47999999999999999999988877776443

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

Probab=98.23  E-value=5.5e-07  Score=86.06  Aligned_cols=56  Identities=25%  Similarity=0.482  Sum_probs=49.1

Q ss_pred             CCCccchHHHHHHHHHHHHHHHHhHhcCCC--------CCCCCchhhHHHHHHHHHHHHHHHHH
Q 018897          178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPK--------ISKMDRTSILADTIDYMKELLDKISS  233 (349)
Q Consensus       178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~--------~~K~dKaSIL~~AI~YIk~Lq~~v~~  233 (349)
                      .++..|-+.||+||.|||+-|..|+.|||.        .+|++||.||.-|++|++.|+.....
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            355678899999999999999999999993        37899999999999999999976544

>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=98.22  E-value=1.6e-05  Score=61.37  Aligned_cols=49  Identities=27%  Similarity=0.375  Sum_probs=44.6

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecc
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGV  323 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~  323 (349)
                      ..|.|.|.+++|||.+|..+|..+||+|+.|.|.+. ++.+++++.....
T Consensus         2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~   51 (73)
T cd04900           2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDP   51 (73)
T ss_pred             EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECC
Confidence            468999999999999999999999999999999988 6899999987653

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

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

Probab=98.04  E-value=6.4e-05  Score=58.46  Aligned_cols=67  Identities=16%  Similarity=0.115  Sum_probs=54.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeeccc-CCccCC---HHHHHHHHHHHh
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVE-QRETLS---CEDIKQALFRNA  342 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e-~~~~is---~edIkqaL~~~~  342 (349)
                      .|+|.+.++||+|.+|..+|..+|++|+.|.+++.++.+++++.+.... +.....   .+.|+++|.+++
T Consensus         2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~~l   72 (74)
T cd04925           2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGAPIDDPIRLASIEDRLDNVL   72 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHHHh
Confidence            5889999999999999999999999999999999999999999876543 222222   356777776655

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.

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

Probab=97.94  E-value=7.9e-06  Score=88.68  Aligned_cols=51  Identities=24%  Similarity=0.423  Sum_probs=47.9

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHH
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDK  230 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~  230 (349)
                      |..|+.+|||||++||..|..|.+|||.+    -|+||..||.+||.+||.+++.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            67999999999999999999999999975    5999999999999999999874

>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=97.91  E-value=0.00015  Score=55.99  Aligned_cols=71  Identities=21%  Similarity=0.319  Sum_probs=56.7

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHhhcCCCCC
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL  349 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~g~gg~cl  349 (349)
                      .+|.|.+++++|+|.+|..+|.++|++|++|.+.+.++.++.++.....++.. .+. +..++|.+.+|  --||
T Consensus         2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~~~~~~-~~~-~~~~~l~~~l~--~~~~   72 (72)
T cd04926           2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTDANGNP-VDP-KTIEAVRQEIG--PACL   72 (72)
T ss_pred             eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEECCCCCc-CCH-HHHHHHHHHhc--cccC
Confidence            46888999999999999999999999999999999988888888776543332 344 56667888887  5565

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.

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

Probab=97.84  E-value=5e-05  Score=72.03  Aligned_cols=65  Identities=26%  Similarity=0.389  Sum_probs=54.5

Q ss_pred             CCCCCccchHHHHHHHHHHHHHHHHhHhcCCCC--CCCC-chhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897          176 LGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKI--SKMD-RTSILADTIDYMKELLDKISSLQQEIQA  240 (349)
Q Consensus       176 ~~~~~~~h~~aER~RR~kin~~~~~LrslvP~~--~K~d-KaSIL~~AI~YIk~Lq~~v~~L~~~~e~  240 (349)
                      ....|..|+.-||+||..|++.|..|+.+||..  .+.. .++||..|+.||+.|+.+..+....+++
T Consensus        56 ~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~  123 (232)
T KOG2483|consen   56 AASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIED  123 (232)
T ss_pred             CCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHH
Confidence            345789999999999999999999999999974  2333 6899999999999999888777765544

>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=97.79  E-value=0.00027  Score=52.99  Aligned_cols=64  Identities=25%  Similarity=0.365  Sum_probs=50.6

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHH---HHHHHHHH
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCE---DIKQALFR  340 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~e---dIkqaL~~  340 (349)
                      +|.|.+.+++|+|.+|+.+|.++|++|.++.+.+.++.++..+......+.. .+.+   .|+++|.+
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~~-~~~~~~~~i~~~l~~   68 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQP-LDPERQEALRAALGE   68 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCCc-CCHHHHHHHHHHHHh
Confidence            6889999999999999999999999999999999988888888776643333 4442   34444443

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

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

Probab=97.75  E-value=0.0003  Score=54.82  Aligned_cols=64  Identities=20%  Similarity=0.266  Sum_probs=54.2

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .|-|.|+++||+|.+|..+|..+||+|+.|.|.+. ++++++++.+...   ..-...++.++|++++
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~---~~~~~~~~~~~~~~~~   67 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGW---KRGETAALGHALQKEI   67 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecC---CccchHHHHHHHHHhh
Confidence            57889999999999999999999999999999875 6799998887763   3345678899998865

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.

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

Probab=97.65  E-value=0.0005  Score=65.72  Aligned_cols=56  Identities=25%  Similarity=0.430  Sum_probs=47.3

Q ss_pred             cchHHHHHHHHHHHHHHHHhHhcC-CC-CCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 018897          182 KNLMAERRRRKRLNDRLSMLRSIV-PK-ISKMDRTSILADTIDYMKELLDKISSLQQE  237 (349)
Q Consensus       182 ~h~~aER~RR~kin~~~~~Lrslv-P~-~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~  237 (349)
                      .-.|.||||=+|+|+.|.+|+.-. ++ ...+-|..||..||+||..||.=++++.+.
T Consensus       121 AATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~  178 (284)
T KOG3960|consen  121 AATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQA  178 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            446899999999999999997543 33 467889999999999999999988888763

>PRK05007 PII uridylyl-transferase; Provisional

Probab=97.44  E-value=0.00064  Score=75.36  Aligned_cols=70  Identities=17%  Similarity=0.282  Sum_probs=59.3

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~  342 (349)
                      +....|+|.|.+|||||.+|.++|..+||+|++|.|+|.++.+.++|.+... ++..++   .+.|+++|..++
T Consensus       806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~-~g~~l~~~~~~~l~~~L~~~l  878 (884)
T PRK05007        806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATA-DRRALNEELQQELRQRLTEAL  878 (884)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcC-CCCcCCHHHHHHHHHHHHHHH
Confidence            4467899999999999999999999999999999999999999999998764 333444   367777777766

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.35  E-value=0.00045  Score=56.09  Aligned_cols=51  Identities=22%  Similarity=0.522  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhHhcCCCC------CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          191 RKRLNDRLSMLRSIVPKI------SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       191 R~kin~~~~~LrslvP~~------~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      -++|++.+.+|+.|+|..      .|...+-+|+++.+||+.|+++|..|.+++...
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            378999999999999953      455566799999999999999999999987554

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.26  E-value=0.00022  Score=69.73  Aligned_cols=53  Identities=28%  Similarity=0.485  Sum_probs=46.1

Q ss_pred             ccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHHHHH
Q 018897          181 SKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDKISS  233 (349)
Q Consensus       181 ~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~v~~  233 (349)
                      .--+.-||+|=.-||..|..||+|+|.  .-|.+||.||+.+.+||.+|+.+.-+
T Consensus        62 eIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~  116 (373)
T KOG0561|consen   62 EIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTE  116 (373)
T ss_pred             HhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccc
Confidence            344567999999999999999999995  57999999999999999999876443

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.24  E-value=0.0013  Score=72.60  Aligned_cols=70  Identities=19%  Similarity=0.256  Sum_probs=58.7

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~  342 (349)
                      +....|+|.+.++||||.+|.++|.++|++|..|.|+|.++.+.++|.+....+. .++   .+.|+++|..++
T Consensus       781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g~-~l~~~~~~~l~~~L~~~l  853 (854)
T PRK01759        781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQGQ-ALDEEERKALKSRLLSNL  853 (854)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCCC-cCChHHHHHHHHHHHHHh
Confidence            3457999999999999999999999999999999999999999999998765333 333   267777777664

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=97.18  E-value=0.0024  Score=71.05  Aligned_cols=71  Identities=17%  Similarity=0.262  Sum_probs=59.8

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~  342 (349)
                      .....|.|.+.++||||.+|..+|..+||+|+.|.|+|.++.++++|.+....+....+   .+.|+++|.+++
T Consensus       812 ~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~~l~~~~~~~~l~~~L~~~L  885 (895)
T PRK00275        812 RPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQPLSDPQLCSRLQDAICEQL  885 (895)
T ss_pred             CCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999999999999987754433323   256888888776

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

Probab=97.17  E-value=0.004  Score=45.57  Aligned_cols=62  Identities=19%  Similarity=0.205  Sum_probs=46.3

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC--eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND--FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d--~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .|.|.|+++||+|.+|.++|.++|+.|.++.+.+..+  ..+..+...     .....+.+.++|.+..
T Consensus         2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~~~   65 (66)
T PF01842_consen    2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIVV-----DEEDLEKLLEELEALP   65 (66)
T ss_dssp             EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEE-----EGHGHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEEC-----CCCCHHHHHHHHHccc
Confidence            5788999999999999999999999999999999877  222222111     1334567777776654

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 ....

>PRK04374 PII uridylyl-transferase; Provisional

Probab=97.07  E-value=0.0037  Score=69.33  Aligned_cols=71  Identities=20%  Similarity=0.278  Sum_probs=59.0

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccC--CHHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETL--SCEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~i--s~edIkqaL~~~~  342 (349)
                      +....|.|.+.++||||.+|..+|..+||+|+.|.|+|.++.+++++.+....+....  ..+.|+++|..++
T Consensus       794 ~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~~~~~~~~~~l~~~L~~~l  866 (869)
T PRK04374        794 GRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDRPLSESARQALRDALCACL  866 (869)
T ss_pred             CCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCCcCChHHHHHHHHHHHHHh
Confidence            3467999999999999999999999999999999999999999999988765333221  2267888887765

>PRK05092 PII uridylyl-transferase; Provisional

Probab=97.06  E-value=0.0041  Score=69.39  Aligned_cols=70  Identities=21%  Similarity=0.275  Sum_probs=59.7

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~  342 (349)
                      ....|.|.|.++||+|.+|..+|..+|++|..|.|+|.++.+++++.+....+....+   .+.|+++|..++
T Consensus       842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~~~~~l~~~L~~~L  914 (931)
T PRK05092        842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEARQAAIRRALLAAL  914 (931)
T ss_pred             CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999999999999887654443333   367888888877

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

Probab=97.02  E-value=0.00063  Score=63.87  Aligned_cols=60  Identities=20%  Similarity=0.356  Sum_probs=51.9

Q ss_pred             CCCccchHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 018897          178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMKELLDKISSLQQE  237 (349)
Q Consensus       178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~  237 (349)
                      ..+..++..||+|=+.+|..|..||.+||.    .+|.+|..+|.-||.||+.|++-++.-+..
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            456677788999999999999999999995    468899999999999999999877766543

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

Probab=96.99  E-value=0.0093  Score=44.10  Aligned_cols=48  Identities=29%  Similarity=0.411  Sum_probs=42.1

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecc
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGV  323 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~  323 (349)
                      .|.|.|.+++|+|.+|..+|.++|+.|.++.+.+.++.....+.....
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~   49 (70)
T cd04873           2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDS   49 (70)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECC
Confidence            578999999999999999999999999999999987777667766654

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

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.88  E-value=0.0042  Score=68.78  Aligned_cols=71  Identities=11%  Similarity=0.174  Sum_probs=56.5

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .....|.|.|.++||||.+|..+|..+||+|+.|.|+|.++.+++++.+........-..+.|+++|.+++
T Consensus       784 ~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~~~~~~~~~~~~l~~~L~~~L  854 (856)
T PRK03059        784 GQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDGSGLSDNRLQIQLETELLDAL  854 (856)
T ss_pred             CCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcCCCCCCHHHHHHHHHHHHHHh
Confidence            34678999999999999999999999999999999999999999999884321111112357777777665

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=96.59  E-value=0.011  Score=65.41  Aligned_cols=70  Identities=24%  Similarity=0.282  Sum_probs=56.8

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccC--CHHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETL--SCEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~i--s~edIkqaL~~~~  342 (349)
                      ....|.|.|.++||+|.+|.++|..+|++|.+|.|+|.++.+.+++......+...-  ..+.|+++|..++
T Consensus       778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~~~~~~~~~~l~~~L~~~l  849 (850)
T TIGR01693       778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGLKLTDEEEQRLLEVLAASV  849 (850)
T ss_pred             CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999999988888887654332221  2467777777654

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=96.57  E-value=0.012  Score=64.66  Aligned_cols=51  Identities=22%  Similarity=0.350  Sum_probs=47.8

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecc
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGV  323 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~  323 (349)
                      ....|.|.+.++||||.+|..+|..+|++|+.|.|+|.++.+++++.+...
T Consensus       706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~  756 (774)
T PRK03381        706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGA  756 (774)
T ss_pred             CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECC
Confidence            357999999999999999999999999999999999999999999988764

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

Probab=96.44  E-value=0.035  Score=43.37  Aligned_cols=67  Identities=15%  Similarity=0.119  Sum_probs=53.1

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh-hcC
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA-GYG  345 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~-g~g  345 (349)
                      +.|.+.|+++||+...|-+.|.++|..|+.++....++..+.....+..    ..+.++|+++|...+ .+|
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~----~~~~~~l~~~l~~~~~~~~   69 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS----WDAIAKLEAALPGLARRLD   69 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec----cccHHHHHHHHHHHHHHcC
Confidence            5789999999999999999999999999999999988744444344432    247789998888866 444

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

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=96.43  E-value=0.018  Score=63.55  Aligned_cols=72  Identities=17%  Similarity=0.247  Sum_probs=58.7

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe-eeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHhh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS-CFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNAG  343 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS-t~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~g  343 (349)
                      ...+.|.|.+.+++|+|.+|..+|..+||+|+.|.|. +.++.+++++.+....+.....   .+.|+++|..++.
T Consensus       666 ~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~~~~~~~~~~~i~~~L~~~L~  741 (850)
T TIGR01693       666 SGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGSPPAAERVFQELLQGLVDVLA  741 (850)
T ss_pred             CCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCCCCCcHHHHHHHHHHHHHHHc
Confidence            4567899999999999999999999999999999999 6788999999988754332222   3457778877774

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

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=96.41  E-value=0.02  Score=63.47  Aligned_cols=78  Identities=18%  Similarity=0.300  Sum_probs=61.0

Q ss_pred             Cceeeee--ecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccCCH---HHHHHH
Q 018897          264 PKFDVER--TNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETLSC---EDIKQA  337 (349)
Q Consensus       264 p~VeV~~--~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~is~---edIkqa  337 (349)
                      |.|.|+.  ..+...|.|.|.+++|||.+|..+|..+||+|+.|.|.+ .++.+++++.+....+. .++.   +.|+++
T Consensus       665 ~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~-~~~~~~~~~l~~~  743 (854)
T PRK01759        665 LLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGK-LLEFDRRRQLEQA  743 (854)
T ss_pred             CEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCC-CCCHHHHHHHHHH
Confidence            4455543  245679999999999999999999999999999999987 78899999988775333 2343   356777


Q ss_pred             HHHHh
Q 018897          338 LFRNA  342 (349)
Q Consensus       338 L~~~~  342 (349)
                      |.+++
T Consensus       744 L~~aL  748 (854)
T PRK01759        744 LTKAL  748 (854)
T ss_pred             HHHHH
Confidence            77766

>PRK03381 PII uridylyl-transferase; Provisional

Probab=96.41  E-value=0.019  Score=63.07  Aligned_cols=71  Identities=14%  Similarity=0.127  Sum_probs=59.8

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHhh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAG  343 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~g  343 (349)
                      .+.+.|.|.|.++||++.+|..+|..+|++|+.|.|.+.++.+++++.+....+ .....+.|+++|.+++.
T Consensus       597 ~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~~~-~~~~~~~l~~~L~~~L~  667 (774)
T PRK03381        597 PHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPRFG-SPPDAALLRQDLRRALD  667 (774)
T ss_pred             CCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCC-CcchHHHHHHHHHHHHc
Confidence            466789999999999999999999999999999999998889999888776433 23345789999887763

>PRK05007 PII uridylyl-transferase; Provisional

Probab=96.41  E-value=0.021  Score=63.53  Aligned_cols=78  Identities=21%  Similarity=0.223  Sum_probs=60.7

Q ss_pred             Cceeeeee--cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCH---HHHHHH
Q 018897          264 PKFDVERT--NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSC---EDIKQA  337 (349)
Q Consensus       264 p~VeV~~~--~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~---edIkqa  337 (349)
                      |.|.|+..  .+.+.|.|.|.+++|+|..|..+|..+||+|+.|.|.|.++ .+++++.+....+. .++.   +.|+++
T Consensus       689 p~V~i~~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~-~~~~~~~~~I~~~  767 (884)
T PRK05007        689 PLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGS-PLSQDRHQVIRKA  767 (884)
T ss_pred             CeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCC-CCCHHHHHHHHHH
Confidence            44555432  45779999999999999999999999999999999988765 99999988765333 2343   347788


Q ss_pred             HHHHh
Q 018897          338 LFRNA  342 (349)
Q Consensus       338 L~~~~  342 (349)
                      |.+++
T Consensus       768 L~~aL  772 (884)
T PRK05007        768 LEQAL  772 (884)
T ss_pred             HHHHH
Confidence            87776

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

Probab=96.40  E-value=0.011  Score=64.77  Aligned_cols=68  Identities=21%  Similarity=0.372  Sum_probs=56.6

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      ....|++.+.+|||||..|-.+|..++|+|++|.|+|+|..+.++++.-...+ ..+ ..+++|.|.+.+
T Consensus       790 ~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~-~~l-~~~~~q~l~~~l  857 (867)
T COG2844         790 DKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADG-QAL-NAELRQSLLQRL  857 (867)
T ss_pred             CceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEecccc-ccC-CHHHHHHHHHHH
Confidence            35689999999999999999999999999999999999999999999887533 333 445666666544

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

Probab=96.33  E-value=0.028  Score=43.78  Aligned_cols=65  Identities=15%  Similarity=0.124  Sum_probs=49.8

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.+.+++|||++..|..+|.+.|.+|..++.++.++...-...++..    .-+.++|+.+|.+.+
T Consensus         2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~----~~~~~~l~~~L~~l~   66 (76)
T PF13740_consen    2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP----EDSLERLESALEELA   66 (76)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES----HHHHHHHHHHHHHHH
T ss_pred             EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC----cccHHHHHHHHHHHH
Confidence            46799999999999999999999999999999999999944334444432    226688999988875

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

Probab=95.86  E-value=0.077  Score=40.62  Aligned_cols=65  Identities=18%  Similarity=0.148  Sum_probs=47.0

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      |.|.|++++|++.+|.+.|-++|+.|......+. ++..+.+.. +........+.++|+++|....
T Consensus         2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~-~~~~~~~~~~~~~l~~~l~~l~   67 (74)
T cd04875           2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRV-EFELEGFDLSREALEAAFAPVA   67 (74)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEE-EEEeCCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999999999999888763 222233221 1110111257899999998876

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.

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

Probab=95.81  E-value=0.11  Score=39.95  Aligned_cols=65  Identities=14%  Similarity=0.236  Sum_probs=49.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC------C-eEEEEEeeecccCCccCCHHHHHHHHHHHh-hcC
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN------D-FAMQASCSEGVEQRETLSCEDIKQALFRNA-GYG  345 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~------d-~vl~a~~se~~e~~~~is~edIkqaL~~~~-g~g  345 (349)
                      |.|.|.+++|++.+|-+.|.++|++|...+..+.+      + +.+. .....   ....+..+|+.+|.... .+|
T Consensus         2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~-~~v~~---p~~~~~~~l~~~l~~l~~~~~   74 (81)
T cd04869           2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQ-ATLAL---PAGTDLDALREELEELCDDLN   74 (81)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEE-EEEec---CCCCCHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999998876      2 2221 12222   23467889999998876 444

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

>PRK03059 PII uridylyl-transferase; Provisional

Probab=95.79  E-value=0.051  Score=60.42  Aligned_cols=70  Identities=11%  Similarity=0.153  Sum_probs=55.9

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe-eeCCeEEEEEeeecccCCccC---CHHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS-CFNDFAMQASCSEGVEQRETL---SCEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS-t~~d~vl~a~~se~~e~~~~i---s~edIkqaL~~~~  342 (349)
                      .+.+.|.|.|.+++|||.+|..+|..+||+|+.|.|. +-+|++++++.+....+. ..   -.+.|+++|.+++
T Consensus       676 ~~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~~-~~~~~~~~~i~~~l~~~l  749 (856)
T PRK03059        676 GEGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEED-VHYRDIINLVEHELAERL  749 (856)
T ss_pred             CCeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCCC-CChHHHHHHHHHHHHHHH
Confidence            3567999999999999999999999999999999995 467899999988764333 11   2456777777665

>PRK05092 PII uridylyl-transferase; Provisional

Probab=95.75  E-value=0.065  Score=59.97  Aligned_cols=71  Identities=18%  Similarity=0.148  Sum_probs=56.5

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccC---CHHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETL---SCEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~i---s~edIkqaL~~~~  342 (349)
                      .+.+.|.|.|.+++|+|.+|..+|..+|++|+.|.|.+ .++++++++.+....+....   ..+.|+++|.+++
T Consensus       730 ~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~~~~l~~~L~~~l  804 (931)
T PRK05092        730 RGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRRLARLAKAIEDAL  804 (931)
T ss_pred             CCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999988 57799998877654332222   2456777777666

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.69  E-value=0.059  Score=60.19  Aligned_cols=70  Identities=17%  Similarity=0.236  Sum_probs=56.1

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe-eeCCeEEEEEeeecccCCccCC----HHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS-CFNDFAMQASCSEGVEQRETLS----CEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS-t~~d~vl~a~~se~~e~~~~is----~edIkqaL~~~~  342 (349)
                      +.+.|.|.|.++||+|.+|..+|..+||+|+.|.|. +-+|++++++.+....+.....    .+.|+++|.+++
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 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGEPIGDNPARIEQIREGLTEAL  777 (895)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCCCccchHHHHHHHHHHHHHHH
Confidence            567999999999999999999999999999999985 4577999999887654443222    245777777765

>PRK00194 hypothetical protein; Validated

Probab=95.67  E-value=0.069  Score=42.38  Aligned_cols=67  Identities=12%  Similarity=0.150  Sum_probs=50.0

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|+++||++.+|.+.|-++|++|...+..+.++...-.+..+..  ....+.++|++.|....
T Consensus         3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~--~~~~~~~~l~~~l~~l~   69 (90)
T PRK00194          3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDIS--ESKKDFAELKEELEELG   69 (90)
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEec--CCCCCHHHHHHHHHHHH
Confidence            45799999999999999999999999999998888776632222233321  11345788988888765

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

Probab=95.57  E-value=0.071  Score=42.35  Aligned_cols=66  Identities=11%  Similarity=0.182  Sum_probs=50.3

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      ..|.+.|+++||++..|.+.|-.+|++|...+..+.++...-.......  ....+.++++.+|.+..
T Consensus         2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~--~~~~~~~~L~~~l~~l~   67 (88)
T cd04872           2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDIS--ESNLDFAELQEELEELG   67 (88)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeC--CCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999999999999888876632222223321  11456889999888876

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.

>PRK04374 PII uridylyl-transferase; Provisional

Probab=95.31  E-value=0.086  Score=58.76  Aligned_cols=71  Identities=15%  Similarity=0.106  Sum_probs=57.0

Q ss_pred             cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.+.|.|.|.+++|||.+|..+|..+||+|+.|.|.+ .+|.+++++.+....+...-..+.|+++|.+++
T Consensus       688 ~~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~~l~~~l  759 (869)
T PRK04374        688 NDALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAAALRQVL  759 (869)
T ss_pred             CCeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHHHHHHHH
Confidence            35679999999999999999999999999999999998 577999999887654432223455777777665

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

Probab=94.99  E-value=0.14  Score=39.73  Aligned_cols=66  Identities=17%  Similarity=0.137  Sum_probs=50.5

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRN  341 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~  341 (349)
                      .|.|.|+++.||-.+|..++-+.||.|..+.+++.|..-+-++-+......-.+.=+-+|+.|..+
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            589999999999999999999999999999999999954444443332223345557777777653

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.

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

Probab=94.75  E-value=0.32  Score=37.45  Aligned_cols=62  Identities=16%  Similarity=0.253  Sum_probs=49.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      |.+.+.+|||++.++.++|.++|++|...+.++.++ |++.. .....   ...+.++++.+|....
T Consensus         2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~-~v~~p---~~~~~~~l~~~l~~l~   64 (75)
T cd04870           2 ITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGI-LVQIP---DSADSEALLKDLLFKA   64 (75)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEE-EEEcC---CCCCHHHHHHHHHHHH
Confidence            678899999999999999999999999998888877 44433 23332   2257889999988766

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.

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

Probab=94.59  E-value=0.47  Score=36.64  Aligned_cols=61  Identities=20%  Similarity=0.242  Sum_probs=41.9

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CCeEEEEEeeecccCCccCCHHHHHHHHHH
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--NDFAMQASCSEGVEQRETLSCEDIKQALFR  340 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d~vl~a~~se~~e~~~~is~edIkqaL~~  340 (349)
                      .+.|+|.+.+++|+|.+|.++|.+.|+.|.+.++...  ++...-.+..++      -+.+++.+.+.+
T Consensus         6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V------~d~~~L~~ii~~   68 (80)
T PF13291_consen    6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEV------KDLEHLNQIIRK   68 (80)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEE------SSHHHHHHHHHH
T ss_pred             EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEE------CCHHHHHHHHHH
Confidence            4678999999999999999999999999999999995  343333333443      134455554444

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

Probab=93.24  E-value=0.99  Score=32.77  Aligned_cols=34  Identities=15%  Similarity=0.237  Sum_probs=29.2

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      +.|.++++||.|.+|+++|.+.|++|.+......
T Consensus         1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~   34 (73)
T cd04886           1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRA   34 (73)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEec
Confidence            3577899999999999999999999997766543

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

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

Probab=92.82  E-value=1.5  Score=32.87  Aligned_cols=35  Identities=17%  Similarity=0.240  Sum_probs=31.9

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN  311 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~  311 (349)
                      |+|.+.+++|+|.+|+++|.+.|..|.+.++....
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~   36 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQG   36 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEec
Confidence            67889999999999999999999999988887764

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.

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

Probab=91.76  E-value=1  Score=29.56  Aligned_cols=35  Identities=20%  Similarity=0.370  Sum_probs=30.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN  311 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~  311 (349)
                      |.|.|.+++|.+.+|+.+|...|+.|.........
T Consensus         1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            46788899999999999999999999988776643

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

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=91.69  E-value=0.11  Score=46.74  Aligned_cols=52  Identities=27%  Similarity=0.416  Sum_probs=46.2

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDK  230 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~  230 (349)
                      ++.-|++-||+|=..+|+.|.+||.++|.  +.|.+|.-.|.-|..||..|-+-
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence            56789999999999999999999999996  57888888999999999988643

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=91.51  E-value=0.99  Score=44.28  Aligned_cols=67  Identities=19%  Similarity=0.237  Sum_probs=49.8

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe---eeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS---CFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS---t~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|++++|+...|-+.|-+.|++|+..+..   ..+.|.+.+.....  ....++.++|+++|...+
T Consensus         9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~--~~~~~~~~~l~~~l~~l~   78 (289)
T PRK13010          9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQ--SAEAASVDTFRQEFQPVA   78 (289)
T ss_pred             CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcC--CCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999999999999998885   23445443322211  123567889999998865

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

Probab=91.28  E-value=0.92  Score=31.55  Aligned_cols=35  Identities=17%  Similarity=0.267  Sum_probs=30.7

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN  311 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~  311 (349)
                      |+|.+.+++|.+.+|++.|...+++|.+..+...+
T Consensus         1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (71)
T cd04876           1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDD   35 (71)
T ss_pred             CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECC
Confidence            46778899999999999999999999988777654

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

>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=91.24  E-value=2.2  Score=31.42  Aligned_cols=35  Identities=20%  Similarity=0.331  Sum_probs=31.5

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      .|.|.+.+++|+|.+|+..|.+.|..|.+......
T Consensus         2 yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~   36 (79)
T cd04881           2 YLRLTVKDKPGVLAKITGILAEHGISIESVIQKEA   36 (79)
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence            58889999999999999999999999998877655

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

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

Probab=90.79  E-value=2.3  Score=30.86  Aligned_cols=36  Identities=19%  Similarity=0.168  Sum_probs=31.7

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN  311 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~  311 (349)
                      .|.|.+.+++|.|.+|++.|.+.++.|.+......+
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~   37 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIER   37 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccC
Confidence            477889999999999999999999999987776653

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.

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

Probab=90.58  E-value=1.4  Score=33.17  Aligned_cols=36  Identities=8%  Similarity=0.158  Sum_probs=31.3

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      +.|.|.+.+++|+|.+|+++|.+.|++|...+.+..
T Consensus         1 ~~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~   36 (76)
T cd04888           1 VTLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIP   36 (76)
T ss_pred             CEEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCC
Confidence            357888999999999999999999999998776543

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.

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

Probab=90.27  E-value=2.4  Score=31.52  Aligned_cols=61  Identities=16%  Similarity=0.243  Sum_probs=41.4

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--NDFAMQASCSEGVEQRETLSCEDIKQALFRN  341 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d~vl~a~~se~~e~~~~is~edIkqaL~~~  341 (349)
                      .+|.+..++++|.|.++++.|.+.|+.|.+......  .+...-.+..+.      .+.++++++|.+.
T Consensus         2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~------~~~~~~~~~L~~~   64 (72)
T cd04883           2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQT------MNPRPIIEDLRRA   64 (72)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEec------CCHHHHHHHHHHC
Confidence            467788899999999999999999999997654332  223332333322      2345777777553

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.

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

Probab=89.59  E-value=3.2  Score=31.65  Aligned_cols=35  Identities=20%  Similarity=0.349  Sum_probs=32.2

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      .|+|.|.+++|+|.+|+.++.+.+..|...++.+.
T Consensus         2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~   36 (74)
T cd04877           2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK   36 (74)
T ss_pred             EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC
Confidence            58899999999999999999999999998888765

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

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=89.54  E-value=0.2  Score=52.44  Aligned_cols=56  Identities=16%  Similarity=0.214  Sum_probs=46.9

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDKISSL  234 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~v~~L  234 (349)
                      +|+.++..||.|=..||+.|.+|-.+.---    ....|--||..|+.-|-.|++||.+-
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            667888999999889999999998876532    23457889999999999999999864

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=89.46  E-value=2.7  Score=41.04  Aligned_cols=62  Identities=16%  Similarity=0.101  Sum_probs=48.0

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--C-eEEEEEeeecccCCccCCHHHHHHHHHH
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--D-FAMQASCSEGVEQRETLSCEDIKQALFR  340 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d-~vl~a~~se~~e~~~~is~edIkqaL~~  340 (349)
                      .|.+.|++++|+...|-+.|-++|+.|+..+.+...  + |.+ ....+.  .....+.++|+++|..
T Consensus         2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~m-r~~v~~--~~~~~~~~~l~~~l~~   66 (280)
T TIGR00655         2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFM-RVEFQL--EGFRLEESSLLAAFKS   66 (280)
T ss_pred             EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEE-EEEEEe--CCCCCCHHHHHHHHHH
Confidence            578999999999999999999999999998888753  4 333 223332  1224678899999888

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.

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

Probab=89.38  E-value=2.2  Score=30.80  Aligned_cols=34  Identities=21%  Similarity=0.229  Sum_probs=28.2

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      |.|.-+++||.|.++++.|.+.|+.|.+......
T Consensus         2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~   35 (65)
T cd04882           2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVE   35 (65)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEcc
Confidence            4566689999999999999999999986655443

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.

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=89.33  E-value=0.3  Score=51.70  Aligned_cols=42  Identities=38%  Similarity=0.644  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHH
Q 018897          184 LMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMK  225 (349)
Q Consensus       184 ~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk  225 (349)
                      .---+|-|+|+|..|..|.+|+|-    ++|.||-|||.-++.|++
T Consensus        30 SNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   30 SNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             CCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            334567799999999999999994    689999999999999975

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

Probab=89.32  E-value=0.23  Score=53.76  Aligned_cols=46  Identities=33%  Similarity=0.491  Sum_probs=40.3

Q ss_pred             ccchHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHHH
Q 018897          181 SKNLMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMKE  226 (349)
Q Consensus       181 ~~h~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk~  226 (349)
                      .+-.-|-|-||.|-|+-|..|..+||-    .+.+|||||+.-||.|++-
T Consensus        48 EkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   48 EKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            444568899999999999999999993    4689999999999999874

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

Probab=88.94  E-value=3.5  Score=30.67  Aligned_cols=37  Identities=22%  Similarity=0.373  Sum_probs=31.7

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND  312 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d  312 (349)
                      +|.|..+++||.|.+|++.|.+.|+.|.+..+...++
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            5778889999999999999999999999777655544

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.

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=88.43  E-value=3.4  Score=40.37  Aligned_cols=66  Identities=18%  Similarity=0.260  Sum_probs=50.1

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee--eCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC--FND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt--~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.+.|.+|||+...|-++|-++|++|...+.++  .++ |.+.... ..  .....+.++|+++|....
T Consensus         6 ~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v-~~--~~~~~~~~~L~~~L~~l~   74 (286)
T PRK06027          6 RYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEF-EG--DGLIFNLETLRADFAALA   74 (286)
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEE-Ee--CCCCCCHHHHHHHHHHHH
Confidence            467999999999999999999999999999999998  766 3333322 21  122345788998888755

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=88.27  E-value=0.48  Score=48.74  Aligned_cols=44  Identities=32%  Similarity=0.429  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHHHH
Q 018897          184 LMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMKEL  227 (349)
Q Consensus       184 ~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk~L  227 (349)
                      +-+-|.||++-|-.|..|..++|-    .+..||++|+.-|..|||.-
T Consensus         6 KnaA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    6 KNAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             hhHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            357799999999999999999995    35699999999999999853

>PRK04435 hypothetical protein; Provisional

Probab=87.97  E-value=2.4  Score=37.46  Aligned_cols=70  Identities=10%  Similarity=-0.009  Sum_probs=47.0

Q ss_pred             eecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897          270 RTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGVEQRETLSCEDIKQALFRN  341 (349)
Q Consensus       270 ~~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~e~~~~is~edIkqaL~~~  341 (349)
                      ..+..+.|.+.+.+++|+|.+|+++|.+.|.+|...+.+.. ++...-.+..+..  +.....++|.++|.+.
T Consensus        65 ~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs--~~~~~L~~Li~~L~~i  135 (147)
T PRK04435         65 VKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTS--SMEGDIDELLEKLRNL  135 (147)
T ss_pred             CCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeC--ChHHHHHHHHHHHHcC
Confidence            35778899999999999999999999999999998776543 3422222233331  1122445666665543

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

Probab=87.70  E-value=3  Score=29.90  Aligned_cols=60  Identities=17%  Similarity=0.137  Sum_probs=42.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--CeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--DFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      +.|...+++|+|.+|++.|.+.|+.|.+..+..-.  +...-.+..+.    .  ..++|.+.|...-
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~~----~--~~~~l~~~l~~~~   63 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDS----P--VPEEVLEELKALP   63 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcCC----C--CCHHHHHHHHcCC
Confidence            66788999999999999999999999988877654  43333332221    1  2457777776543

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

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

Probab=87.29  E-value=3.2  Score=31.33  Aligned_cols=34  Identities=21%  Similarity=0.258  Sum_probs=29.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      +.+.-+++||.|.++++.|.+.|..|++......
T Consensus         2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~   35 (72)
T cd04884           2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFE   35 (72)
T ss_pred             EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence            5566789999999999999999999997765554

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.

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

Probab=86.90  E-value=4.3  Score=29.22  Aligned_cols=33  Identities=18%  Similarity=0.255  Sum_probs=29.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISC  309 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt  309 (349)
                      |.+.+.+++|.|.+|...|.+.|+.|.+.....
T Consensus         2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~   34 (71)
T cd04903           2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSR   34 (71)
T ss_pred             EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEe
Confidence            567889999999999999999999999877665

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.

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=86.34  E-value=5.4  Score=39.03  Aligned_cols=65  Identities=15%  Similarity=0.170  Sum_probs=48.5

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CC--eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-ND--FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d--~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|.++||+...|-+.|-++|++|...+..+- .+  |.+.+... .   ....+.++|+++|...+
T Consensus         7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~-~---p~~~~~~~L~~~L~~l~   74 (286)
T PRK13011          7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFH-S---EEGLDEDALRAGFAPIA   74 (286)
T ss_pred             eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEe-c---CCCCCHHHHHHHHHHHH
Confidence            4678999999999999999999999999998887642 22  44433322 1   12356889998888765

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

Probab=86.33  E-value=4.7  Score=29.85  Aligned_cols=35  Identities=17%  Similarity=0.294  Sum_probs=30.2

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      -+.+.+++++|.|.+|++.|.+.|++|........
T Consensus         3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            36778899999999999999999999997765554

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.

>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=85.53  E-value=3.8  Score=29.29  Aligned_cols=43  Identities=21%  Similarity=0.349  Sum_probs=32.6

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC-CeEEEEEe
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN-DFAMQASC  319 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~-d~vl~a~~  319 (349)
                      |.|...++||.|.++...|.+.|+.|....+.... +..+-.+.
T Consensus         1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~   44 (56)
T cd04889           1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLI   44 (56)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEE
Confidence            35678899999999999999999999877666544 44433333

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

>PRK08577 hypothetical protein; Provisional

Probab=85.27  E-value=7.6  Score=33.42  Aligned_cols=66  Identities=15%  Similarity=0.249  Sum_probs=44.6

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--CeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--DFAMQASCSEGVEQRETLSCEDIKQALFRN  341 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d~vl~a~~se~~e~~~~is~edIkqaL~~~  341 (349)
                      .+.|.|.+.+++|+|.+|++.|.+++.++.+.+..+..  +...-.+..+..  ......+++.+.|.+.
T Consensus        56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~--~~~~~l~~l~~~L~~l  123 (136)
T PRK08577         56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLS--KSDIDLEELEEELKKL  123 (136)
T ss_pred             EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeC--CchhhHHHHHHHHHcC
Confidence            56799999999999999999999999999987776654  322112223331  1113345666666543

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

Probab=84.50  E-value=12  Score=26.72  Aligned_cols=35  Identities=14%  Similarity=0.271  Sum_probs=30.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      .|.|.+.+++|+|.+|+..|.+.++.|.+......
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04878           2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPT   36 (72)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeec
Confidence            36677889999999999999999999998877654

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

>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=84.22  E-value=9.5  Score=29.42  Aligned_cols=63  Identities=11%  Similarity=0.081  Sum_probs=39.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      |.+...+++|.|.+|++.|.++|+.+.+.......+ .....+..+.. .  ..+.+.++.+|...-
T Consensus         4 l~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~-~--~~~~~~~~~~l~~l~   67 (80)
T cd04905           4 IVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE-G--HIEDPNVAEALEELK   67 (80)
T ss_pred             EEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE-C--CCCCHHHHHHHHHHH
Confidence            455567899999999999999999999776555432 22222223321 1  234456666665443

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

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

Probab=84.12  E-value=4.7  Score=44.91  Aligned_cols=55  Identities=18%  Similarity=0.210  Sum_probs=47.6

Q ss_pred             eeecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecc
Q 018897          269 ERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGV  323 (349)
Q Consensus       269 ~~~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~  323 (349)
                      ........|-|.|+++|.++..|..++...|++|+.|.|-+- +|+.++++.+...
T Consensus       679 r~~~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~~  734 (867)
T COG2844         679 RPHSGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLEP  734 (867)
T ss_pred             cccCCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEecC
Confidence            334567899999999999999999999999999999998775 6679999977754

>PRK07334 threonine dehydratase; Provisional

Probab=83.11  E-value=8.1  Score=39.19  Aligned_cols=37  Identities=16%  Similarity=0.239  Sum_probs=34.0

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF  310 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~  310 (349)
                      .+.|.|.+.+|+|+|.+|+++|.+.++.|.+.++.+.
T Consensus       326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~  362 (403)
T PRK07334        326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRL  362 (403)
T ss_pred             EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEec
Confidence            4889999999999999999999999999998887654

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

Probab=81.06  E-value=12  Score=28.29  Aligned_cols=34  Identities=15%  Similarity=0.218  Sum_probs=27.7

Q ss_pred             EEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897          278 EICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN  311 (349)
Q Consensus       278 ~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~  311 (349)
                      .+...++||.|.++++.|...|+.+.+.......
T Consensus         3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~   36 (75)
T cd04880           3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSR   36 (75)
T ss_pred             EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecC
Confidence            3455789999999999999999999987555443

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

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

Probab=80.53  E-value=1.6  Score=42.13  Aligned_cols=52  Identities=29%  Similarity=0.435  Sum_probs=44.6

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCC---CCCCCchhhHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK---ISKMDRTSILADTIDYMKELLDK  230 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~---~~K~dKaSIL~~AI~YIk~Lq~~  230 (349)
                      +|.+=+..||+|=-.+|+.|..||.++|.   ..|+.|...|.-|-+||..|++-
T Consensus        72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            45666788998889999999999999994   47889999999999999988753

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=80.21  E-value=5.6  Score=36.79  Aligned_cols=65  Identities=14%  Similarity=0.190  Sum_probs=49.8

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      ..+.|.+.+.+|||+...|-++|.++|..|..++.+.+++ |.+-..+ ...    ......|+.+|....
T Consensus         7 ~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lv-s~~----~~~~~~le~~L~~l~   72 (190)
T PRK11589          7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLL-SGS----WNAITLIESTLPLKG   72 (190)
T ss_pred             cEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEE-eCC----hhHHHHHHHHHHhhh
Confidence            4567899999999999999999999999999999999988 4443333 221    225667777776544

---

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	349
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	5e-14
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	3e-11
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	4e-11
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	5e-11
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-08
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	4e-08
4f3l_A	361	Mclock, circadian locomoter output cycles protein	4e-05
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	2e-04
1a0a_A	63	BHLH, protein (phosphate system positive regulator	4e-04
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	4e-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 = 65.9 bits (161), Expect = 5e-14
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKI-SKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
             E+R R  +ND++  L+ +V    +K++++++L   IDY++ L      L+QE  +
Sbjct: 12  AIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLS 68

>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 = 57.7 bits (140), Expect = 3e-11
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKI--SKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
             ER+RR  + D    LR  VP +   K  R  IL    +Y++ +  K  + QQ+I  
Sbjct: 18  ALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD 75

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

 Score = 57.4 bits (139), Expect = 4e-11
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKI--SKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
             ER+RR  + D    LR  VP +   K  R  IL    +Y++ +  K  + QQ+I  
Sbjct: 8   ALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD 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 = 57.3 bits (139), Expect = 5e-11
 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 8/71 (11%)

Query: 177 GGQPSK----NLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLD 229
           G    K    N + ER+RR  L      LR  +P++    K  +  IL     Y+  +  
Sbjct: 1   GHMNVKRRTHN-VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQA 59

Query: 230 KISSLQQEIQA 240
           +   L  E   
Sbjct: 60  EEQKLISEEDL 70

>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 = 49.3 bits (118), Expect = 2e-08
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 6/49 (12%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP------KISKMDRTSILADTIDYMKEL 227
             ERRRR ++N+ +  L  I+P        S   +  IL+   DY++EL
Sbjct: 11  EVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

>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 = 49.1 bits (117), Expect = 4e-08
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKISKMDRTS---ILADTIDYMKELLDKISSLQQEIQ 239
             E+ RR  L   L  L+ +VP      R +   +L     ++K+L D       +I 
Sbjct: 7   EMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQID 64

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

 Score = 44.2 bits (104), Expect = 4e-05
 Identities = 16/57 (28%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 170 KSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKI-SKMDRTSILADTIDYMK 225
           +  +K    + S+N  +E++RR + N  +  L S++P    KMD++++L  +ID+++
Sbjct: 4   EEDDKDKAKRVSRNK-SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59

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

 Score = 41.9 bits (98), Expect = 2e-04
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 170 KSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVP----KISKMDRTSILADTIDYMK 225
                K   +       E+RRR ++N  +  L S+VP       K+D+ ++L   + +MK
Sbjct: 6   HQGRIKNAREAHSQ--IEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 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 = 37.5 bits (87), Expect = 4e-04
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPK-------ISKMDRTSILADTIDYMKELLDKISS 233
            AE+ RR RL   L  L S++P         +   + + +     Y++ L    S+
Sbjct: 8   HAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST 63

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus} Length = 60

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 16/61 (26%)

Query: 187 ERRRRKRLNDRLSMLRSIVP------KISKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
           ER R   LN  L  LR +VP      K+SK++    L    +Y       I +L + +++
Sbjct: 10  ERNRMHGLNAALDNLRKVVPCYSKTQKLSKIE---TLRLAKNY-------IWALSEILRS 59

Query: 241 G 241
           G
Sbjct: 60  G 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	349
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.58
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.49
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.48
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.47
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.47
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.46
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.45
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.42
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.36
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.35
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.28
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.0
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.99
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.87
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.7
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.45
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.34
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.86
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	96.7
1u8s_A	192	Glycine cleavage system transcriptional repressor,	95.99
2nyi_A	195	Unknown protein; protein structure initiative, PSI	95.34
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	94.92
2nyi_A	195	Unknown protein; protein structure initiative, PSI	94.67
1u8s_A	192	Glycine cleavage system transcriptional repressor,	93.86
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	91.32
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	89.77
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	89.3
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	88.76
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	87.46
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	87.24
3nrb_A	287	Formyltetrahydrofolate deformylase; N-terminal ACT	80.19

>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=99.58  E-value=1.5e-15  Score=120.50  Aligned_cols=63  Identities=25%  Similarity=0.422  Sum_probs=58.6

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI-SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~-~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      ++..|+++||+||.+||++|..|+++||+. .|++|++||.+||+||++|+.+++.|+++.+..
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            457999999999999999999999999986 899999999999999999999999999977654

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

Probab=99.49  E-value=3.9e-14  Score=119.50  Aligned_cols=59  Identities=27%  Similarity=0.534  Sum_probs=52.1

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDKISSLQQE  237 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~  237 (349)
                      .+..|+++||+||.+||++|..|++|||++    .|++|++||.+||+||++||++++.|+++
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999975    37889999999999999999999999874

>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=99.48  E-value=1.7e-14  Score=109.18  Aligned_cols=54  Identities=30%  Similarity=0.497  Sum_probs=49.6

Q ss_pred             CCCccchHHHHHHHHHHHHHHHHhHhcCCCCC------CCCchhhHHHHHHHHHHHHHHH
Q 018897          178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPKIS------KMDRTSILADTIDYMKELLDKI  231 (349)
Q Consensus       178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~~~------K~dKaSIL~~AI~YIk~Lq~~v  231 (349)
                      ..+..|+.+||+||.+||+.|..|++|||...      |++|++||.+||+||+.|+++.
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            35689999999999999999999999999754      7899999999999999999764

>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=99.47  E-value=3.1e-14  Score=112.12  Aligned_cols=63  Identities=29%  Similarity=0.461  Sum_probs=58.2

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC--CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI--SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~--~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      .+..|+.+||+||.+||+.|..|+++||..  .|++|++||..||+||+.|+++++.|+.+++.+
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457999999999999999999999999974  699999999999999999999999999987643

>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=99.47  E-value=8.9e-15  Score=110.82  Aligned_cols=54  Identities=24%  Similarity=0.356  Sum_probs=48.9

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC-------CCCCchhhHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI-------SKMDRTSILADTIDYMKELLDKIS  232 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~-------~K~dKaSIL~~AI~YIk~Lq~~v~  232 (349)
                      ++.+|+++||+||.+||..|..|++|||+.       ++.+||+||+.||+||++||++++
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            467999999999999999999999999953       577899999999999999998753

>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=99.46  E-value=5e-14  Score=111.47  Aligned_cols=62  Identities=29%  Similarity=0.422  Sum_probs=57.1

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      +..|+.+||+||.+||+.|..|+++||.  ..|++|++||..||+||+.|+++++.|+.+++..
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            4689999999999999999999999997  4799999999999999999999999998877554

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

Probab=99.45  E-value=2.5e-14  Score=110.83  Aligned_cols=57  Identities=25%  Similarity=0.472  Sum_probs=52.2

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCC-CCCCCchhhHHHHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK-ISKMDRTSILADTIDYMKELLDKISSLQ  235 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~-~~K~dKaSIL~~AI~YIk~Lq~~v~~L~  235 (349)
                      .+.+|+++||+||.+||++|..|++|||. ..|+||++||..||+||+.||+++.=|+
T Consensus         8 kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            8 KRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            45799999999999999999999999996 4699999999999999999999887654

>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=99.42  E-value=1.5e-13  Score=110.48  Aligned_cols=61  Identities=23%  Similarity=0.353  Sum_probs=55.6

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKISSLQQEIQA  240 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~  240 (349)
                      +..|+.+||+||.+||+.|..|+.+||..   .|++|++||.+||+||++|+.+.+.|..+++.
T Consensus         7 R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~   70 (88)
T 1nkp_A            7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL   70 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999974   59999999999999999999999988776543

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

Probab=99.36  E-value=6.8e-14  Score=108.92  Aligned_cols=51  Identities=29%  Similarity=0.470  Sum_probs=47.4

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLD  229 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~  229 (349)
                      ++..|+.+||+||++||+.|..|++|||.+    .|+||++||..||+||+.|+.
T Consensus         9 rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            457999999999999999999999999964    799999999999999999973

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

Probab=99.35  E-value=1.2e-12  Score=103.55  Aligned_cols=62  Identities=26%  Similarity=0.240  Sum_probs=56.4

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      +..|+..||+||..||+.|..|+++||..   .|.+|++||..|++||+.|+++.+.|..+++..
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            46899999999999999999999999964   688899999999999999999999999877543

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

Probab=99.28  E-value=1.4e-12  Score=102.26  Aligned_cols=58  Identities=17%  Similarity=0.286  Sum_probs=48.7

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCC---CCCC-CchhhHHHHHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK---ISKM-DRTSILADTIDYMKELLDKISSLQQ  236 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~---~~K~-dKaSIL~~AI~YIk~Lq~~v~~L~~  236 (349)
                      +|..|+..||+||..||+.|..|+.+||.   ..|. +|.+||..||+||+.|++++++++.
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            56799999999999999999999999994   3455 6889999999999999999987653

>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=99.00  E-value=7.8e-11  Score=90.46  Aligned_cols=53  Identities=23%  Similarity=0.427  Sum_probs=48.9

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDKI  231 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~v  231 (349)
                      ++..|+..||+|+..||+.|..||.+||.  ..|++|..||..||+||+.|++.+
T Consensus        12 rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            56789999999999999999999999996  468999999999999999999765

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

Probab=98.99  E-value=2.7e-10  Score=85.44  Aligned_cols=53  Identities=28%  Similarity=0.357  Sum_probs=48.3

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHHH
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKIS  232 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v~  232 (349)
                      +..|+..||+|+..||+.|..||.+||..   .|++|..+|..||+||+.|++.++
T Consensus         3 R~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            3 RMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999964   589999999999999999998764

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

Probab=98.87  E-value=1.2e-09  Score=105.95  Aligned_cols=52  Identities=25%  Similarity=0.524  Sum_probs=42.7

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCC-CCCCCCchhhHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVP-KISKMDRTSILADTIDYMKELLDK  230 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP-~~~K~dKaSIL~~AI~YIk~Lq~~  230 (349)
                      .+.+|+.+||+||++||..|..|++||| ...|+||++||..||+|||.|+..
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            5678999999999999999999999999 567999999999999999999864

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

Probab=98.70  E-value=4.7e-09  Score=102.92  Aligned_cols=52  Identities=29%  Similarity=0.445  Sum_probs=48.4

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCC----CCCCCCchhhHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVP----KISKMDRTSILADTIDYMKELLDK  230 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP----~~~K~dKaSIL~~AI~YIk~Lq~~  230 (349)
                      ++.+|+.+||+||++||..|..|++|||    ...|+||++||..||+|||.|+..
T Consensus        13 ~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            4679999999999999999999999999    578999999999999999999853

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

Probab=98.45  E-value=3.6e-08  Score=75.51  Aligned_cols=46  Identities=26%  Similarity=0.395  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHH
Q 018897          184 LMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLD  229 (349)
Q Consensus       184 ~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~  229 (349)
                      +..||+|+..||+.|..||.+||..   .|++|..+|..||+||..||.
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            3568899999999999999999964   689999999999999999984

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

Probab=98.34  E-value=7e-07  Score=70.86  Aligned_cols=48  Identities=25%  Similarity=0.497  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 018897          191 RKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDKISSLQQEI  238 (349)
Q Consensus       191 R~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~  238 (349)
                      |..||+++..|..|||..    .|.+|++||..|++||+.||++++.+.++.
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            889999999999999964    578999999999999999999988887643

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

Probab=97.86  E-value=1.9e-05  Score=64.36  Aligned_cols=48  Identities=29%  Similarity=0.405  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHhHhcCCC---CCCCCchhhHHHHHHHHHHHHHHHHH
Q 018897          186 AERRRRKRLNDRLSMLRSIVPK---ISKMDRTSILADTIDYMKELLDKISS  233 (349)
Q Consensus       186 aER~RR~kin~~~~~LrslvP~---~~K~dKaSIL~~AI~YIk~Lq~~v~~  233 (349)
                      .||.|=..+|+.|..||.+||.   ..|++|..+|.-||+||+.|++-++.
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            3567778999999999999996   36899999999999999999987653

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

Probab=96.70  E-value=0.019  Score=43.93  Aligned_cols=66  Identities=11%  Similarity=0.210  Sum_probs=51.6

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|.++||+|.+|..+|-+.|..|.+.+.....+...-.+..+..   .....+.|.++|.+..
T Consensus         5 ~~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~---~~~~l~~l~~~L~~~~   70 (91)
T 1zpv_A            5 KAIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSD---EKQDFTYLRNEFEAFG   70 (91)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES---SCCCHHHHHHHHHHHH
T ss_pred             eEEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeC---CCCCHHHHHHHHHHHH
Confidence            46799999999999999999999999999999888877633333333332   2457789999998765

>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=95.99  E-value=0.025  Score=49.59  Aligned_cols=65  Identities=14%  Similarity=0.117  Sum_probs=50.9

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|+++||++..|..+|.+.|++|+.+.+.+..+..+..+.+...  .  ...+.|+++|...+
T Consensus         6 ~~~itv~~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~~--~--~~~~~l~~~L~~~~   70 (192)
T 1u8s_A            6 HLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGS--P--SNITRVETTLPLLG   70 (192)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEEC--H--HHHHHHHHHHHHHH
T ss_pred             EEEEEEEcCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEecC--C--CCHHHHHHHHHHHH
Confidence            36799999999999999999999999999999999887743334444332  1  25678888888765

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

Probab=95.34  E-value=0.045  Score=48.50  Aligned_cols=68  Identities=15%  Similarity=0.208  Sum_probs=48.3

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|++++|++..|..+|.++|+.|+.+.+.+..+ |.+ .+.............+.|+++|...+
T Consensus         5 ~~~ltv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m-~~~v~~~~~~~~~~~~~l~~~L~~~~   73 (195)
T 2nyi_A            5 SFVVSVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFAM-IVLVSLNAKDGKLIQSALESALPGFQ   73 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEE-EEEEEESSSSSHHHHHHHHHHSTTCE
T ss_pred             EEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEE-EEEEEecCccchhHHHHHHHHHHHHH
Confidence            467999999999999999999999999999999998776 444 33333211100001566777765443

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

Probab=94.92  E-value=0.18  Score=37.75  Aligned_cols=39  Identities=13%  Similarity=0.185  Sum_probs=35.2

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND  312 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d  312 (349)
                      .+.|.|.+.++||+|.+|..+|.+.|+.|.+..+...++
T Consensus         5 ~~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~   43 (88)
T 2ko1_A            5 LAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDG   43 (88)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSS
T ss_pred             EEEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCC
Confidence            457888999999999999999999999999998887666

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

Probab=94.67  E-value=0.097  Score=46.31  Aligned_cols=65  Identities=15%  Similarity=0.148  Sum_probs=49.7

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC------C-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN------D-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~------d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      ....|.|.|+++||++..|-..|-++|+.|..+.+.+.+      + |.+.... ...   .... ++|+++|...+
T Consensus        92 ~~~iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~-~~~---~~~~-~~l~~~l~~~a  163 (195)
T 2nyi_A           92 REYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRV-AFP---FPLY-QEVVTALSRVE  163 (195)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEE-EEE---GGGH-HHHHHHHHHHH
T ss_pred             cEEEEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEE-EcC---CCcc-HHHHHHHHHHH
Confidence            456899999999999999999999999999999999886      2 3333222 211   1335 88999998765

>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=93.86  E-value=0.31  Score=42.45  Aligned_cols=66  Identities=9%  Similarity=0.061  Sum_probs=50.3

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC------C---eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN------D---FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~------d---~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      ....|.|.|++++|++..|.++|.+.|++|..+...+.+      +   |.+... ...   ....+.+.|+++|...+
T Consensus        92 ~~~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~-~~~---~~~~~~~~l~~~l~~~~  166 (192)
T 1u8s_A           92 YTVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAIS-ARV---DSGCNLMQLQEEFDALC  166 (192)
T ss_dssp             EEEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEE-EEE---CTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEE-EeC---CCCCCHHHHHHHHHHHH
Confidence            456899999999999999999999999999999998875      1   222222 111   12457889999998765

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

Probab=91.32  E-value=0.44  Score=46.10  Aligned_cols=67  Identities=7%  Similarity=0.070  Sum_probs=50.9

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|++|||+...|...|-++|..|+.++.+..++..+-.......  ....+.++|+.+|...+
T Consensus        12 ~~~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~--~~~~~~~~l~~~l~~~~   78 (415)
T 3p96_A           12 SVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCP--ADVADGPALRHDVEAAI   78 (415)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEEC--HHHHTSHHHHHHHHHHH
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEec--CCcCCHHHHHHHHHHHH
Confidence            46799999999999999999999999999999999888833333233321  11234578988887764

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

Probab=89.77  E-value=1.7  Score=41.45  Aligned_cols=66  Identities=15%  Similarity=0.193  Sum_probs=50.3

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--ND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.+.|++++|+...|-..|-+.|+.|+.++....  ++ |.+.+. ...  .....+.++|+++|...+
T Consensus        22 ~~iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~FfMr~~-~~~--~~~~~~~~~L~~~l~~la   90 (302)
T 3o1l_A           22 TFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHE-IRA--DTLPFDLDGFREAFTPIA   90 (302)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEEEEEE-EEG--GGSSSCHHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEEEEEE-Eec--CCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999999999999999888865  34 444332 222  122467889999987654

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

Probab=89.30  E-value=0.59  Score=38.87  Aligned_cols=36  Identities=22%  Similarity=0.409  Sum_probs=33.1

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN  311 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~  311 (349)
                      .|+|.|.+|+|+|.+|+++|-+.++++...++...+
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            589999999999999999999999999999887663

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

Probab=88.76  E-value=2  Score=40.56  Aligned_cols=65  Identities=8%  Similarity=-0.020  Sum_probs=49.8

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--ND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|++++|+...|-..|-+.|+.|..++..+.  ++ |.+.+. .... .  ..+.++|+++|...+
T Consensus         8 ~~vLtv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~-~~~~-~--~~~~~~L~~~f~~la   75 (286)
T 3n0v_A            8 TWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVE-FRQP-D--DFDEAGFRAGLAERS   75 (286)
T ss_dssp             CEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEE-EECC-S--SCCHHHHHHHHHHHH
T ss_pred             cEEEEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeEEEEE-EecC-C--CCCHHHHHHHHHHHH
Confidence            4679999999999999999999999999999888742  33 444332 2221 1  477899999997755

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

Probab=87.46  E-value=2.3  Score=40.17  Aligned_cols=66  Identities=14%  Similarity=0.168  Sum_probs=49.4

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--ND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.+.|++++|+...|-..|-+.|+.|..++..+.  ++ |.+.+. ...  .....+.++|+++|...+
T Consensus         6 ~~iLtv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~-~~~--~~~~~~~~~L~~~f~~la   74 (288)
T 3obi_A            6 QYVLTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVV-FNA--AAKVIPLASLRTGFGVIA   74 (288)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEE-EEE--SSCCCCHHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEE-EEc--CCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999999999999998887632  33 444332 222  122467899999997755

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

Probab=87.24  E-value=2.2  Score=40.46  Aligned_cols=68  Identities=10%  Similarity=0.222  Sum_probs=48.4

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee--eCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC--FND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt--~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.+.|++++|+...|-..|-+.|+.|+.++..+  .++ |.+.+. ..........+.++|+++|...+
T Consensus        10 ~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~-~~~~~~~~~~~~~~L~~~f~~la   80 (292)
T 3lou_A           10 QFVLTLSCPSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFFVRCV-FHATDDADALRVDALRREFEPIA   80 (292)
T ss_dssp             EEEEEEEEESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEE-EEECC----CCHHHHHHHHHHHH
T ss_pred             cEEEEEEcCCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceEEEEE-EEccCcccCCCHHHHHHHHHHHH
Confidence            467999999999999999999999999999988874  233 444332 22110011367889999987654

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

Probab=80.19  E-value=5.5  Score=37.56  Aligned_cols=64  Identities=20%  Similarity=0.204  Sum_probs=45.5

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee--eCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC--FND-FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt--~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.+.|++++|+...|-..|-+.|+.|+.++..+  .++ |.+.+. ....  .  .+.++|+++|...+
T Consensus         7 ~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~-~~~~--~--~~~~~L~~~f~~la   73 (287)
T 3nrb_A            7 QYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVS-VEIP--V--AGVNDFNSAFGKVV   73 (287)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEE-EECC--C-----CHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCCEEeeeeeecCCCCeEEEEEE-EEcC--C--CCHHHHHHHHHHHH
Confidence            467999999999999999999999999999988863  233 444332 2221  1  23448888887654

---

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	349
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-12
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	7e-12
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-11
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	2e-11
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	3e-11
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	5e-11
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	6e-10
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	9e-10

>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 = 60.1 bits (146), Expect = 1e-12
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 191 RKRLNDRLSMLRSIVPKI-SKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
           R  +ND++  L+ +V    +KM ++ +L   IDY+K L      L+QE   
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMV 51

>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 = 58.7 bits (142), Expect = 7e-12
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP--KISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239
             ER+RR  + D    LR  VP  +  K  R  IL    +Y++ +  K  + QQ+I 
Sbjct: 8   ALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 64

>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 = 57.6 bits (139), Expect = 1e-11
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKIS---KMDRTSILADTIDYMKELLDKISSLQQEIQA 240
           + ER+RR  L      LR  +P++    K  +  IL     Y+  +  +   L  E   
Sbjct: 12  VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL 70

>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 = 56.8 bits (137), Expect = 2e-11
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP-------KISKMDRTSILADTIDYMKELLDKISS 233
            AE+ RR RL   L  L S++P         +   + + +     Y++ L    S+
Sbjct: 8   HAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST 63

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

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

 Score = 56.8 bits (137), Expect = 3e-11
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKISKMDRTS---ILADTIDYMKELLDKISSLQQEIQA 240
             E+ RR  L   L  L+ +VP      R +   +L     ++K+L D       +I  
Sbjct: 7   EMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQ 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 = 56.1 bits (135), Expect = 5e-11
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 185 MAERRRRKRLNDRLSMLRSIVP-KISKMDRTSILADTIDYMKELLDKISSLQQEIQA 240
             E+R R  +ND++  L+ +V    +K++++++L   IDY++ L      L+QE  +
Sbjct: 12  AIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLS 68

>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 = 52.6 bits (126), Expect = 6e-10
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 167 LERKSRNKKLGGQPSKNLMAERRRRKRLNDRLSMLRSIVP--KISKMDRTSILADTIDYM 224
           L+RK+ N     +     M ERRR  ++N+    L+         ++ +  IL + I Y+
Sbjct: 3   LKRKTTNAD---RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYI 59

Query: 225 KELLDKI 231
           + L   +
Sbjct: 60  EGLQALL 66

>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 = 52.1 bits (125), Expect = 9e-10
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 6/49 (12%)

Query: 185 MAERRRRKRLNDRLSMLRSIVPKI------SKMDRTSILADTIDYMKEL 227
             ERRRR ++N+ +  L  I+P        S   +  IL+   DY++EL
Sbjct: 11  EVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	349
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.46
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.41
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.4
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.4
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.36
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.27
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	97.09
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.43
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	96.26
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	93.4
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	91.82
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	89.34
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	82.85

>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=99.47  E-value=2.2e-14  Score=111.02  Aligned_cols=62  Identities=26%  Similarity=0.453  Sum_probs=56.9

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI-SKMDRTSILADTIDYMKELLDKISSLQQEIQA  240 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~-~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~  240 (349)
                      .+..|+++||+||.+||+.|..|++|||+. .|++|++||..||+||+.|+++++.|.++.+.
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~   68 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLS   68 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356899999999999999999999999974 68999999999999999999999999987654

>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=99.46  E-value=1.4e-14  Score=107.56  Aligned_cols=53  Identities=23%  Similarity=0.354  Sum_probs=49.0

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCC-------CCCCCchhhHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK-------ISKMDRTSILADTIDYMKELLDKI  231 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~-------~~K~dKaSIL~~AI~YIk~Lq~~v  231 (349)
                      ++..|+++||+||.+||+.|..|++|||.       ..|++|++||..||+||+.||+++
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       478999999999999999999875

>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=99.45  E-value=5.7e-14  Score=108.22  Aligned_cols=61  Identities=26%  Similarity=0.268  Sum_probs=55.8

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKISSLQQEIQA  240 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~  240 (349)
                      +..|+.+||+||.+||+.|..|+++||..   .|++|++||..||+||+.|+.+++.|..+++.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   65 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQ   65 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999963   58999999999999999999999999887654

>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=99.41  E-value=8.8e-14  Score=108.06  Aligned_cols=61  Identities=30%  Similarity=0.452  Sum_probs=56.3

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDKISSLQQEIQA  240 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~  240 (349)
                      +..|+.+||+||.+||+.|..|+++||+  ..|++|++||..||+||+.|++++..|..+.+.
T Consensus         3 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   65 (83)
T d1nkpb_           3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD   65 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999995  478999999999999999999999999987654

>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=99.40  E-value=1.9e-14  Score=108.53  Aligned_cols=54  Identities=22%  Similarity=0.418  Sum_probs=49.6

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC--CCCCchhhHHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI--SKMDRTSILADTIDYMKELLDKIS  232 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~--~K~dKaSIL~~AI~YIk~Lq~~v~  232 (349)
                      ++..|+..||+||.+||+.|..|+++||..  .|++|++||..||+||++|++.|+
T Consensus        12 rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            457899999999999999999999999974  588999999999999999998764

>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=99.40  E-value=1.3e-13  Score=108.15  Aligned_cols=62  Identities=23%  Similarity=0.323  Sum_probs=56.3

Q ss_pred             CccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       180 ~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      +..|+.+||+||.+||+.|..|+++||+.   .|++|++||..||+||+.|+++++.|..+++..
T Consensus         7 R~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   71 (88)
T d1nkpa_           7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999963   679999999999999999999999998876543

>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=99.36  E-value=2.4e-13  Score=101.40  Aligned_cols=53  Identities=30%  Similarity=0.513  Sum_probs=48.3

Q ss_pred             CCccchHHHHHHHHHHHHHHHHhHhcCCCC------CCCCchhhHHHHHHHHHHHHHHH
Q 018897          179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI------SKMDRTSILADTIDYMKELLDKI  231 (349)
Q Consensus       179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~------~K~dKaSIL~~AI~YIk~Lq~~v  231 (349)
                      ++..|+.+||+||.+||+.|..|+++||..      .|++|++||..||+||+.||++.
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            467899999999999999999999999953      48999999999999999998753

>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=99.27  E-value=1e-12  Score=96.86  Aligned_cols=51  Identities=31%  Similarity=0.458  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHhHhcCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897          191 RKRLNDRLSMLRSIVPKI-SKMDRTSILADTIDYMKELLDKISSLQQEIQAG  241 (349)
Q Consensus       191 R~kin~~~~~LrslvP~~-~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~  241 (349)
                      |++||++|..||++||+. .|+||++||.+||+||+.|+++++.|+++....
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            678999999999999985 699999999999999999999999999977543

>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=97.09  E-value=0.0028  Score=47.16  Aligned_cols=65  Identities=11%  Similarity=0.224  Sum_probs=52.1

Q ss_pred             eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      +.|.+.|++|||++..|...|-+.|..|...+....++.-.-......   ....+.++|+.+|...+
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~---~~~~~~~~l~~~l~~la   67 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSS---DEKQDFTYLRNEFEAFG   67 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE---SSCCCHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEE---ecCCCHHHHHHHHHHHH
Confidence            568999999999999999999999999999999888873333333333   23457889999998866

>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=96.43  E-value=0.0076  Score=45.13  Aligned_cols=66  Identities=14%  Similarity=0.115  Sum_probs=52.3

Q ss_pred             CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      ..+.|.+.|++|||++.+|...|-+.|..|..+....+++...-...++..    .-+.+.++.+|.+.+
T Consensus         4 ~~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~----~~~~~~l~~~L~~l~   69 (86)
T d1u8sa1           4 QHLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGS----PSNITRVETTLPLLG   69 (86)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEEC----HHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcC----cccHHHHHHHHHHHH
Confidence            356799999999999999999999999999999999999844444444432    124678888888765

>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=96.26  E-value=0.021  Score=43.21  Aligned_cols=65  Identities=9%  Similarity=0.053  Sum_probs=49.3

Q ss_pred             eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC---------eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897          274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND---------FAMQASCSEGVEQRETLSCEDIKQALFRNA  342 (349)
Q Consensus       274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d---------~vl~a~~se~~e~~~~is~edIkqaL~~~~  342 (349)
                      .+.|.|.|++|||++.+|-..|-++|+.|...+..+...         |.+++...-    ....+.++|+++|...+
T Consensus         6 tv~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~----p~~~~~~~l~~~l~~l~   79 (93)
T d1u8sa2           6 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARV----DSGCNLMQLQEEFDALC   79 (93)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEE----CTTSCHHHHHHHHHHHH
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEc----CccccHHHHHHHHHHHH
Confidence            467889999999999999999999999999877665431         444443222    12467889999998765

>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=93.40  E-value=0.25  Score=35.47  Aligned_cols=46  Identities=26%  Similarity=0.245  Sum_probs=38.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeee
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSE  321 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se  321 (349)
                      .|.|..+++||.|.+++++|.+.|+.|........+++.+-.+..+
T Consensus         1 ViaV~v~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~vd   46 (71)
T d2f06a1           1 VVGISCPNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRPS   46 (71)
T ss_dssp             EEEEEEESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEES
T ss_pred             CEEEEecCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEEC
Confidence            3677789999999999999999999999888888788766555443

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

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

Probab=91.82  E-value=0.61  Score=33.44  Aligned_cols=56  Identities=18%  Similarity=0.202  Sum_probs=42.8

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHH
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALF  339 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~  339 (349)
                      .|.|..+++||.|.++...|...|+.|...++....++.+--+.+.        .++...+.|.
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Riiv~--------~~e~a~~~L~   60 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGILRGIVS--------DPDKAYKALK   60 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEEES--------CHHHHHHHHH
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEEEEC--------ChHHHHHHHH
Confidence            4788899999999999999999999999888888777655433222        4555555553

>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=89.34  E-value=0.13  Score=37.65  Aligned_cols=34  Identities=21%  Similarity=0.142  Sum_probs=27.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee
Q 018897          276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC  309 (349)
Q Consensus       276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt  309 (349)
                      -|.|.|.+|+|+|.+|..++-+.|..|.+.+...
T Consensus         3 ~i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~   36 (77)
T d1y7pa2           3 GLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFL   36 (77)
T ss_dssp             EEEEEEECCTTHHHHHHHHCC----CEEEEEEEE
T ss_pred             eEEEEEecCCChHHHHHHHHHHcCCCeEEEEeec
Confidence            4889999999999999999999999999888765

>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=82.85  E-value=2.6  Score=30.49  Aligned_cols=48  Identities=13%  Similarity=0.212  Sum_probs=37.6

Q ss_pred             ceeeeeecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCe
Q 018897          265 KFDVERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDF  313 (349)
Q Consensus       265 ~VeV~~~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~  313 (349)
                      .|+....+ ..+|-|.-.++||+|.+|..+|-+.|+.|.+....+.++.
T Consensus         3 ~v~l~~~~-~~rl~i~~~d~PGvla~I~~~l~~~~iNI~~~~~~~~~~~   50 (84)
T d1sc6a3           3 EVSLPLHG-GRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQM   50 (84)
T ss_dssp             CCCCCCCS-SEEEEEEEESCTTHHHHHHHHHHHTTCEEEEEEEEECSSE
T ss_pred             CccCCCCC-CeEEEEEeCCcCCHHHHHHHHHHHcCCCHHHhccccCCCC
Confidence            34444333 3567777789999999999999999999998888887763