Citrus Sinensis ID: 039361

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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---
Protein Sequence
MIRKMAPTVLVHQFEHSDDPFPFHYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSIK
Secondary Structure (PSIPRED)
ccccccccEEEEEccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEccccEEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEccccccccccHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cHHccccEEEEEEEccccccccccccccHHHcccccHHHHcccHHEEEccccccccccccccEEEEEcccccccccccccccccEHHHHHHHHHHHHHHHHHHHHHHcccHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEccccEEEEEEEcccccccccHHHHHHHHHHcccEEEEEEEEEEcccEEEEEEEEEccccccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mirkmaptvlvhqfehsddpfpfhynpyqehsniqqDQILQGQALLERninsskmgkgqqHKLLFVATTkvndgnsdnnnnkkMILRKDIERQRRQHLSMLHASLRSLlplqsitgkrsiSDHINEARNYINYLNKNIQELGLkrdklknlselgavghgssnwdnclqncvtihpysgGVEIVINSVHKEENLKLSKVMEAVLEEGLDVircastqtdegFFHTIQAeesqvgdltcVDLRVLQLKLDHSIK
Flexible Loop (DISEMBL)
MIRKMAPTVLVHQFEHSDDPFPFHYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATtkvndgnsdnnnnkkmilRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAeesqvgdltCVDLRVLQlkldhsik
Low Complexity Region (SEG)
MIRKMAPTVLVHQFEHSDDPFPFHYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATTKVndgnsdnnnnKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSIK
Disordered region (IsUnstruct)
*********LVHQF******FPFHYNPY**********************************LLFVAT************************************LRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKL*****
Disordered Region (DISOPRED)
******P*************************************************************************************QRRQHLSMLHASLRSLLPL**********DHINEARNYINYL******************************************YSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSI*
Disordered Region (DISEMBL)
MIRKMAPTVLVHQFEHSDDPFPFHYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSIK
Disordered Region (DISPRO)
MIRKMAPTVLVHQFEHSDDPFPFHYNPYQEHSNIQQDQILQGQALLERNINSS**GKGQQHKLLFVATTK***********KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLS***************LQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSIK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIRKMAPTVLVHQFEHSDDPFPFHYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYxxxxxxxxxxxxxxxxxxxxxSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSIK
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	253	2.2.26 [Sep-21-2011]
Q9STJ6	221	Transcription factor bHLH	yes	no	0.671	0.769	0.396	1e-25
Q9STJ7	163	Transcription factor bHLH	no	no	0.588	0.914	0.401	6e-22
Q9FLI1	174	Transcription factor bHLH	no	no	0.644	0.936	0.368	2e-21
Q9FLI0	204	Transcription factor bHLH	no	no	0.660	0.818	0.365	2e-21
Q9LQ08	259	Transcription factor bHLH	no	no	0.715	0.698	0.336	3e-18
Q9LN95	257	Transcription factor bHLH	no	no	0.667	0.657	0.340	4e-18

>sp|Q9STJ6|BH126_ARATH Transcription factor bHLH126 OS=Arabidopsis thaliana GN=BHLH126 PE=2 SV=1

 Score =  116 bits (291), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 71/179 (39%), Positives = 106/179 (59%), Gaps = 9/179 (5%)

Query: 76  SDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLN 135
           +D+N  KK +L +DIERQRRQ ++ L A+LR+ LPL+ I GKR++SDH+N A N+I    
Sbjct: 36  TDDNKKKKKLLHRDIERQRRQEMATLFATLRTHLPLKYIKGKRAVSDHVNGAVNFIKDTE 95

Query: 136 KNIQELGLKRDKLKNLSELGA-----VGHGSSNWDNCLQNCVTIHPYSGGVEIVINS-VH 189
             I+EL  +RD+L   +  G       G   S+        V + P+  G+E+V++S   
Sbjct: 96  ARIKELSARRDELSRETGQGYKSNPDPGKTGSDVGKSEPATVMVQPHVSGLEVVVSSNSS 155

Query: 190 KEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKL 248
             E L LSKV+E + E+GL+V+   +T+ ++   HTIQ E +  G   C+DL  LQ KL
Sbjct: 156 GPEALPLSKVLETIQEKGLEVMSSFTTRVNDRLMHTIQVEVNSFG---CIDLLWLQQKL 211

Arabidopsis thaliana (taxid: 3702)

>sp|Q9STJ7|BH118_ARATH Transcription factor bHLH118 OS=Arabidopsis thaliana GN=BHLH118 PE=2 SV=1

 Score =  104 bits (260), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/157 (40%), Positives = 92/157 (58%), Gaps = 8/157 (5%)

Query: 85  ILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLK 144
           ++ K+IE++RRQ ++ L+ASLRSLLPL+ I GKRS SD +  A NYI+YL +NI+++  K
Sbjct: 4   LVHKEIEKRRRQEMASLYASLRSLLPLEFIQGKRSTSDQVKGAVNYIDYLQRNIKDINSK 63

Query: 145 RDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVL 204
           RD L  LS           W N + N V I P   G+EIV++ +        S V++ + 
Sbjct: 64  RDDLVLLSGRSFRSSNEQEW-NEISNHVVIRPCLVGIEIVLSILQT----PFSSVLQVLR 118

Query: 205 EEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDL 241
           E GL V+    +  ++   HT+QAE   V DL  +DL
Sbjct: 119 EHGLYVLGYICSSVNDRLIHTLQAE---VNDLALIDL 152

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLI1|BH036_ARATH Transcription factor bHLH36 OS=Arabidopsis thaliana GN=BHLH36 PE=2 SV=1

 Score =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 63/171 (36%), Positives = 102/171 (59%), Gaps = 8/171 (4%)

Query: 85  ILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLK 144
           ++ ++ ERQRRQ ++ L+ASLRSLLPL  I GKRS SD +NEA NYI YL + I+EL ++
Sbjct: 4   MMHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKELSVR 63

Query: 145 RDKLKNLSELGAVGHGSSNWDNCLQ-----NCVTIHPYSGGVEIVINSVHKEENLKLSKV 199
           RD L  LS    +G  + ++   ++     N V +     GVEI+++S       + S V
Sbjct: 64  RDDLMVLSRGSLLGSSNGDFKEDVEMISGKNHVVVRQCLVGVEIMLSSRCCGGQPRFSSV 123

Query: 200 MEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVG---DLTCVDLRVLQLK 247
           ++ + E GL ++   S+  D+   +TIQAE + +    DL  ++ R++++K
Sbjct: 124 LQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMIDLAELEKRLIRMK 174

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLI0|BH120_ARATH Transcription factor bHLH120 OS=Arabidopsis thaliana GN=BHLH120 PE=2 SV=2

 Score =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 100/178 (56%), Gaps = 11/178 (6%)

Query: 77  DNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNK 136
           D    +K +L ++IERQRRQ +++L ASLRS LPL+ I GKR++SDH+N A ++I     
Sbjct: 21  DETKKEKKLLHRNIERQRRQEMAILFASLRSQLPLKYIKGKRAMSDHVNGAVSFIKDTQT 80

Query: 137 NIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQN-----CVTIHPYSGGVEIVINSVHKE 191
            I++L  +RD+LK   E+G     + +      +      V + P   G E+V++S+   
Sbjct: 81  RIKDLSARRDELKR--EIGDPTSLTGSGSGSGSSRSEPASVMVQPCVSGFEVVVSSLASG 138

Query: 192 -ENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKL 248
            E   LS+V+E +  +GL+VI   + + +E   +TIQ E   V    C DL  LQ KL
Sbjct: 139 LEAWPLSRVLEVLHGQGLEVISSLTARVNERLMYTIQVE---VNSFDCFDLAWLQQKL 193

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ08|BH125_ARATH Transcription factor bHLH125 OS=Arabidopsis thaliana GN=BHLH125 PE=2 SV=1

 Score = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 103/205 (50%), Gaps = 24/205 (11%)

Query: 52  SSKMGKGQQHKLLFVATTKVNDGN-SDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLP 110
           ++K+G   + + L   T   N+ N +D++   K +  +DIERQRRQ +S L   LR+LLP
Sbjct: 42  TNKIGGSNKKRSLCDITYGANEANKNDDDRESKKMKHRDIERQRRQEVSSLFKRLRTLLP 101

Query: 111 LQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGS--------- 161
            Q I GKRS SDHI +A NYI  L   I+EL  KR+++K +       H +         
Sbjct: 102 FQYIQGKRSTSDHIVQAVNYIKDLQIKIKELNEKRNRVKKVISATTTTHSAIEECTSSLS 161

Query: 162 -------SNWDNCLQN---CVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVL-EEGLDV 210
                  S+  +C+ +    V + P   GVEI+I+         LS V++ +  E+   V
Sbjct: 162 SSAASTLSSSCSCVGDKHITVVVTPCLVGVEIIISCCLGRNKSCLSSVLQMLAQEQRFSV 221

Query: 211 IRCASTQTDEGFFHTIQAEESQVGD 235
           + C S +  + F HTI    SQV D
Sbjct: 222 VSCLSARRQQRFMHTIV---SQVED 243

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LN95|BH055_ARATH Transcription factor bHLH55 OS=Arabidopsis thaliana GN=BHLH55 PE=2 SV=1

 Score = 92.0 bits (227), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 62/182 (34%), Positives = 105/182 (57%), Gaps = 13/182 (7%)

Query: 58  GQQHKLLFVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGK 117
           G+Q+    +  +++  G+ +  N +     K++ERQRRQ  + L   LR LLP Q I GK
Sbjct: 52  GRQNCETTMTLSEIMKGDDEPKNKRAK--HKELERQRRQENTSLFKILRYLLPSQYIKGK 109

Query: 118 RSISDHINEARNYINYLNKNIQELGLKRDKLK-NLSELGAVGHGS-----SNWDNCLQN- 170
           RS +DH+ EA NYI  L K I+E+  KRD++K +++   + G  S     S+  +C+ + 
Sbjct: 110 RSSADHVLEAVNYIKDLQKKIKEVSEKRDRIKRSITHPSSRGEFSIRSLASSTCSCVGDT 169

Query: 171 --CVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVL-EEGLDVIRCASTQTDEGFFHTIQ 227
              V + P   G+EIV++  ++ E+  LS V++ +  E+  +++ C ST+  +GF HTI 
Sbjct: 170 NIAVVVRPCLIGLEIVVSCCNRHESC-LSSVLQLLAQEQCFNIVSCISTRLHQGFIHTIA 228

Query: 228 AE 229
           +E
Sbjct: 229 SE 230

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	253
255539627	243	DNA binding protein, putative [Ricinus c	0.873	0.909	0.448	2e-43
224122512	243	predicted protein [Populus trichocarpa]	0.920	0.958	0.458	1e-42
224134615	247	predicted protein [Populus trichocarpa]	0.905	0.927	0.462	3e-41
224122516	240	predicted protein [Populus trichocarpa]	0.877	0.925	0.441	5e-40
225455629	204	PREDICTED: transcription factor bHLH120	0.703	0.872	0.5	4e-39
224134607	246	predicted protein [Populus trichocarpa]	0.743	0.764	0.466	5e-39
296084086	231	unnamed protein product [Vitis vinifera]	0.830	0.909	0.428	4e-36
147810508	196	hypothetical protein VITISV_004405 [Viti	0.723	0.933	0.494	4e-36
359490223	195	PREDICTED: transcription factor bHLH120-	0.719	0.933	0.489	2e-35
147843674	254	hypothetical protein VITISV_043103 [Viti	0.731	0.728	0.451	5e-35

>gi|255539627|ref|XP_002510878.1| DNA binding protein, putative [Ricinus communis] gi|223549993|gb|EEF51480.1| DNA binding protein, putative [Ricinus communis]

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 110/245 (44%), Positives = 149/245 (60%), Gaps = 24/245 (9%)

Query: 21  FPF----HYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATTKVNDGNS 76
           FP+     ++P        QD I   Q L E++++SS + +  Q  ++          NS
Sbjct: 2   FPYDQNNRFSPQAIFFYPHQDIIQDNQILGEKSVDSSNLDQEGQIPIIL--------SNS 53

Query: 77  DNNNN------KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNY 130
           + NN+      +K I+RK+IERQRRQ +S LHASLRSLLPL+S+ GKRS+SDHINEA  Y
Sbjct: 54  NTNNDVNLACVEKKIIRKEIERQRRQQMSTLHASLRSLLPLESLKGKRSMSDHINEAAKY 113

Query: 131 INYLNKNIQELGLKRDKLKNLSELGAVGHG---SSNWDNCLQNCVTIHPYSGGVEIVINS 187
           I +L  N+QEL  KRDKLKNLS   +  HG    S  D  + + V++  Y GGVEIVI+ 
Sbjct: 114 IKHLRSNVQELSAKRDKLKNLSNSSSYEHGINYESAHDTFMNSIVSVRSYLGGVEIVISC 173

Query: 188 VHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLK 247
              +EN  LS+V+EAV+EEG DV+ C ST++D+  ++TIQ    Q    T VDL  LQ K
Sbjct: 174 DSGDENFLLSRVLEAVIEEGFDVVSCISTKSDQRIYNTIQC---QANHNTYVDLAALQQK 230

Query: 248 LDHSI 252
           L+  I
Sbjct: 231 LNDVI 235

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122512|ref|XP_002318855.1| predicted protein [Populus trichocarpa] gi|222859528|gb|EEE97075.1| predicted protein [Populus trichocarpa]

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 110/240 (45%), Positives = 147/240 (61%), Gaps = 7/240 (2%)

Query: 15  EHSDDPFP-FHYNPYQEHSNIQQDQILQGQALLERNINSS-KMGKGQQHKLLFVATTKVN 72
           ++SD+ +P    NPYQE        ++ GQ  L    N +  + + Q+HK+L  AT+K N
Sbjct: 6   QNSDEFWPQIFSNPYQEDIGKDFQDLIYGQDSLHGISNQTISVDEIQKHKIL--ATSKAN 63

Query: 73  DGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYIN 132
           D +     ++K I RK+IERQRRQH+S LHASLR+LLPL+SI GKRSISDH+NEA  YI 
Sbjct: 64  DHSGKIIRDEKKIARKEIERQRRQHISTLHASLRNLLPLESIKGKRSISDHMNEAAKYIK 123

Query: 133 YLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEE 192
           +L+ NI+EL  KRDK K LS       G+    + L + V + PY GGVEIV++    EE
Sbjct: 124 HLSSNIRELSAKRDKFKKLSNSSTFEQGTEISGHNLLDFVKVRPYLGGVEIVVSGGCGEE 183

Query: 193 NLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSI 252
              LS+V+EA+LEEG D +   STQ DE  + TIQ    Q  +  C+D   LQ KL+  I
Sbjct: 184 GFLLSRVLEALLEEGFDAVSYVSTQKDERHYTTIQC---QATNRNCIDSDGLQRKLNGVI 240

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134615|ref|XP_002321866.1| predicted protein [Populus trichocarpa] gi|222868862|gb|EEF05993.1| predicted protein [Populus trichocarpa]

 Score =  174 bits (441), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 111/240 (46%), Positives = 148/240 (61%), Gaps = 11/240 (4%)

Query: 14  FEHSDDPF--PFHYNPYQEHSNIQQDQILQGQALLE--RNINSSKMGK-GQQHKLLFVAT 68
           F+ S D F      NPYQE  +  Q QIL GQ  L    N+N+S + +  Q H +L  AT
Sbjct: 4   FQQSYDEFWSQISSNPYQEDIDQDQHQIL-GQDSLHGISNLNNSSVEEVPQAHTIL--AT 60

Query: 69  TKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEAR 128
           +  ND + +   ++K + RK+IERQRRQ +S LHASLR+LLP  SI G+RSISDH++EA 
Sbjct: 61  SNANDDSGNIRCDEKKVARKEIERQRRQQMSTLHASLRNLLPPDSIKGRRSISDHMSEAV 120

Query: 129 NYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSV 188
             I +L  NIQ+L +KRDKLKNLS      HG+   D+ L + VT+  Y  G+EIV+   
Sbjct: 121 KCIKHLKSNIQDLSVKRDKLKNLSSSSTFEHGTEISDHNLLDSVTVRHYLDGLEIVLTRG 180

Query: 189 HKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKL 248
             EE + LS+V+EAVLEEG DV+ C STQ  +  + TIQ    Q  +L C+D   L+ KL
Sbjct: 181 PGEEGILLSRVLEAVLEEGFDVVGCTSTQKGQRHYTTIQC---QASNLNCIDADRLKGKL 237

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122516|ref|XP_002318856.1| predicted protein [Populus trichocarpa] gi|222859529|gb|EEE97076.1| predicted protein [Populus trichocarpa]

 Score =  170 bits (430), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 146/229 (63%), Gaps = 7/229 (3%)

Query: 21  FPFHYNPYQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLLFVATTKVNDGNSDNNN 80
           F    +P+Q+H NI QD IL   A L+ +  ++KM   ++  L+ + +      +   NN
Sbjct: 12  FNISSDPHQQH-NIPQDLILARYAALQGSDTTNKMENDRRRFLISMDSNHEVARDHSKNN 70

Query: 81  NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQE 140
           NKKM+ R +IERQRRQ ++ L+ASLR+LLPL+ I GKRSISDH+NE+ NYI YL K I+E
Sbjct: 71  NKKMMHR-NIERQRRQEMTTLYASLRALLPLEFIKGKRSISDHMNESVNYIKYLQKKIKE 129

Query: 141 LGLKRDKLKNLSELGA-VGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKV 199
           L  KRD LK    L      GSSN  + + + VT+ PY GG+E+V +S  + ++  LS+V
Sbjct: 130 LSAKRDGLKKSPNLSFDSPSGSSNKYSPI-SPVTLQPYPGGIEVVFDSDFRGQDSPLSRV 188

Query: 200 MEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKL 248
           ++ +LEEG+ V+ C ST+ +E  FHT+Q E   V D  C++L  L+ KL
Sbjct: 189 LQVLLEEGISVVNCVSTKVNERLFHTVQTE---VNDPACLNLSELRQKL 234

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455629|ref|XP_002271172.1| PREDICTED: transcription factor bHLH120 [Vitis vinifera] gi|296084087|emb|CBI24475.3| unnamed protein product [Vitis vinifera]

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 92/184 (50%), Positives = 122/184 (66%), Gaps = 6/184 (3%)

Query: 65  FVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHI 124
            +AT   NDGN+   + K  I+R+D+ERQRRQ ++ L+ASLRSLLP++ I GKRSISDH+
Sbjct: 19  LLATPGDNDGNTSGGDRK--IMRRDMERQRRQEMANLNASLRSLLPIEYIKGKRSISDHM 76

Query: 125 NEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIV 184
           +EA NYIN L   IQ+LG KRD LK    + A    S + + C  NCV + P  GGVEI+
Sbjct: 77  HEAVNYINDLQMKIQDLGNKRDALKRQCNMSASHLESRSSEICPPNCVVVSPCLGGVEIL 136

Query: 185 INSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVL 244
           ++   +EE L LS+VME + EE L V+ C ST+ +EG  HTI     +V D +CVDL +L
Sbjct: 137 VSGGFREEGL-LSRVMELLFEERLSVVSCVSTKVNEGLLHTINC---KVADPSCVDLSML 192

Query: 245 QLKL 248
           Q KL
Sbjct: 193 QQKL 196

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134607|ref|XP_002321864.1| predicted protein [Populus trichocarpa] gi|222868860|gb|EEF05991.1| predicted protein [Populus trichocarpa]

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 91/195 (46%), Positives = 127/195 (65%), Gaps = 7/195 (3%)

Query: 55  MGKGQQHKLLFVATTKVNDGNSDNNNN-KKMILRKDIERQRRQHLSMLHASLRSLLPLQS 113
           M KG++  ++ +     N+   DNNNN KK ++ +DIERQRRQ ++ L+ASLR+LLPL+ 
Sbjct: 46  MEKGRRRNIISMDN---NEAARDNNNNSKKKMMHRDIERQRRQEMTTLYASLRALLPLEF 102

Query: 114 ITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVT 173
           I GKRSISDH+NEA NYI YL K I+E   KRD+LK LS+  +V   S   +    + V 
Sbjct: 103 IKGKRSISDHMNEAVNYIKYLQKKIKETSAKRDELKKLSDFSSVASPSGCSNKSSSSSVA 162

Query: 174 IHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQV 233
           + PY GG+EI  +S     +L LS+V++ +LEEG+ VI C ST+ +E  FH++Q E   V
Sbjct: 163 LQPYPGGIEITFDSDLMGRDLPLSRVLQVLLEEGISVINCVSTKVNERLFHSVQTE---V 219

Query: 234 GDLTCVDLRVLQLKL 248
            D TC++L  L  KL
Sbjct: 220 NDPTCLNLSELWQKL 234

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296084086|emb|CBI24474.3| unnamed protein product [Vitis vinifera]

 Score =  157 bits (397), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 102/238 (42%), Positives = 142/238 (59%), Gaps = 28/238 (11%)

Query: 29  QEHSNIQQDQILQGQALLERNINSSK--------------MGKGQQHKLLFVATTKVNDG 74
           +E+S IQ +Q        +RN+N+S               M K  + K++        + 
Sbjct: 3   REYSAIQSNQN-------KRNLNASTHSIAFGLGNNLPKNMEKSPRQKVVLTPGKNTENT 55

Query: 75  NSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYL 134
           +S N    K ILR+D+ERQRRQ ++ L+ASLRSLLPL+ + GKRSISDH++EA NYIN+L
Sbjct: 56  SSSN----KKILRRDMERQRRQEMANLNASLRSLLPLEYVKGKRSISDHMHEAVNYINHL 111

Query: 135 NKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENL 194
              IQ+LG KRD+L+N S + A    S +     ++CV + P   GVEI+I+   K E L
Sbjct: 112 QMKIQDLGTKRDELRNQSNMSACDSESGSSYKRSRHCVIVSPCMDGVEILISGGFK-EGL 170

Query: 195 KLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSI 252
            LSKVME +LEEGL V RC ST+ +EG  HT+  +  QV D T  DL  L+ KL +++
Sbjct: 171 LLSKVMEVLLEEGLGVHRCVSTKVNEGLLHTMNCK--QVSDPTGFDLCGLRQKLWNAV 226

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147810508|emb|CAN67627.1| hypothetical protein VITISV_004405 [Vitis vinifera]

 Score =  157 bits (397), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 93/188 (49%), Positives = 125/188 (66%), Gaps = 5/188 (2%)

Query: 65  FVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHI 124
            V T   N  N+ ++N K  ILR+D+ERQRRQ ++ L+ASLRSLLPL+ + GKRSISDH+
Sbjct: 9   VVLTPGKNTENTSSSNKK--ILRRDMERQRRQEMANLNASLRSLLPLEYVKGKRSISDHM 66

Query: 125 NEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIV 184
           +EA NYIN+L   IQ+LG KRD+L+N S + A    S +     ++CV + P   GVEI+
Sbjct: 67  HEAVNYINHLQMKIQDLGTKRDELRNQSNMSACDSESGSSYKRSRHCVIVSPCMDGVEIL 126

Query: 185 INSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVL 244
           I+   K E L LSKVME +LEEGL V RC ST+ +EG  HT+  +  QV D T  DL  L
Sbjct: 127 ISGGFK-EGLLLSKVMEVLLEEGLGVHRCVSTKVNEGLLHTMNCK--QVSDPTGFDLCGL 183

Query: 245 QLKLDHSI 252
           + KL +++
Sbjct: 184 RQKLWNAV 191

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359490223|ref|XP_002271208.2| PREDICTED: transcription factor bHLH120-like [Vitis vinifera]

 Score =  155 bits (391), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 92/188 (48%), Positives = 124/188 (65%), Gaps = 6/188 (3%)

Query: 65  FVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHI 124
            V T   N  N+ ++N K  ILR+D+ERQRRQ ++ L+ASLRSLLPL+ + GKRSISDH+
Sbjct: 9   VVLTPGKNTENTSSSNKK--ILRRDMERQRRQEMANLNASLRSLLPLEYVKGKRSISDHM 66

Query: 125 NEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIV 184
           +EA NYIN+L   IQ+LG KRD+L+N S + A    S +     ++CV + P   GVEI+
Sbjct: 67  HEAVNYINHLQMKIQDLGTKRDELRNQSNMSACDSESGSSYKRSRHCVIVSPCMDGVEIL 126

Query: 185 INSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVL 244
           I+   K E L LSKVME +LEEGL V RC ST+ +EG  HT+     +V D T  DL  L
Sbjct: 127 ISGGFK-EGLLLSKVMEVLLEEGLGVHRCVSTKVNEGLLHTMNC---KVSDPTGFDLCGL 182

Query: 245 QLKLDHSI 252
           + KL +++
Sbjct: 183 RQKLWNAV 190

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147843674|emb|CAN81995.1| hypothetical protein VITISV_043103 [Vitis vinifera]

 Score =  153 bits (387), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 88/195 (45%), Positives = 120/195 (61%), Gaps = 10/195 (5%)

Query: 65  FVATTKVNDGNSDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHI 124
            +AT   NDGN+   + K  I+R+D+ERQRRQ ++ L+ASLRSLLP++ I GKRSISDH+
Sbjct: 58  LLATPGDNDGNTSGGDRK--IMRRDMERQRRQEMANLNASLRSLLPIEYIKGKRSISDHM 115

Query: 125 NEARNYINYLNKNIQELGLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIV 184
           +EA NYIN L   IQ+LG KRD LK    + A    S + + C  NCV + P  GGVEI+
Sbjct: 116 HEAVNYINDLQMKIQDLGNKRDALKRQCNMSASHLESRSSEICPPNCVVVSPCLGGVEIL 175

Query: 185 INSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTI-------QAEESQVGDLT 237
           ++   +EE L  S+VME + EE L V+ C ST+ +EG  HTI       Q E S   + T
Sbjct: 176 VSGGFREEGLX-SRVMELLFEEXLSVVSCVSTKVNEGLLHTINCKVGLGQVERSIQPETT 234

Query: 238 CVDLRVLQLKLDHSI 252
              +   QL +++ I
Sbjct: 235 SFCMESFQLHIEYGI 249

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	253
TAIR|locus:2138019	163	AT4G25400 "AT4G25400" [Arabido	0.604	0.938	0.397	3.8e-23
TAIR|locus:2165311	174	AT5G51780 "AT5G51780" [Arabido	0.652	0.948	0.373	2.1e-22
TAIR|locus:504956298	259	AT1G62975 "AT1G62975" [Arabido	0.636	0.621	0.327	1.3e-12
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.573	0.763	0.273	6.8e-08
TAIR|locus:2040287	242	BHLH100 "basic helix-loop-heli	0.632	0.661	0.267	1.5e-05
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.549	0.560	0.298	0.00012
TAIR|locus:2080600	253	bHLH38 "basic helix-loop-helix	0.616	0.616	0.248	0.00028

TAIR|locus:2138019 AT4G25400 "AT4G25400" [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 64/161 (39%), Positives = 94/161 (58%)

Query:    85 ILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLK 144
             ++ K+IE++RRQ ++ L+ASLRSLLPL+ I GKRS SD +  A NYI+YL +NI+++  K
Sbjct:     4 LVHKEIEKRRRQEMASLYASLRSLLPLEFIQGKRSTSDQVKGAVNYIDYLQRNIKDINSK 63

Query:   145 RDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVL 204
             RD L  LS           W N + N V I P   G+EIV++ +        S V++ + 
Sbjct:    64 RDDLVLLSGRSFRSSNEQEW-NEISNHVVIRPCLVGIEIVLSILQTP----FSSVLQVLR 118

Query:   205 EEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQ 245
             E GL V+    +  ++   HT+QAE   V DL  +DL  L+
Sbjct:   119 EHGLYVLGYICSSVNDRLIHTLQAE---VNDLALIDLADLK 156

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2165311 AT5G51780 "AT5G51780" [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 65/174 (37%), Positives = 104/174 (59%)

Query:    82 KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQEL 141
             +KM + ++ ERQRRQ ++ L+ASLRSLLPL  I GKRS SD +NEA NYI YL + I+EL
Sbjct:     2 EKM-MHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKEL 60

Query:   142 GLKRDKLKNLSELGAVGHGSSNWDNCLQ-----NCVTIHPYSGGVEIVINSVHKEENLKL 196
              ++RD L  LS    +G  + ++   ++     N V +     GVEI+++S       + 
Sbjct:    61 SVRRDDLMVLSRGSLLGSSNGDFKEDVEMISGKNHVVVRQCLVGVEIMLSSRCCGGQPRF 120

Query:   197 SKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVG---DLTCVDLRVLQLK 247
             S V++ + E GL ++   S+  D+   +TIQAE + +    DL  ++ R++++K
Sbjct:   121 SSVLQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMIDLAELEKRLIRMK 174

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:504956298 AT1G62975 "AT1G62975" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 1.3e-12, P = 1.3e-12
 Identities = 57/174 (32%), Positives = 87/174 (50%)

Query:    82 KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQEL 141
             KKM   +DIERQRRQ +S L   LR+LLP Q I GKRS SDHI +A NYI  L   I+EL
Sbjct:    74 KKM-KHRDIERQRRQEVSSLFKRLRTLLPFQYIQGKRSTSDHIVQAVNYIKDLQIKIKEL 132

Query:   142 GLKRDKLKNLSELGAVGHGSSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVME 201
               KR+++K +       H +      ++ C T    S     + +S     +  ++ V+ 
Sbjct:   133 NEKRNRVKKVISATTTTHSA------IEEC-TSSLSSSAASTLSSSCSCVGDKHITVVVT 185

Query:   202 AVLEEGLDVI-RCASTQTDEGFFHTIQ--AEESQVGDLTCVDLRVLQLKLDHSI 252
               L  G+++I  C   +        +Q  A+E +   ++C+  R  Q +  H+I
Sbjct:   186 PCLV-GVEIIISCCLGRNKSCLSSVLQMLAQEQRFSVVSCLSAR-RQQRFMHTI 237

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2133089 AT4G20970 "AT4G20970" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 44/161 (27%), Positives = 77/161 (47%)

Query:    87 RKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRD 146
             RK +E+ RR  +  L++ L SLLP  S T   ++ D ++EA NYI  L  N+++   KR+
Sbjct:    16 RKTVEKNRRMQMKSLYSELISLLPHHSSTEPLTLPDQLDEAANYIKKLQVNVEK---KRE 72

Query:   147 KLKNL------SELGAVGHGS--SNWDNCL-QNCVTIH-PYSGGVEIVINSVHKEENLKL 196
             + +NL       +L +VG  S  S+ D  + +    I    +G +  +      E     
Sbjct:    73 RKRNLVATTTLEKLNSVGSSSVSSSVDVSVPRKLPKIEIQETGSIFHIFLVTSLEHKFMF 132

Query:   197 SKVMEAVLEE-GLDVIRCASTQTDEGFFHTI--QAEESQVG 234
              +++  + EE G ++     +  D+  FHT+  + EE   G
Sbjct:   133 CEIIRVLTEELGAEITHAGYSIVDDAVFHTLHCKVEEHDYG 173

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:0050832 "defense response to fungus" evidence=IEP

TAIR|locus:2040287 BHLH100 "basic helix-loop-helix protein 100" [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 46/172 (26%), Positives = 86/172 (50%)

Query:    91 ERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLK- 149
             ER+RR+ ++ + +SLRS LP  + T K S+S  +++A  YI  L + +++L  K+++L  
Sbjct:    70 ERERRKKINTMFSSLRSCLPPTNQTKKLSVSATVSQALKYIPELQEQVKKLMKKKEELSF 129

Query:   150 NLS---ELGAVGHGSSNWDNCLQNCVTIHPYS-GGVEIVIN-SVHKEENLKLSKVMEAVL 204
              +S   +L      S + +       T+        E+++  S  + E      V+  V 
Sbjct:   130 QISGQRDLVYTDQNSKSEEGVTSYASTVSSTRLSETEVMVQISSLQTEKCSFGNVLSGVE 189

Query:   205 EEGLDVIRCASTQTD-EGFFHT--IQAEESQVGDLTCVDLRVLQL--KLDHS 251
             E+GL ++  +S+++  E  F++  +Q +  QV      D R+L L  K  HS
Sbjct:   190 EDGLVLVGASSSRSHGERLFYSMHLQIKNGQVNSEELGD-RLLYLYEKCGHS 240

GO:0003677 "DNA binding" evidence=IEA;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:0010106 "cellular response to iron ion starvation" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0055072 "iron ion homeostasis" evidence=IGI

UNIPROTKB|Q941Z7 P0431G06.13-1 "BHLH transcription factor-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 115 (45.5 bits), Expect = 0.00012, P = 0.00012
 Identities = 45/151 (29%), Positives = 71/151 (47%)

Query:    91 ERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN 150
             ER RR+ L+ L++SLR+LLP    T K SI   ++    YI  L K ++ L  K+ +L  
Sbjct:    77 ERDRRKQLNELYSSLRALLPDADHTKKLSIPTTVSRVLKYIPELQKQVENLERKKKELTT 136

Query:   151 LSEL----GAVGHG-SSNWDNCLQNCVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLE 205
              S      G +G    S     + +   I+     V++ + S      L LSK ++ +  
Sbjct:   137 TSTTNCKPGVLGSQLMSEGMAPIVSATCINDMEIMVQVSLLSNVAGSVLPLSKCIKVLEN 196

Query:   206 EGLDVIRCASTQTDEGF----FHTIQAEESQ 232
             EGL  I   S+ T  GF    F++I  + S+
Sbjct:   197 EGLHFI---SSSTSSGFGNRTFYSIHLQRSE 224

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2080600 bHLH38 "basic helix-loop-helix 38" [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 0.00028, P = 0.00028
 Identities = 41/165 (24%), Positives = 82/165 (49%)

Query:    91 ERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDK-LK 149
             ER RR+ ++ L +SLRS LP    + K SI + ++++  YI  L + ++ L  K+++ L 
Sbjct:    80 ERDRRKKINTLFSSLRSCLPASDQSKKLSIPETVSKSLKYIPELQQQVKRLIQKKEEILV 139

Query:   150 NLSELGAVGHGSSNWDNCLQNCV-TIHPYS-GGVEIVIN-SVHKEENLKLSKVMEAVLEE 206
              +S               + + + T+     G  E+++  S  K  N  +S V+  + E+
Sbjct:   140 RVSGQRDFELYDKQQPKAVASYLSTVSATRLGDNEVMVQVSSSKIHNFSISNVLGGIEED 199

Query:   207 GLDVIRCASTQTD-EGFFHTIQAEESQVGD--LTCVDL--RVLQL 246
             G  ++  +S+++  E  F+T+  +   + D  + C +L  R+L L
Sbjct:   200 GFVLVDVSSSRSQGERLFYTLHLQVENMDDYKINCEELSERMLYL 244


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.133   0.380    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      253       243   0.00097  113 3  11 22  0.44    33
                                                     32  0.45    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  598 (64 KB)
  Total size of DFA:  186 KB (2106 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.35u 0.14s 22.49t   Elapsed:  00:00:01
  Total cpu time:  22.35u 0.14s 22.49t   Elapsed:  00:00:01
  Start:  Fri May 10 22:23:09 2013   End:  Fri May 10 22:23:10 2013

GO:0003677 "DNA binding" evidence=IEA;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:0010106 "cellular response to iron ion starvation" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0055072 "iron ion homeostasis" evidence=IGI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00121197 hypothetical protein (243 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	253
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-05
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	3e-04

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 82  KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQ 139
            +       ER+RR+ ++     LRSLLP    + K S ++ + +A +YI  L + +Q
Sbjct: 3   SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 37.4 bits (88), Expect = 3e-04
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 90  IERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYL 134
            ER+RR  ++     LR LLP      K S ++ +  A  YI +L
Sbjct: 8   RERRRRDRINDAFEELRELLP-TPPNKKLSKAEILRLAIEYIKHL 51

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	253
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.34
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.34
smart00353	53	HLH helix loop helix domain.	99.32
KOG1318	411	consensus Helix loop helix transcription factor EB	98.23
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	97.93
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	97.79
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.57
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.46
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.44
PLN03217	93	transcription factor ATBS1; Provisional	97.43
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.41
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.39
KOG4304	250	consensus Transcriptional repressors of the hairy/	97.27
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.22
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.06
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.0
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	96.96
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	96.8
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	96.69
KOG0561	373	consensus bHLH transcription factor [Transcription	96.57
KOG3960	284	consensus Myogenic helix-loop-helix transcription	96.03
PRK05007	884	PII uridylyl-transferase; Provisional	95.62
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	95.58
PRK03381	774	PII uridylyl-transferase; Provisional	95.55
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	95.54
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	95.34
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.2
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.57
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	94.56
PRK04374	869	PII uridylyl-transferase; Provisional	94.51
PRK00194	90	hypothetical protein; Validated	94.42
PRK05092	931	PII uridylyl-transferase; Provisional	94.35
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.0
PRK03381	774	PII uridylyl-transferase; Provisional	93.89
PRK03059	856	PII uridylyl-transferase; Provisional	93.86
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	93.76
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	93.66
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	93.64
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	93.56
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	93.51
PRK05007	884	PII uridylyl-transferase; Provisional	93.47
PRK00275	895	glnD PII uridylyl-transferase; Provisional	92.92
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	92.76
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	92.62
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	92.58
PRK03059	856	PII uridylyl-transferase; Provisional	92.24
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	91.92
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	91.49
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	91.24
PRK04374	869	PII uridylyl-transferase; Provisional	91.03
PRK05092	931	PII uridylyl-transferase; Provisional	90.81
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	90.07
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	89.78
PRK04435	147	hypothetical protein; Provisional	88.78
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	88.64
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	88.14
KOG3910	632	consensus Helix loop helix transcription factor [T	87.95
cd02116	60	ACT ACT domains are commonly involved in specifica	86.86
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	86.38
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	85.89
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	84.93
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	84.43
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	84.38
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	84.34
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	83.83
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	82.06
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	80.9
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	80.66

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

Probab=99.34  E-value=1e-12  Score=92.27  Aligned_cols=53  Identities=28%  Similarity=0.382  Sum_probs=48.5

Q ss_pred             ccccchHHHHHHHHHHHhcHhhhhccCCCC--CcCCCCchhhhHHHHHHHHHHHH
Q 039361           83 KMILRKDIERQRRQHLSMLHASLRSLLPLQ--SITGKRSISDHINEARNYINYLN  135 (253)
Q Consensus        83 kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~--~~k~K~Sis~il~eAI~YIKeLq  135 (253)
                      ++..|+..||.||..||..|..|+.+||..  ....|.|.+++|..||+||++||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            477899999999999999999999999996  25668899999999999999997

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

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

Probab=99.34  E-value=1.2e-12  Score=92.29  Aligned_cols=58  Identities=29%  Similarity=0.366  Sum_probs=52.4

Q ss_pred             cccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 039361           82 KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQ  139 (253)
Q Consensus        82 ~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVk  139 (253)
                      .++..|+..||+||.+||..|..|+++||......|.|.+++|..||+||+.|+..++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            5688999999999999999999999999998655677888889999999999998763

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

>smart00353 HLH helix loop helix domain

Probab=99.32  E-value=2.6e-12  Score=88.95  Aligned_cols=52  Identities=33%  Similarity=0.432  Sum_probs=46.4

Q ss_pred             hHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 039361           88 KDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQ  139 (253)
Q Consensus        88 ~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVk  139 (253)
                      +..||+||.+||+.|..|+++||......|.|.+++|.+||+||++|+++++
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            3689999999999999999999976545677888889999999999999876

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

Probab=98.23  E-value=1.9e-06  Score=83.13  Aligned_cols=63  Identities=21%  Similarity=0.317  Sum_probs=53.0

Q ss_pred             CcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcC-CCCchhhhHHHHHHHHHHHHHHHHHH
Q 039361           79 NNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSIT-GKRSISDHINEARNYINYLNKNIQEL  141 (253)
Q Consensus        79 ~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k-~K~Sis~il~eAI~YIKeLq~rVkeL  141 (253)
                      -...||.+|+++||+||.++|++.-.|.-|||..+.- .|+.+..|+.-+++||++||+..+..
T Consensus       229 rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~  292 (411)
T KOG1318|consen  229 RDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRA  292 (411)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999977422 25556777999999999999887743

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

Probab=97.93  E-value=2.5e-05  Score=70.51  Aligned_cols=66  Identities=21%  Similarity=0.244  Sum_probs=54.9

Q ss_pred             CcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCc-hhhhHHHHHHHHHHHHHHHHHHHHhH
Q 039361           79 NNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRS-ISDHINEARNYINYLNKNIQELGLKR  145 (253)
Q Consensus        79 ~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~S-is~il~eAI~YIKeLq~rVkeLe~kK  145 (253)
                      +..+.+..|++-||.||-+++..|..|+-+||...- .|++ .+.+|..|..||+.|+.+..+.+...
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~-~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~  121 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNG-ETRSTTLSILDKALEHIQSLERKSATQQQDI  121 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCC-cchhhhhHhhhhHHHHHHHHHhHHHHHHHHH
Confidence            455678999999999999999999999999998753 3344 68899999999999998776665443

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=97.79  E-value=3.7e-05  Score=67.31  Aligned_cols=65  Identities=18%  Similarity=0.268  Sum_probs=56.2

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCC----CCchhhhHHHHHHHHHHHHHHHHHHHHhH
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITG----KRSISDHINEARNYINYLNKNIQELGLKR  145 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~----K~Sis~il~eAI~YIKeLq~rVkeLe~kK  145 (253)
                      +.+|..|-.+||+||.-+|.-|..|.-|||.-...+    |.|.+-||-.||+||-.|...+.+-+.+-
T Consensus        60 ~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~  128 (229)
T KOG1319|consen   60 DRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEV  128 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345889999999999999999999999999765544    88999999999999999998877666543

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

Probab=97.57  E-value=5.6e-05  Score=67.44  Aligned_cols=64  Identities=31%  Similarity=0.380  Sum_probs=57.2

Q ss_pred             cccccccchHHHHHHHHHHHhcHhhhhccCCCCCc-CCCCchhhhHHHHHHHHHHHHHHHHHHHH
Q 039361           80 NNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSI-TGKRSISDHINEARNYINYLNKNIQELGL  143 (253)
Q Consensus        80 ~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~-k~K~Sis~il~eAI~YIKeLq~rVkeLe~  143 (253)
                      ....+..+++.||+|=+.+|..|..||.+||.... ..|.|.-++|-.||.||+.|++-++.-+.
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            45678889999999999999999999999999887 67889999999999999999998776664

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

Probab=97.46  E-value=0.00012  Score=76.06  Aligned_cols=62  Identities=21%  Similarity=0.366  Sum_probs=52.9

Q ss_pred             CCCCcccccccchHHHHHHHHHHHhcHhhhhccCCCCC-cCCCCchhhhHHHHHHHHHHHHHH
Q 039361           76 SDNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQS-ITGKRSISDHINEARNYINYLNKN  137 (253)
Q Consensus        76 ~~~~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~-~k~K~Sis~il~eAI~YIKeLq~r  137 (253)
                      +++...+++..|..+||+||.|||.+...|.+|||.-. .-+|.|...||-.||.+||.+++.
T Consensus        13 ~d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   13 SDSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             ccchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            35566678999999999999999999999999999765 234667788899999999998874

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

Probab=97.44  E-value=0.0016  Score=48.67  Aligned_cols=62  Identities=8%  Similarity=0.036  Sum_probs=48.6

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccH----HHHHHHH
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDL----RVLQLKL  248 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~----~~l~~kL  248 (253)
                      .|+|.+.  .++++|++|..+|.++||+|..|-+++.|+++.-+|.+   .-.++..++-    ..|+++|
T Consensus         3 viev~a~--DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV---~d~~g~kl~d~~~~~~l~~~L   68 (72)
T cd04895           3 LVKVDSA--RKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHV---TDQLGNKLTDDSLIAYIEKSL   68 (72)
T ss_pred             EEEEEEC--CcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEE---ECCCCCCCCCHHHHHHHHHHh
Confidence            4566674  56889999999999999999999999999999999998   5555545543    3444444

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.

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.43  E-value=0.00024  Score=54.86  Aligned_cols=56  Identities=23%  Similarity=0.339  Sum_probs=48.8

Q ss_pred             HHHHhcHhhhhccCCCCCc---CCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhhh
Q 039361           96 QHLSMLHASLRSLLPLQSI---TGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNL  151 (253)
Q Consensus        96 ~kMn~lf~~LRSLLP~~~~---k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~~  151 (253)
                      .+|+++.+.|+.|||....   .+|+|-+-+|.|+-+||+.|+..|..|.++-.+|...
T Consensus        20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6899999999999998632   3588999999999999999999999999987776643

>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains

Probab=97.41  E-value=0.0019  Score=47.28  Aligned_cols=66  Identities=15%  Similarity=0.145  Sum_probs=49.1

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeee-CCeEEEEEEeeccccCCCccccH----HHHHHHHHhh
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQT-DEGFFHTIQAEESQVGDLTCVDL----RVLQLKLDHS  251 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~-~~~~~~tI~a~~~kv~~~~~id~----~~l~~kL~~~  251 (253)
                      .+|.+.|.  .++++|+++..+|..+|++|++|.+.+. ++.++-+|..   .-.++..++.    .+|+++|.++
T Consensus         2 ~~i~v~~~--Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v---~~~~~~~~~~~~~~~~l~~~L~~~   72 (73)
T cd04900           2 TEVFIYTP--DRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVV---LDPDGEPIGERERLARIREALEDA   72 (73)
T ss_pred             EEEEEEec--CCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEE---ECCCCCCCChHHHHHHHHHHHHhh
Confidence            36777774  4678999999999999999999999877 6899999998   5444434432    3455555544

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.

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

Probab=97.39  E-value=0.0018  Score=48.84  Aligned_cols=66  Identities=9%  Similarity=0.053  Sum_probs=53.6

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc----HHHHHHHHHhhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD----LRVLQLKLDHSI  252 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id----~~~l~~kL~~~I  252 (253)
                      .|+|.|.  .++++|.+|..+|-++|++|.+|.+++.++++.-+|..   .-.+|..+.    ..+|+++|.+++
T Consensus         3 vveV~~~--DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV---~d~~g~kl~~~~~~~~l~~~L~~al   72 (75)
T cd04897           3 VVTVQCR--DRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYI---RHKDGRTLSTEGERQRVIKCLEAAI   72 (75)
T ss_pred             EEEEEeC--CcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEE---EcCCCCccCCHHHHHHHHHHHHHHH
Confidence            3667774  56889999999999999999999999999999999998   666554443    347777777765

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.

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

Probab=97.27  E-value=0.00011  Score=66.93  Aligned_cols=63  Identities=17%  Similarity=0.261  Sum_probs=54.8

Q ss_pred             CCCcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcC-----CCCchhhhHHHHHHHHHHHHHHHH
Q 039361           77 DNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSIT-----GKRSISDHINEARNYINYLNKNIQ  139 (253)
Q Consensus        77 ~~~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k-----~K~Sis~il~eAI~YIKeLq~rVk  139 (253)
                      ......+|..+-..||+||-.||+.+..|+.|||...++     .|...++||.=|++|++.|+....
T Consensus        26 ~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   26 SKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             hhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            344567899999999999999999999999999988877     377788899999999999987643

>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=97.22  E-value=0.0046  Score=46.04  Aligned_cols=66  Identities=12%  Similarity=0.001  Sum_probs=49.2

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCeEEEEEEeeccccCCCcccc---HHHHHHHHHhhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEGFFHTIQAEESQVGDLTCVD---LRVLQLKLDHSI  252 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~~~~tI~a~~~kv~~~~~id---~~~l~~kL~~~I  252 (253)
                      .++|.|.  .++++|+++..+|..+|++|++|.+++ .|+.++-+|.+   .-.++...+   ..+|+++|.+++
T Consensus         2 ~~ei~~~--Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V---~d~~~~~~~~~~~~~l~~~L~~~L   71 (76)
T cd04927           2 LLKLFCS--DRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFI---TDARELLHTKKRREETYDYLRAVL   71 (76)
T ss_pred             EEEEEEC--CCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEE---eCCCCCCCCHHHHHHHHHHHHHHH
Confidence            5677774  467899999999999999999999996 89999999998   443333112   335666665543

This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=97.06  E-value=0.0069  Score=45.69  Aligned_cols=66  Identities=11%  Similarity=0.069  Sum_probs=51.4

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEee--eeCCeEEEEEEeeccccCCCcccc---HHHHHHHHHhhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCAST--QTDEGFFHTIQAEESQVGDLTCVD---LRVLQLKLDHSI  252 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS--~~~~~~~~tI~a~~~kv~~~~~id---~~~l~~kL~~~I  252 (253)
                      .|+|+|.  .++++|++|..+|.++|++|.+|-++  +.|+++.-+|..   ...+..-.|   ...|+++|.+++
T Consensus         2 vlev~a~--DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv---~~~g~kl~d~~~~~~L~~~L~~~l   72 (75)
T cd04896           2 LLQIRCV--DQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV---QSDGKKIMDPKKQAALCARLREEM   72 (75)
T ss_pred             EEEEEeC--CcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE---eCCCCccCCHHHHHHHHHHHHHHh
Confidence            3567774  56889999999999999999999999  999998888887   544432123   457888887764

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.

>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=97.00  E-value=0.011  Score=41.88  Aligned_cols=65  Identities=15%  Similarity=0.168  Sum_probs=48.8

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccH---HHHHHHHHhhh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDL---RVLQLKLDHSI  252 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~---~~l~~kL~~~I  252 (253)
                      |.+.+.  .+++.|.+++.+|.++|+.|+++.+.+.++.++.+|.+   +-.++..++.   .+|+++|.++|
T Consensus         3 l~v~~~--d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i---~~~~~~~~~~~~~~~i~~~l~~~~   70 (70)
T cd04899           3 LELTAL--DRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYV---TDADGQPLDPERQEALRAALGEAL   70 (70)
T ss_pred             EEEEEc--CCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEE---ECCCCCcCCHHHHHHHHHHHHhhC
Confidence            455553  45778999999999999999999999888899999998   6555433333   35777776653

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

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

Probab=96.96  E-value=0.011  Score=43.32  Aligned_cols=64  Identities=17%  Similarity=0.147  Sum_probs=46.6

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+|.|.+.  .++++|++|..+|.++|++|+++.+.+.++..+.+|++   .-.++..++.+ ..++|.+
T Consensus         2 tri~V~~~--D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v---~~~~~~~~~~~-~~~~l~~   65 (72)
T cd04926           2 VRLELRTE--DRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYV---TDANGNPVDPK-TIEAVRQ   65 (72)
T ss_pred             eEEEEEEC--CccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEE---ECCCCCcCCHH-HHHHHHH
Confidence            45666664  45789999999999999999999998888888889988   54444334433 3334443

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.

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

Probab=96.80  E-value=0.017  Score=42.84  Aligned_cols=64  Identities=16%  Similarity=0.145  Sum_probs=52.0

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCeEEEEEEeeccccCCCccccHHHHHHHHHhhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHSI  252 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~I  252 (253)
                      +|.|.+.  .++++|+++..+|..+||+|++|.+.+ .+|.++-+|.+   .  +..+=+...|.++|.+++
T Consensus         3 eI~V~~~--Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V---~--d~~~~~~~~~~~~~~~~~   67 (68)
T cd04928           3 EITFAAG--DKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVV---T--GWKRGETAALGHALQKEI   67 (68)
T ss_pred             EEEEEEC--CCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEE---e--cCCccchHHHHHHHHHhh
Confidence            6777774  468899999999999999999999875 57889999988   4  333457888999998775

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.

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

Probab=96.69  E-value=0.023  Score=41.90  Aligned_cols=65  Identities=15%  Similarity=0.196  Sum_probs=50.0

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCC-Cccc-c---HHHHHHHHHhhh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGD-LTCV-D---LRVLQLKLDHSI  252 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~-~~~i-d---~~~l~~kL~~~I  252 (253)
                      |++.+.  .++++|++|-.+|.++|+.|++|.+++.|+.++-+|.+   .-.+ +..+ +   ..+|++.|.+++
T Consensus         3 ~~v~~~--Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V---~d~~~~~~~~~~~~~~~i~~~L~~~l   72 (74)
T cd04925           3 IELTGT--DRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYV---RDEETGAPIDDPIRLASIEDRLDNVL   72 (74)
T ss_pred             EEEEEC--CCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEE---EcCcCCCCCCCHHHHHHHHHHHHHHh
Confidence            556663  46889999999999999999999999999999999998   4322 2222 2   457777777765

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.

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=96.57  E-value=0.0014  Score=61.23  Aligned_cols=51  Identities=33%  Similarity=0.406  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHH
Q 039361           90 IERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQEL  141 (253)
Q Consensus        90 ~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeL  141 (253)
                      -||+|=+-+|.-|.+||+|||.. -..|.|.+.||..+.+||.+|+..--+|
T Consensus        67 NERRRMQSINAGFqsLr~LlPr~-eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   67 NERRRMQSINAGFQSLRALLPRK-EGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             hHHHHHHhhhHHHHHHHHhcCcc-cchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            69999999999999999999975 3468999999999999999998764443

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

Probab=96.03  E-value=0.015  Score=53.19  Aligned_cols=59  Identities=19%  Similarity=0.187  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHHhcHhhhh-ccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHh
Q 039361           88 KDIERQRRQHLSMLHASLR-SLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKL  148 (253)
Q Consensus        88 ~~~ERqRR~kMn~lf~~LR-SLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l  148 (253)
                      -+.||+|=+|.|+.|.+|. .-.+++..  +.....||-.||.||..||.-++++.+....+
T Consensus       123 TMRERRRLkKVNEAFE~LKRrT~~NPNQ--RLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  123 TMRERRRLKKVNEAFETLKRRTSSNPNQ--RLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCccc--cccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            4579999999999999995 34454442  44556779999999999999999998766544

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.62  E-value=0.083  Score=55.98  Aligned_cols=79  Identities=13%  Similarity=0.144  Sum_probs=59.8

Q ss_pred             CceEEEEEe--CCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc---HHH
Q 039361          169 QNCVTIHPY--SGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD---LRV  243 (253)
Q Consensus       169 ~p~V~V~~~--~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id---~~~  243 (253)
                      ++.|.+...  +.-..|+|++.  .++++|++|..+|.++|++|.+|-++|.|+++.-+|.+   .-.++..++   ...
T Consensus       795 ~~~V~~d~~~s~~~TvlEV~a~--DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV---~~~~g~~l~~~~~~~  869 (884)
T PRK05007        795 PTEVSFLPTHTDRRSYMELIAL--DQPGLLARVGKIFADLGISLHGARITTIGERVEDLFIL---ATADRRALNEELQQE  869 (884)
T ss_pred             CCEEEEccCCCCCeEEEEEEeC--CchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEE---EcCCCCcCCHHHHHH
Confidence            456666532  23567788884  56899999999999999999999999999999999988   544554555   346


Q ss_pred             HHHHHHhhh
Q 039361          244 LQLKLDHSI  252 (253)
Q Consensus       244 l~~kL~~~I  252 (253)
                      |+++|..++
T Consensus       870 l~~~L~~~l  878 (884)
T PRK05007        870 LRQRLTEAL  878 (884)
T ss_pred             HHHHHHHHH
Confidence            677776654

>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=95.58  E-value=0.2  Score=34.49  Aligned_cols=60  Identities=18%  Similarity=0.261  Sum_probs=44.0

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCC--e-EEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDE--G-FFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~--~-~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .|.+.|.  .+++.|.+|..+|.++|+.|.++.....++  . ++.++..        ..-+...+.++|.++
T Consensus         2 ~v~v~~~--drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~l~~~   64 (66)
T PF01842_consen    2 RVRVIVP--DRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIVV--------DEEDLEKLLEELEAL   64 (66)
T ss_dssp             EEEEEEE--TSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEE--------EGHGHHHHHHHHHHH
T ss_pred             EEEEEcC--CCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEEC--------CCCCHHHHHHHHHcc
Confidence            3556664  457899999999999999999999998876  3 3333333        345677788887765

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 ....

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.55  E-value=0.12  Score=53.92  Aligned_cols=78  Identities=18%  Similarity=0.086  Sum_probs=61.4

Q ss_pred             ceEEEEEe-CCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHH
Q 039361          170 NCVTIHPY-SGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKL  248 (253)
Q Consensus       170 p~V~V~~~-~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL  248 (253)
                      |.|.+... .+.++|.|.|.  .++++|++|..+|..+|++|++|++.+.||.++-+|.+   .-..+......+|++.|
T Consensus       588 ~~v~~~~~~~~~~~V~V~~~--DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V---~~~~~~~~~~~~l~~~L  662 (774)
T PRK03381        588 VHVEIAPADPHMVEVTVVAP--DRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVV---SPRFGSPPDAALLRQDL  662 (774)
T ss_pred             CEEEEeeCCCCeEEEEEEec--CCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE---ECCCCCcchHHHHHHHH
Confidence            45555432 36788888874  56889999999999999999999999988999999999   65555445567888888


Q ss_pred             Hhhh
Q 039361          249 DHSI  252 (253)
Q Consensus       249 ~~~I  252 (253)
                      .+++
T Consensus       663 ~~~L  666 (774)
T PRK03381        663 RRAL  666 (774)
T ss_pred             HHHH
Confidence            8764

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

Probab=95.54  E-value=0.19  Score=35.08  Aligned_cols=45  Identities=11%  Similarity=0.171  Sum_probs=37.2

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEe
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQA  228 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a  228 (253)
                      .|.+.|.  .+++.|.++..+|.++|+.|.++.+.+.++.....|++
T Consensus         2 ~l~i~~~--d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v   46 (70)
T cd04873           2 VVEVYAP--DRPGLLADITRVLADLGLNIHDARISTTGERALDVFYV   46 (70)
T ss_pred             EEEEEeC--CCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            3556664  45778999999999999999999998877777778888

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

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

Probab=95.34  E-value=0.18  Score=37.22  Aligned_cols=63  Identities=13%  Similarity=0.117  Sum_probs=50.2

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      +.|.+.+.  .+++.++.+..+|.+.|.++..+..++.++.+...+.+   .+.   .-+.++|+..|.++
T Consensus         3 ~vItv~G~--DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v---~~~---~~~~~~l~~~L~~l   65 (76)
T PF13740_consen    3 LVITVVGP--DRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLV---SIP---EDSLERLESALEEL   65 (76)
T ss_dssp             EEEEEEEE----TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEE---EES---HHHHHHHHHHHHHH
T ss_pred             EEEEEEec--CCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEE---EeC---cccHHHHHHHHHHH
Confidence            45666664  45889999999999999999999999999999999988   555   22778888888765

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.20  E-value=0.19  Score=53.45  Aligned_cols=79  Identities=15%  Similarity=0.026  Sum_probs=60.5

Q ss_pred             CceEEEEEeC--CeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc----HH
Q 039361          169 QNCVTIHPYS--GGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD----LR  242 (253)
Q Consensus       169 ~p~V~V~~~~--~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id----~~  242 (253)
                      +|.|.+....  +..+|.|.+.  .++++|++|..+|..+|++|++|.+++.|++++-+|.+   .-.++..+.    ..
T Consensus       801 ~~~V~i~~~~~~~~T~i~V~a~--DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V---~d~~g~~l~~~~~~~  875 (895)
T PRK00275        801 PTQVTISNDAQRPVTVLEIIAP--DRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFI---TDADNQPLSDPQLCS  875 (895)
T ss_pred             CCEEEEEECCCCCeEEEEEEEC--CCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEE---ECCCCCCCCCHHHHH
Confidence            3667666543  3567777774  56889999999999999999999999999999999999   554544332    34


Q ss_pred             HHHHHHHhhh
Q 039361          243 VLQLKLDHSI  252 (253)
Q Consensus       243 ~l~~kL~~~I  252 (253)
                      +|+++|.+++
T Consensus       876 ~l~~~L~~~L  885 (895)
T PRK00275        876 RLQDAICEQL  885 (895)
T ss_pred             HHHHHHHHHH
Confidence            6778777664

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=94.57  E-value=0.24  Score=52.38  Aligned_cols=79  Identities=14%  Similarity=0.098  Sum_probs=59.6

Q ss_pred             CceEEEEEeCC--eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc---HHH
Q 039361          169 QNCVTIHPYSG--GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD---LRV  243 (253)
Q Consensus       169 ~p~V~V~~~~~--~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id---~~~  243 (253)
                      +|.|.+....+  -..|+|.+.  .++++|++|..+|.++|++|.+|-++|.++++.-+|.+   .-.++..++   ..+
T Consensus       770 ~~~V~~dn~~s~~~T~iev~a~--DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv---~~~~g~~l~~~~~~~  844 (854)
T PRK01759        770 KTEVRFLNEEKQEQTEMELFAL--DRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFIL---TNQQGQALDEEERKA  844 (854)
T ss_pred             CCEEEEccCCCCCeEEEEEEeC--CchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEE---ECCCCCcCChHHHHH
Confidence            46666643322  467788884  56889999999999999999999999999999988888   444443333   367


Q ss_pred             HHHHHHhhh
Q 039361          244 LQLKLDHSI  252 (253)
Q Consensus       244 l~~kL~~~I  252 (253)
                      |+++|.+++
T Consensus       845 l~~~L~~~l  853 (854)
T PRK01759        845 LKSRLLSNL  853 (854)
T ss_pred             HHHHHHHHh
Confidence            777777665

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

Probab=94.56  E-value=0.42  Score=35.35  Aligned_cols=63  Identities=16%  Similarity=0.103  Sum_probs=51.0

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      +.|.+.|+  .+++...+|-..|.+.|..++.++....++.+++.+..   .+..   .+.+.|+++|..+
T Consensus         2 ~iltv~g~--Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~---~~~~---~~~~~l~~~l~~~   64 (77)
T cd04893           2 LVISALGT--DRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLV---EGSW---DAIAKLEAALPGL   64 (77)
T ss_pred             EEEEEEeC--CCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEE---Eecc---ccHHHHHHHHHHH
Confidence            34566774  45788999999999999999999999999999998888   5442   3678888887754

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

>PRK04374 PII uridylyl-transferase; Provisional

Probab=94.51  E-value=0.37  Score=51.22  Aligned_cols=79  Identities=14%  Similarity=0.031  Sum_probs=60.1

Q ss_pred             CceEEEEEeCC--eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc---HHH
Q 039361          169 QNCVTIHPYSG--GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD---LRV  243 (253)
Q Consensus       169 ~p~V~V~~~~~--~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id---~~~  243 (253)
                      +|.|.+....+  -..|+|.+.  .++++|++|-.+|.++|++|++|.+++.|+++.-+|.+   .-.++..++   ..+
T Consensus       783 ~~~V~~~~~~~~~~t~leI~a~--DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V---~d~~g~~~~~~~~~~  857 (869)
T PRK04374        783 APRVEFSESAGGRRTRISLVAP--DRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQI---TDEHDRPLSESARQA  857 (869)
T ss_pred             CCeEEEeecCCCCeEEEEEEeC--CcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE---ECCCCCcCChHHHHH
Confidence            46677765333  467777774  46889999999999999999999999999999999998   544443332   357


Q ss_pred             HHHHHHhhh
Q 039361          244 LQLKLDHSI  252 (253)
Q Consensus       244 l~~kL~~~I  252 (253)
                      |+++|.+++
T Consensus       858 l~~~L~~~l  866 (869)
T PRK04374        858 LRDALCACL  866 (869)
T ss_pred             HHHHHHHHh
Confidence            777777665

>PRK00194 hypothetical protein; Validated

Probab=94.42  E-value=0.24  Score=37.24  Aligned_cols=65  Identities=14%  Similarity=0.171  Sum_probs=50.6

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      +.|.+.|.  .+++.+.+|...|-++|++|++.+..+.++.++..+.+   .... ...+.+.|++.|.++
T Consensus         4 ~~ltv~g~--DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v---~~~~-~~~~~~~l~~~l~~l   68 (90)
T PRK00194          4 AIITVIGK--DKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLV---DISE-SKKDFAELKEELEEL   68 (90)
T ss_pred             EEEEEEcC--CCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEE---EecC-CCCCHHHHHHHHHHH
Confidence            45667774  46889999999999999999999988888877777777   5433 245678888877654

>PRK05092 PII uridylyl-transferase; Provisional

Probab=94.35  E-value=0.4  Score=51.14  Aligned_cols=79  Identities=13%  Similarity=-0.005  Sum_probs=60.7

Q ss_pred             CceEEEEEeCC--eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc----HH
Q 039361          169 QNCVTIHPYSG--GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD----LR  242 (253)
Q Consensus       169 ~p~V~V~~~~~--~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id----~~  242 (253)
                      +|.|.+....+  ...|.|.+.  .++++|++|..+|.++|++|.+|.+++.++++.-+|.+   .-.++..+.    ..
T Consensus       830 ~~~V~~~~~~s~~~t~i~I~~~--DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v---~d~~g~~i~~~~~~~  904 (931)
T PRK05092        830 PPRVTIDNEASNRFTVIEVNGR--DRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYV---TDLFGLKITNEARQA  904 (931)
T ss_pred             CCEEEEeeCCCCCeEEEEEEEC--CcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEE---eCCCCCcCCCHHHHH
Confidence            46677765433  467777774  46889999999999999999999999999999999999   554543332    35


Q ss_pred             HHHHHHHhhh
Q 039361          243 VLQLKLDHSI  252 (253)
Q Consensus       243 ~l~~kL~~~I  252 (253)
                      +|+++|.+++
T Consensus       905 ~l~~~L~~~L  914 (931)
T PRK05092        905 AIRRALLAAL  914 (931)
T ss_pred             HHHHHHHHHh
Confidence            6788887765

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=94.00  E-value=0.59  Score=49.51  Aligned_cols=79  Identities=16%  Similarity=0.182  Sum_probs=58.5

Q ss_pred             CceEEEEEe--CCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCeEEEEEEeeccccCCCccccHH---
Q 039361          169 QNCVTIHPY--SGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEGFFHTIQAEESQVGDLTCVDLR---  242 (253)
Q Consensus       169 ~p~V~V~~~--~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~~~~tI~a~~~kv~~~~~id~~---  242 (253)
                      .|.|.+...  .+..+|.|.+.  .++++|++|..+|..+|++|++|.+.+ .+|.++-+|.+   .-.++..++.+   
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~~--DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V---~d~~g~~~~~~~~~  738 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYCQ--DQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIV---TELNGKLLEFDRRR  738 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEec--CCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEE---eCCCCCCCCHHHHH
Confidence            366666543  34678888884  468899999999999999999999876 89999999998   54454444433   


Q ss_pred             HHHHHHHhhh
Q 039361          243 VLQLKLDHSI  252 (253)
Q Consensus       243 ~l~~kL~~~I  252 (253)
                      +|++.|.+++
T Consensus       739 ~l~~~L~~aL  748 (854)
T PRK01759        739 QLEQALTKAL  748 (854)
T ss_pred             HHHHHHHHHH
Confidence            5666666654

>PRK03381 PII uridylyl-transferase; Provisional

Probab=93.89  E-value=0.51  Score=49.45  Aligned_cols=74  Identities=8%  Similarity=0.022  Sum_probs=54.7

Q ss_pred             ceEEEEEeCC--eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc--HHHHH
Q 039361          170 NCVTIHPYSG--GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD--LRVLQ  245 (253)
Q Consensus       170 p~V~V~~~~~--~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id--~~~l~  245 (253)
                      +.|.+....+  ...|+|.+.  .++++|++|..+|.++|++|++|.+++.|++++-+|.+   .-.++..+.  ...|+
T Consensus       695 ~~v~~~~~~~~~~t~i~V~a~--DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V---~d~~g~~~~~~~~~l~  769 (774)
T PRK03381        695 PRVLWLDGASPDATVLEVRAA--DRPGLLARLARALERAGVDVRWARVATLGADVVDVFYV---TGAAGGPLADARAAVE  769 (774)
T ss_pred             cEEEEEECCCCCeEEEEEEeC--CchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEE---ECCCCCcCchHHHHHH
Confidence            4565654433  467777773  56889999999999999999999999999999999999   655554443  33444


Q ss_pred             HHH
Q 039361          246 LKL  248 (253)
Q Consensus       246 ~kL  248 (253)
                      ++|
T Consensus       770 ~~L  772 (774)
T PRK03381        770 QAV  772 (774)
T ss_pred             HHh
Confidence            443

>PRK03059 PII uridylyl-transferase; Provisional

Probab=93.86  E-value=0.51  Score=49.99  Aligned_cols=78  Identities=13%  Similarity=0.038  Sum_probs=58.1

Q ss_pred             ceEEEEEeC--CeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCC-ccccHHHHHH
Q 039361          170 NCVTIHPYS--GGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDL-TCVDLRVLQL  246 (253)
Q Consensus       170 p~V~V~~~~--~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~-~~id~~~l~~  246 (253)
                      +.|.+....  +..+|+|.+.  .++++|++|-.+|..+|++|++|.+++.|++++-+|.+   .-... ..-...+|++
T Consensus       774 ~~V~~~~~~~~~~T~i~V~a~--DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V---~~~~~~~~~~~~~l~~  848 (856)
T PRK03059        774 PRVDLRPDERGQYYILSVSAN--DRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI---DGSGLSDNRLQIQLET  848 (856)
T ss_pred             ceEEEEEcCCCCEEEEEEEeC--CcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE---cCCCCCCHHHHHHHHH
Confidence            556665432  3567777774  56889999999999999999999999999999999988   42221 1123457888


Q ss_pred             HHHhhh
Q 039361          247 KLDHSI  252 (253)
Q Consensus       247 kL~~~I  252 (253)
                      +|.+++
T Consensus       849 ~L~~~L  854 (856)
T PRK03059        849 ELLDAL  854 (856)
T ss_pred             HHHHHh
Confidence            887765

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=93.76  E-value=0.42  Score=50.38  Aligned_cols=78  Identities=21%  Similarity=0.086  Sum_probs=58.0

Q ss_pred             ceEEEEE--eCCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEee-eeCCeEEEEEEeeccccCCCcccc----HH
Q 039361          170 NCVTIHP--YSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCAST-QTDEGFFHTIQAEESQVGDLTCVD----LR  242 (253)
Q Consensus       170 p~V~V~~--~~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS-~~~~~~~~tI~a~~~kv~~~~~id----~~  242 (253)
                      |.|.+..  ..+..+|.|.+.  .++++|++|..+|..+|++|++|.++ +.|+.++-+|.+   +-.++..++    ..
T Consensus       656 ~~v~~~~~~~~~~t~i~V~~~--DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V---~~~~g~~~~~~~~~~  730 (850)
T TIGR01693       656 PLALIDGTRPSGGTEVFIYAP--DQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVV---QDLFGSPPAAERVFQ  730 (850)
T ss_pred             CEEEEeccCCCCeEEEEEEeC--CCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEE---ECCCCCCCCcHHHHH
Confidence            4555533  234678888884  56889999999999999999999988 678999999999   665554443    33


Q ss_pred             HHHHHHHhhh
Q 039361          243 VLQLKLDHSI  252 (253)
Q Consensus       243 ~l~~kL~~~I  252 (253)
                      +|++.|.+++
T Consensus       731 ~i~~~L~~~L  740 (850)
T TIGR01693       731 ELLQGLVDVL  740 (850)
T ss_pred             HHHHHHHHHH
Confidence            5667776654

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.

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

Probab=93.66  E-value=0.39  Score=36.11  Aligned_cols=64  Identities=16%  Similarity=0.197  Sum_probs=50.5

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .|.+.|+  .+++.+++|...|-++|+++++++..+.++.++..+.+   .... ...+.++|++.|..+
T Consensus         3 vl~i~g~--D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v---~~~~-~~~~~~~L~~~l~~l   66 (88)
T cd04872           3 VITVVGK--DRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIV---DISE-SNLDFAELQEELEEL   66 (88)
T ss_pred             EEEEEcC--CCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEE---EeCC-CCCCHHHHHHHHHHH
Confidence            4666674  46889999999999999999999988888888777777   5432 246788888887754

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

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

Probab=93.64  E-value=0.52  Score=34.12  Aligned_cols=64  Identities=6%  Similarity=0.035  Sum_probs=44.2

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcc-ccHHHHHHHHHhh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTC-VDLRVLQLKLDHS  251 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~-id~~~l~~kL~~~  251 (253)
                      |.+.|.  .+++.+.+|-..|-++|+.+++.+..+..+.-.+.+.+   ++..+.. ++...|+++|..+
T Consensus         2 i~v~g~--D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~---~~~~~~~~~~~~~l~~~l~~l   66 (74)
T cd04875           2 LTLSCP--DRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRV---EFELEGFDLSREALEAAFAPV   66 (74)
T ss_pred             EEEEcC--CCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEE---EEEeCCCCCCHHHHHHHHHHH
Confidence            455564  45788999999999999999999888532212234444   4444332 6788999888754

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=93.56  E-value=0.75  Score=33.45  Aligned_cols=62  Identities=10%  Similarity=0.114  Sum_probs=47.5

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeC------CeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTD------EGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~------~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      |.+.|.  .+++.+.+|-+.|.++|+++.+.+..+.+      +.++..+.+   .+.  ..++..+++..|..+
T Consensus         2 l~v~g~--D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v---~~p--~~~~~~~l~~~l~~l   69 (81)
T cd04869           2 VEVVGN--DRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATL---ALP--AGTDLDALREELEEL   69 (81)
T ss_pred             EEEEeC--CCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEE---ecC--CCCCHHHHHHHHHHH
Confidence            445563  45788999999999999999999998877      566666666   443  356888998888754

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

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=93.51  E-value=0.56  Score=49.44  Aligned_cols=78  Identities=17%  Similarity=0.018  Sum_probs=58.0

Q ss_pred             ceEEEEEeCC--eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCcccc---HHHH
Q 039361          170 NCVTIHPYSG--GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVD---LRVL  244 (253)
Q Consensus       170 p~V~V~~~~~--~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id---~~~l  244 (253)
                      |.|++....+  ...|.|.+.  .+++.|++|..+|.++|++|.++.+++.+++..-+|.+   ....+..++   ...|
T Consensus       767 ~~V~~d~~~s~~~t~~~v~~~--DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v---~~~~g~~~~~~~~~~l  841 (850)
T TIGR01693       767 PRVTILNTASRKATIMEVRAL--DRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYV---TDLFGLKLTDEEEQRL  841 (850)
T ss_pred             CeEEEccCCCCCeEEEEEEEC--CccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEE---ECCCCCCCCHHHHHHH
Confidence            5566654333  466777774  56889999999999999999999999999998888888   555443333   4567


Q ss_pred             HHHHHhhh
Q 039361          245 QLKLDHSI  252 (253)
Q Consensus       245 ~~kL~~~I  252 (253)
                      +++|.+++
T Consensus       842 ~~~L~~~l  849 (850)
T TIGR01693       842 LEVLAASV  849 (850)
T ss_pred             HHHHHHHh
Confidence            77776654

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

>PRK05007 PII uridylyl-transferase; Provisional

Probab=93.47  E-value=0.85  Score=48.50  Aligned_cols=79  Identities=19%  Similarity=0.198  Sum_probs=57.3

Q ss_pred             CceEEEEEeC--CeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeee-CCeEEEEEEeeccccCCCccccH---H
Q 039361          169 QNCVTIHPYS--GGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQT-DEGFFHTIQAEESQVGDLTCVDL---R  242 (253)
Q Consensus       169 ~p~V~V~~~~--~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~-~~~~~~tI~a~~~kv~~~~~id~---~  242 (253)
                      .|.|.+....  +..+|.|.|.  .++++|++|..+|..+|++|++|.+.+. +|.++-+|.+   .-.++..++.   .
T Consensus       688 ~p~V~i~~~~~~~~t~V~V~a~--DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V---~d~~g~~~~~~~~~  762 (884)
T PRK05007        688 KPLVLLSKQATRGGTEIFIWSP--DRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIV---LEPDGSPLSQDRHQ  762 (884)
T ss_pred             CCeEEEEecCCCCeEEEEEEec--CCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEE---ECCCCCCCCHHHHH
Confidence            3666665433  4778888774  5688999999999999999999997765 5688888888   5555444443   3


Q ss_pred             HHHHHHHhhh
Q 039361          243 VLQLKLDHSI  252 (253)
Q Consensus       243 ~l~~kL~~~I  252 (253)
                      +|++.|.+++
T Consensus       763 ~I~~~L~~aL  772 (884)
T PRK05007        763 VIRKALEQAL  772 (884)
T ss_pred             HHHHHHHHHH
Confidence            4677776654

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=92.92  E-value=0.87  Score=48.53  Aligned_cols=69  Identities=14%  Similarity=0.183  Sum_probs=52.9

Q ss_pred             CeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEe-eeeCCeEEEEEEeeccccCCCccc--c---HHHHHHHHHhhh
Q 039361          179 GGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCAS-TQTDEGFFHTIQAEESQVGDLTCV--D---LRVLQLKLDHSI  252 (253)
Q Consensus       179 ~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsass-S~~~~~~~~tI~a~~~kv~~~~~i--d---~~~l~~kL~~~I  252 (253)
                      +..+|.|.|.  .++++|+++..+|..+|++|++|.+ |+.+|.++-+|.+   .-.++..+  +   ..+|++.|.+++
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 GGTQIFIYAP--DQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIV---LDDDGEPIGDNPARIEQIREGLTEAL  777 (895)
T ss_pred             CeEEEEEEeC--CCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEE---eCCCCCCccchHHHHHHHHHHHHHHH
Confidence            5788888884  5688999999999999999999997 5678888889998   55555432  2   234667776654

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

Probab=92.76  E-value=0.87  Score=33.30  Aligned_cols=62  Identities=21%  Similarity=0.268  Sum_probs=44.1

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeee--CCeEEEEEEeeccccCCCccccHHHHHHHHH
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQT--DEGFFHTIQAEESQVGDLTCVDLRVLQLKLD  249 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~--~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~  249 (253)
                      +.+.+.+.  .+++.|.+|..++.+.|+.+.+++....  ++.....|.+   ++.+.  -....|-++|.
T Consensus         7 ~~l~i~~~--dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v---~V~d~--~~L~~ii~~L~   70 (80)
T PF13291_consen    7 VRLRIEAE--DRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTV---EVKDL--EHLNQIIRKLR   70 (80)
T ss_dssp             EEEEEEEE----TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEE---EESSH--HHHHHHHHHHC
T ss_pred             EEEEEEEE--cCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEE---EECCH--HHHHHHHHHHH
Confidence            34445553  4578999999999999999999999984  6788888998   66553  24445555554

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

Probab=92.62  E-value=1.2  Score=32.36  Aligned_cols=57  Identities=14%  Similarity=0.115  Sum_probs=46.1

Q ss_pred             CCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          190 KEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       190 ~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      ..+++...++-++|-++|+++.+.+.++.++.+...+.+   ..  +..++..+|++.|..+
T Consensus         7 ~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v---~~--p~~~~~~~l~~~l~~l   63 (75)
T cd04870           7 PDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILV---QI--PDSADSEALLKDLLFK   63 (75)
T ss_pred             CCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEE---Ec--CCCCCHHHHHHHHHHH
Confidence            346889999999999999999999988888886666666   43  3346789999988764

The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=92.58  E-value=0.53  Score=49.62  Aligned_cols=75  Identities=16%  Similarity=0.123  Sum_probs=57.6

Q ss_pred             CceEEEEEeCC--eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHH
Q 039361          169 QNCVTIHPYSG--GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQL  246 (253)
Q Consensus       169 ~p~V~V~~~~~--~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~  246 (253)
                      +|.|++....+  ...+++.+-  .++++|+.|-.+|.+++|++++|.++++|+++.-+|.+   ....+..++ .++++
T Consensus       778 ~p~v~i~~t~~~~~t~lEv~al--DRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~v---t~~~~~~l~-~~~~q  851 (867)
T COG2844         778 PPRVTILPTASNDKTVLEVRAL--DRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIV---TDADGQALN-AELRQ  851 (867)
T ss_pred             CCceeeccccCCCceEEEEEeC--CcccHHHHHHHHHHhcccceeeeeeccccccceeEEEE---eccccccCC-HHHHH
Confidence            47788876543  466777774  45889999999999999999999999999998888888   666665553 34444


Q ss_pred             HHH
Q 039361          247 KLD  249 (253)
Q Consensus       247 kL~  249 (253)
                      .|.
T Consensus       852 ~l~  854 (867)
T COG2844         852 SLL  854 (867)
T ss_pred             HHH
Confidence            444

>PRK03059 PII uridylyl-transferase; Provisional

Probab=92.24  E-value=0.98  Score=47.91  Aligned_cols=77  Identities=9%  Similarity=0.169  Sum_probs=56.3

Q ss_pred             ceEEEEEe--CCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEee-eeCCeEEEEEEeeccccCCCcccc----HH
Q 039361          170 NCVTIHPY--SGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCAST-QTDEGFFHTIQAEESQVGDLTCVD----LR  242 (253)
Q Consensus       170 p~V~V~~~--~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS-~~~~~~~~tI~a~~~kv~~~~~id----~~  242 (253)
                      |-|.++..  .+..+|.|.|.  .++++|+++..+|..+|++|++|.+. +.+|.++-+|.+   .-.++. +.    ..
T Consensus       666 ~~v~~~~~~~~~~~~v~i~~~--d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V---~~~~~~-~~~~~~~~  739 (856)
T PRK03059        666 PIVRARLSPAGEGLQVMVYTP--DQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQV---LDPEED-VHYRDIIN  739 (856)
T ss_pred             CeEEEEecCCCCeEEEEEEec--CCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEE---eCCCCC-CChHHHHH
Confidence            44445443  35789988884  56889999999999999999999984 578999999998   544443 22    34


Q ss_pred             HHHHHHHhhh
Q 039361          243 VLQLKLDHSI  252 (253)
Q Consensus       243 ~l~~kL~~~I  252 (253)
                      +|++.|.+++
T Consensus       740 ~i~~~l~~~l  749 (856)
T PRK03059        740 LVEHELAERL  749 (856)
T ss_pred             HHHHHHHHHH
Confidence            5666666553

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=91.92  E-value=0.065  Score=45.82  Aligned_cols=59  Identities=29%  Similarity=0.411  Sum_probs=50.0

Q ss_pred             CCcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHH
Q 039361           78 NNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKN  137 (253)
Q Consensus        78 ~~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~r  137 (253)
                      ++-.+++..|+.-||||-+-+|+.|.+||-.+|-.. -+|.|..-.|.-|.-||.-|-+=
T Consensus        73 dE~q~qrv~anvrerqRtqsLn~AF~~lr~iiptlP-sdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   73 DELQKQRVMANVRERQRTQSLNEAFAALRKIIPTLP-SDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCC-ccccccccchhhcccCCchhhhc
Confidence            344478999999999999999999999999999775 47888877788888898877653

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=91.49  E-value=0.098  Score=55.39  Aligned_cols=63  Identities=25%  Similarity=0.281  Sum_probs=52.8

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhH
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKR  145 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK  145 (253)
                      ..+|..|+.+|++=|--+|++...|+-+||..-.  |...+..+.-||+||.+|+..-+.|....
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~a--Kl~kSavLr~ai~~i~dl~~~nq~lk~~~  336 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEA--KLNKSAVLRKAIDYIEDLQGYNQKLKLEN  336 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHh--hhhhhhhHHHHHHHHHHhhccccccchhh
Confidence            5789999999999999999999999999997654  33446669999999999998776665443

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

Probab=91.24  E-value=1.6  Score=31.04  Aligned_cols=63  Identities=16%  Similarity=0.091  Sum_probs=42.9

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeee-CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQT-DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~-~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+.+.+.  .+++.|.+|+..|.++|+++...+.+.. ++.....|.+   .+.+. .....+|-++|.+
T Consensus         2 ~l~i~~~--d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v---~v~~~-~~~l~~l~~~L~~   65 (76)
T cd04888           2 TLSLLLE--HRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISI---DTSTM-NGDIDELLEELRE   65 (76)
T ss_pred             EEEEEec--CCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEE---EcCch-HHHHHHHHHHHhc
Confidence            3445553  3467899999999999999999987653 4656666666   44443 2255667777664

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.

>PRK04374 PII uridylyl-transferase; Provisional

Probab=91.03  E-value=1.8  Score=46.15  Aligned_cols=70  Identities=13%  Similarity=0.218  Sum_probs=53.6

Q ss_pred             CCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCeEEEEEEeeccccCCCc-cccHHHHHHHHHhhh
Q 039361          178 SGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEGFFHTIQAEESQVGDLT-CVDLRVLQLKLDHSI  252 (253)
Q Consensus       178 ~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~~~~tI~a~~~kv~~~~-~id~~~l~~kL~~~I  252 (253)
                      .+..+|.|.|.  .++++|++|..+|..+|++|++|.+.+ .+|.++-+|.+   .-.++. .-...+|++.|.+++
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 NDALEVFVYSP--DRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEV---LPQDTYADGDPQRLAAALRQVL  759 (869)
T ss_pred             CCeEEEEEEeC--CCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEE---eCCCCCChHHHHHHHHHHHHHH
Confidence            35788888884  568899999999999999999999876 68999999998   543332 223445777776654

>PRK05092 PII uridylyl-transferase; Provisional

Probab=90.81  E-value=2.4  Score=45.36  Aligned_cols=79  Identities=15%  Similarity=0.167  Sum_probs=57.4

Q ss_pred             CceEEEEEeC--CeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCeEEEEEEeeccccCCCccc-c---H
Q 039361          169 QNCVTIHPYS--GGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEGFFHTIQAEESQVGDLTCV-D---L  241 (253)
Q Consensus       169 ~p~V~V~~~~--~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~~~~tI~a~~~kv~~~~~i-d---~  241 (253)
                      ++.|.++...  +..+|.|.|.  .++++|++|..+|..+|++|++|.+.+ .|+.++-+|.+   .-.++..+ +   .
T Consensus       719 ~~~v~~~~~~~~~~t~v~I~~~--Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V---~~~~g~~~~~~~~~  793 (931)
T PRK05092        719 PLATEVRPDPARGVTEVTVLAA--DHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWI---QDAFGRDEDEPRRL  793 (931)
T ss_pred             CcEEEEEecCCCCeEEEEEEeC--CCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEE---ECCCCCCCCCHHHH
Confidence            3566665543  5788888885  467899999999999999999999876 67888888888   54443222 2   4


Q ss_pred             HHHHHHHHhhh
Q 039361          242 RVLQLKLDHSI  252 (253)
Q Consensus       242 ~~l~~kL~~~I  252 (253)
                      ..|++.|.+++
T Consensus       794 ~~l~~~L~~~l  804 (931)
T PRK05092        794 ARLAKAIEDAL  804 (931)
T ss_pred             HHHHHHHHHHH
Confidence            56777776553

>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=90.07  E-value=3.2  Score=29.42  Aligned_cols=54  Identities=13%  Similarity=0.049  Sum_probs=39.9

Q ss_pred             CcchHHHHHHHHHHCCceEEEEEeeee-CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          192 ENLKLSKVMEAVLEEGLDVIRCASTQT-DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       192 ~~~~Ls~Vm~~Lee~gLdVvsassS~~-~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      +++.|.+|+.+|.+.|..+.+++.... ++.....|.+   ++.+.  -.+..+-++|.+
T Consensus         9 ~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~v---ev~~~--~~l~~i~~~L~~   63 (74)
T cd04887           9 RPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITV---DAPSE--EHAETIVAAVRA   63 (74)
T ss_pred             CCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEE---EcCCH--HHHHHHHHHHhc
Confidence            467899999999999999999998876 4676677777   55553  234456666554

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.

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

Probab=89.78  E-value=2.9  Score=28.70  Aligned_cols=55  Identities=11%  Similarity=0.187  Sum_probs=38.5

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeee-----CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQT-----DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~-----~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.|.+|+.+|.+.|++|.+..+...     ++.....|..   ++.+  ..+...+.++|.+
T Consensus         7 d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v---~~~~--~~~l~~l~~~l~~   66 (73)
T cd04886           7 DRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTL---ETRG--AEHIEEIIAALRE   66 (73)
T ss_pred             CCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEE---EeCC--HHHHHHHHHHHHH
Confidence            3567899999999999999999987654     3556666666   4432  2344566666653

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.

>PRK04435 hypothetical protein; Provisional

Probab=88.78  E-value=3.1  Score=34.86  Aligned_cols=68  Identities=18%  Similarity=0.155  Sum_probs=49.9

Q ss_pred             eCCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          177 YSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       177 ~~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+..+.+.+...  .+++.|++|+..|.+.|++|.+.+.+. .++....+|.+   .+.+. ..++.+|-++|.+
T Consensus        66 ~~r~vtL~i~l~--Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tV---evs~~-~~~L~~Li~~L~~  134 (147)
T PRK04435         66 KGKIITLSLLLE--DRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISI---DTSSM-EGDIDELLEKLRN  134 (147)
T ss_pred             CCcEEEEEEEEe--cCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEE---EeCCh-HHHHHHHHHHHHc
Confidence            455677777664  346789999999999999999998764 46777777888   55443 3366777777764

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

Probab=88.64  E-value=3.9  Score=27.75  Aligned_cols=52  Identities=10%  Similarity=0.058  Sum_probs=38.0

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeeeC--CeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQTD--EGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~~--~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.|.+++..|.+.|+.+.+..+...+  +....++.+   +-     .....+.++|.+
T Consensus         8 d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v---~~-----~~~~~l~~~l~~   61 (71)
T cd04879           8 DVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV---DS-----PVPEEVLEELKA   61 (71)
T ss_pred             CCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc---CC-----CCCHHHHHHHHc
Confidence            45678999999999999999999887754  666666665   22     135566666654

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

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

Probab=88.14  E-value=4.3  Score=27.86  Aligned_cols=60  Identities=12%  Similarity=0.089  Sum_probs=39.1

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeee-CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQT-DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~-~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      ++.+.+  ..+++.|.+++..|.++++.+.+.+.... ++....+|..     .+.  .....+.++|.+
T Consensus         2 ~l~i~~--~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~~-----~~~--~~~~~~~~~L~~   62 (72)
T cd04874           2 ALSIIA--EDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYMEL-----EGV--GDIEELVEELRS   62 (72)
T ss_pred             eEEEEe--CCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEEE-----ecc--ccHHHHHHHHhC
Confidence            344555  34577899999999999999998887665 3444444554     221  244466666653

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=87.95  E-value=0.3  Score=48.77  Aligned_cols=63  Identities=16%  Similarity=0.209  Sum_probs=50.2

Q ss_pred             cccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCC-CchhhhHHHHHHHHHHHHHHHHHHH
Q 039361           80 NNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGK-RSISDHINEARNYINYLNKNIQELG  142 (253)
Q Consensus        80 ~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K-~Sis~il~eAI~YIKeLq~rVkeLe  142 (253)
                      ...+|+..++.||-|=+.+|+.|..|--+.=...+.+| ....-||..|+.-|-.|+++|.|-.
T Consensus       523 EkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN  586 (632)
T KOG3910|consen  523 EKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN  586 (632)
T ss_pred             HHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence            44778889999999999999999999876644433343 2557779999999999999998744

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

Probab=86.86  E-value=5.3  Score=24.54  Aligned_cols=37  Identities=16%  Similarity=0.148  Sum_probs=27.6

Q ss_pred             CcchHHHHHHHHHHCCceEEEEEeeeeC--CeEEEEEEe
Q 039361          192 ENLKLSKVMEAVLEEGLDVIRCASTQTD--EGFFHTIQA  228 (253)
Q Consensus       192 ~~~~Ls~Vm~~Lee~gLdVvsassS~~~--~~~~~tI~a  228 (253)
                      +++.+.+++..|...|+.+........+  +....++..
T Consensus         8 ~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~   46 (60)
T cd02116           8 RPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVV   46 (60)
T ss_pred             CCchHHHHHHHHHHCCCcEEEEEeEEcCCCCeEEEEEEE
Confidence            4567999999999999999999877653  333344444

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

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

Probab=86.38  E-value=5.2  Score=28.79  Aligned_cols=38  Identities=13%  Similarity=0.194  Sum_probs=29.7

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeeeCC-eEEEEEEe
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQTDE-GFFHTIQA  228 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~-~~~~tI~a  228 (253)
                      .+++.|++|+..+.++|+.+.+..+....+ .--|.|..
T Consensus         8 d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~i   46 (75)
T cd04880           8 NKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFV   46 (75)
T ss_pred             CcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEE
Confidence            357789999999999999999998887544 44455444

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

>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=85.89  E-value=7.5  Score=28.43  Aligned_cols=38  Identities=13%  Similarity=0.138  Sum_probs=30.7

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeeeC-CeEEEEEEe
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQTD-EGFFHTIQA  228 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~~-~~~~~tI~a  228 (253)
                      .+++.|++++..+.++|+.+++..+.... +...|.|.+
T Consensus        10 d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~v   48 (80)
T cd04905          10 NKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFI   48 (80)
T ss_pred             CCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEE
Confidence            35778999999999999999999877653 456677777

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

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

Probab=84.93  E-value=6.5  Score=25.67  Aligned_cols=55  Identities=16%  Similarity=0.199  Sum_probs=37.2

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeeeC-CeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQTD-EGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~~-~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.+.+++..|.++++++.+......+ +.....+..   .+.+  ..+...+.+.|..
T Consensus         7 ~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~---~~~~--~~~~~~~~~~l~~   62 (71)
T cd04876           7 DRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTL---EVRD--LEHLARIMRKLRQ   62 (71)
T ss_pred             ccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEE---EECC--HHHHHHHHHHHhC
Confidence            34678999999999999999999887655 544444555   3222  2345666666653

ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=84.43  E-value=5.7  Score=36.89  Aligned_cols=67  Identities=9%  Similarity=-0.007  Sum_probs=49.0

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .+.|.+.|.  .+++...+|-+.|-++|+++.+.+..+..+.-+|++.+   .+..+...+...|+++|..+
T Consensus         7 ~~vitv~G~--DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~---~~~~p~~~~~~~L~~~L~~l   73 (286)
T PRK13011          7 TFVLTLSCP--SAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRV---EFHSEEGLDEDALRAGFAPI   73 (286)
T ss_pred             eEEEEEEeC--CCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEE---EEecCCCCCHHHHHHHHHHH
Confidence            456777774  56788999999999999999999987433322333556   55544467899999998764

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

Probab=84.38  E-value=6.5  Score=26.80  Aligned_cols=50  Identities=10%  Similarity=0.119  Sum_probs=36.4

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeeeC--CeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQTD--EGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~~--~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.|.+++..|.++|+.|.+...+...  +...+.|+.   +-       ...+.+.|.+
T Consensus         8 d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~v---e~-------~~~~~~~L~~   59 (65)
T cd04882           8 DKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRT---ED-------IEKAIEVLQE   59 (65)
T ss_pred             CCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEe---CC-------HHHHHHHHHH
Confidence            45788999999999999999877655443  566667777   21       5566666654

Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=84.34  E-value=12  Score=26.23  Aligned_cols=58  Identities=10%  Similarity=0.229  Sum_probs=39.8

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeee--CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQT--DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~--~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      +.+..  ..+++.|.+++..|.+.|+.+.+......  ++.....|+.   ..     .+...+.+.|.+
T Consensus         4 ~~v~~--~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v---~~-----~~~~~~~~~L~~   63 (72)
T cd04883           4 IEVRV--PDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRV---QT-----MNPRPIIEDLRR   63 (72)
T ss_pred             EEEEE--CCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEE---ec-----CCHHHHHHHHHH
Confidence            44444  34567899999999999999998865443  4566677777   33     233477777654

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=83.83  E-value=4.1  Score=29.47  Aligned_cols=58  Identities=10%  Similarity=0.155  Sum_probs=38.1

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      +.+.+.  .+.+.|.+|+.++.++|+.+.++++.+. +.+..++.+     .+  ......|-++|.+
T Consensus         3 l~I~~~--dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~l~i~v-----~~--~~~L~~li~~L~~   60 (74)
T cd04877           3 LEITCE--DRLGITQEVLDLLVEHNIDLRGIEIDPK-GRIYLNFPT-----IE--FEKLQTLMPEIRR   60 (74)
T ss_pred             EEEEEE--ccchHHHHHHHHHHHCCCceEEEEEecC-CeEEEEeEe-----cC--HHHHHHHHHHHhC
Confidence            445553  3467899999999999999999998765 443333333     32  2235555555553

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

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

Probab=82.06  E-value=13  Score=25.16  Aligned_cols=52  Identities=6%  Similarity=0.095  Sum_probs=36.1

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeee--CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQT--DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~--~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.|.++...|.++|+.+.+......  ++.....|..   +  +.   +...+-++|.+
T Consensus         8 d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v---~--~~---~~~~~i~~l~~   61 (71)
T cd04903           8 DKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEV---D--QP---IDEEVIEEIKK   61 (71)
T ss_pred             CCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEe---C--CC---CCHHHHHHHHc
Confidence            4567899999999999999998876652  3555455665   2  11   55566666654

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.

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

Probab=80.90  E-value=7.4  Score=41.36  Aligned_cols=77  Identities=19%  Similarity=0.238  Sum_probs=57.7

Q ss_pred             eEEEEEeCCeeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEee-eeCCeEEEEEEeeccccCCCccccHH---HHHH
Q 039361          171 CVTIHPYSGGVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCAST-QTDEGFFHTIQAEESQVGDLTCVDLR---VLQL  246 (253)
Q Consensus       171 ~V~V~~~~~~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS-~~~~~~~~tI~a~~~kv~~~~~id~~---~l~~  246 (253)
                      .+.++...++.+|.|.|+  .++.+|..+..++...|++|+.|++- +.+|..+-||.+   .--++..++..   .+..
T Consensus       675 ~~~~r~~~~~teV~V~a~--d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv---~~~~g~~~~~dr~~~~~~  749 (867)
T COG2844         675 LISVRPHSGGTEVFVYAP--DRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIV---LEPDGFPVEEDRRAALRG  749 (867)
T ss_pred             eeeecccCCceEEEEEcC--CCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEE---ecCCCCccchhHHHHHHH
Confidence            345667778999999995  56889999999999999999999965 578889999988   54444444433   3445


Q ss_pred             HHHhhh
Q 039361          247 KLDHSI  252 (253)
Q Consensus       247 kL~~~I  252 (253)
                      .|.+++
T Consensus       750 ~l~~~l  755 (867)
T COG2844         750 ELIEAL  755 (867)
T ss_pred             HHHHHH
Confidence            555543

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

Probab=80.66  E-value=15  Score=24.88  Aligned_cols=54  Identities=13%  Similarity=0.049  Sum_probs=37.9

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeee--CCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQT--DEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~--~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.|.+++..|.++|+.+.+.+....  ++...+.|..   .+.  . .....+..+|.+
T Consensus         9 d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~---~~~--~-~~~~~l~~~l~~   64 (72)
T cd04878           9 NEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVV---EGD--D-DVIEQIVKQLNK   64 (72)
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEE---ECC--H-HHHHHHHHHHhC
Confidence            4567899999999999999999987764  4566666666   432  1 345555555553

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

---

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	253
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	5e-04

>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 = 40.0 bits (94), Expect = 5e-05
 Identities = 19/72 (26%), Positives = 29/72 (40%)

Query: 79  NNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNI 138
           + N K      +ERQRR  L     +LR  +P      K      + +A  YI  +    
Sbjct: 2   HMNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEE 61

Query: 139 QELGLKRDKLKN 150
           Q+L  + D L+ 
Sbjct: 62  QKLISEEDLLRK 73

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

 Score = 43.3 bits (101), Expect = 5e-05
 Identities = 49/309 (15%), Positives = 104/309 (33%), Gaps = 70/309 (22%)

Query: 10  LVHQFEHSDDPFPFHYNPYQEHSNIQQDQ---ILQGQ----ALLE-RNINSSKMGK--GQ 59
           L++Q + +      H +  +   +  Q +   +L+ +     LL   N+ ++K       
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL 264

Query: 60  QHKLLFVATTKVNDGNSD--NNNNKKMILRKDIER--QRRQHLSMLHASLR---SLLPLQ 112
             K+L   TT+     +D  +      I            +  S+L   L      LP +
Sbjct: 265 SCKILL--TTR-FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321

Query: 113 SITG--------KRSISDHINEARNYINYLNKNIQEL------GLKRDKLKNLSELGAVG 158
            +T           SI D +    N+ +     +  +       L+  + + + +  +V 
Sbjct: 322 VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381

Query: 159 HGSSN---------WDNCLQNCV-----TIHPYS----GGVE--IVINSVHKEENLKLS- 197
             S++         W + +++ V      +H YS       E  I I S++ E  +KL  
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLEN 441

Query: 198 -KVMEAVLEEGLDVIRC-----ASTQTDEGFF------HTIQAEESQVGDL---TCVDLR 242
              +   + +  ++ +            + +F      H    E  +   L     +D R
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR 501

Query: 243 VLQLKLDHS 251
            L+ K+ H 
Sbjct: 502 FLEQKIRHD 510

>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 = 37.0 bits (86), Expect = 5e-04
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 88  KDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDK 147
             +ER+RR H+     SLR  +P      K S +  +++A  YI Y+ +         D 
Sbjct: 7   NALERKRRDHIKDSFHSLRDSVP-SLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD 65

Query: 148 LKN 150
           LK 
Sbjct: 66  LKR 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	253
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.56
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.56
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.56
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.56
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.53
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.48
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.45
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.39
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.38
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.34
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.26
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.15
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.15
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.66
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.6
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.37
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.15
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.52
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	95.83
1u8s_A	192	Glycine cleavage system transcriptional repressor,	93.03
2nyi_A	195	Unknown protein; protein structure initiative, PSI	91.81
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	90.83
1u8s_A	192	Glycine cleavage system transcriptional repressor,	90.21
2nyi_A	195	Unknown protein; protein structure initiative, PSI	87.56

>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=99.56  E-value=3e-15  Score=113.16  Aligned_cols=69  Identities=22%  Similarity=0.272  Sum_probs=61.6

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhhh
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNL  151 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~~  151 (253)
                      ..++..|+.+||+||.+||+.|..|++|||...  .|+|.++||.+||+||++||.+++.|+.+.+.|...
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~--~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   72 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999852  477888889999999999999999999988777654

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

Probab=99.56  E-value=6.2e-15  Score=111.17  Aligned_cols=67  Identities=21%  Similarity=0.332  Sum_probs=61.7

Q ss_pred             cccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q 039361           84 MILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN  150 (253)
Q Consensus        84 k~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~  150 (253)
                      +..|+..||+||.+||..|..|+++||......|+|.++||..|++||++|+++.++|+.+++.+..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999998877789999999999999999999999999988766643

>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=99.56  E-value=4.4e-15  Score=112.02  Aligned_cols=67  Identities=28%  Similarity=0.409  Sum_probs=60.5

Q ss_pred             ccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q 039361           83 KMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN  150 (253)
Q Consensus        83 kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~  150 (253)
                      ++..|+..||+||..||+.|..|+++||... ..|+|.++||..||+||++|++++++|+.+++.+..
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~   68 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6889999999999999999999999999753 357899999999999999999999999988776654

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

Probab=99.56  E-value=3.1e-15  Score=112.30  Aligned_cols=71  Identities=27%  Similarity=0.402  Sum_probs=63.9

Q ss_pred             CcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q 039361           79 NNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN  150 (253)
Q Consensus        79 ~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~  150 (253)
                      ....++..|+.+||+||..||..|..|++|||... ..|+|.++||..||+||++|++++++|+.+.+.|..
T Consensus         8 ~~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~   78 (80)
T 1hlo_A            8 SDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   78 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             chHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34578999999999999999999999999999764 358899999999999999999999999998877754

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

Probab=99.53  E-value=7.2e-15  Score=112.59  Aligned_cols=69  Identities=28%  Similarity=0.259  Sum_probs=61.4

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhh
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLK  149 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~  149 (253)
                      ..++..|++.||+||.+||+.|..|+++||......|+|.++||..||+||++|+++.+.|...++.+.
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999876567889999999999999999999999887665543

>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=99.48  E-value=4.2e-15  Score=107.37  Aligned_cols=56  Identities=29%  Similarity=0.322  Sum_probs=50.2

Q ss_pred             ccccchHHHHHHHHHHHhcHhhhhccCCCCCcC----CCCchhhhHHHHHHHHHHHHHHH
Q 039361           83 KMILRKDIERQRRQHLSMLHASLRSLLPLQSIT----GKRSISDHINEARNYINYLNKNI  138 (253)
Q Consensus        83 kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k----~K~Sis~il~eAI~YIKeLq~rV  138 (253)
                      ++.+|+.+||.||..||..|..|++|||..+..    .|.|.+++|+.||+||++||+++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999999999999976543    47788888999999999999865

>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=99.45  E-value=1.7e-14  Score=104.09  Aligned_cols=58  Identities=22%  Similarity=0.401  Sum_probs=51.2

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcC---CCCchhhhHHHHHHHHHHHHHHH
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSIT---GKRSISDHINEARNYINYLNKNI  138 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k---~K~Sis~il~eAI~YIKeLq~rV  138 (253)
                      ..++..|+.+||+||..||+.|..|++|||.....   .|+|.++||..||+||++||++.
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            45799999999999999999999999999987642   46778888999999999999764

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

Probab=99.39  E-value=6.4e-14  Score=104.73  Aligned_cols=63  Identities=19%  Similarity=0.228  Sum_probs=51.7

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCC-chhhhHHHHHHHHHHHHHHHHHHHH
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKR-SISDHINEARNYINYLNKNIQELGL  143 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~-Sis~il~eAI~YIKeLq~rVkeLe~  143 (253)
                      ..++..|++.||+||..+|+.|..||.+||.....+|+ |..+||..||+||+.||+.+++++.
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999964456677 7889999999999999999998764

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

Probab=99.38  E-value=3.5e-13  Score=108.33  Aligned_cols=65  Identities=20%  Similarity=0.196  Sum_probs=52.0

Q ss_pred             cccccccchHHHHHHHHHHHhcHhhhhccCCCCCcC-CCCchhhhHHHHHHHHHHHHHHHHHHHHh
Q 039361           80 NNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSIT-GKRSISDHINEARNYINYLNKNIQELGLK  144 (253)
Q Consensus        80 ~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k-~K~Sis~il~eAI~YIKeLq~rVkeLe~k  144 (253)
                      ...++..|+.+||+||.+||+.|..|++|||....+ .|++.++||..||+||++||+.++.|+..
T Consensus        24 ~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           24 ERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            446899999999999999999999999999987654 47888999999999999999999999864

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

Probab=99.34  E-value=7.3e-13  Score=97.80  Aligned_cols=62  Identities=21%  Similarity=0.317  Sum_probs=53.9

Q ss_pred             CcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHH
Q 039361           79 NNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELG  142 (253)
Q Consensus        79 ~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe  142 (253)
                      ....++..|+.+||+||.+||+.|..|++|||...  .|++.++||..||+||++||+.+.=|+
T Consensus         4 k~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~--~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            4 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNA--RKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCC--SCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCC--CCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            35678999999999999999999999999999532  467778889999999999999886554

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

Probab=99.26  E-value=3.6e-12  Score=91.11  Aligned_cols=58  Identities=28%  Similarity=0.320  Sum_probs=53.4

Q ss_pred             cccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 039361           82 KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQ  139 (253)
Q Consensus        82 ~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVk  139 (253)
                      +++..|++.||+|++.||..|..||.+||......|.|..++|-.||+||..|++.++
T Consensus         1 ~rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            1 SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            3678899999999999999999999999988777799999999999999999998764

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

Probab=99.15  E-value=3.8e-12  Score=94.41  Aligned_cols=57  Identities=19%  Similarity=0.225  Sum_probs=48.3

Q ss_pred             cccccccchHHHHHHHHHHHhcHhhhhccCCCCC-cCCCCchhhhHHHHHHHHHHHHH
Q 039361           80 NNKKMILRKDIERQRRQHLSMLHASLRSLLPLQS-ITGKRSISDHINEARNYINYLNK  136 (253)
Q Consensus        80 ~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~-~k~K~Sis~il~eAI~YIKeLq~  136 (253)
                      -..++..|..+||+||.+||+.|..|++|||... ...|.+.++||..||+||+.|+.
T Consensus         6 ~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            6 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            3567899999999999999999999999999652 12366667779999999999974

>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=99.15  E-value=1.6e-11  Score=89.87  Aligned_cols=59  Identities=15%  Similarity=0.164  Sum_probs=52.7

Q ss_pred             cccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 039361           80 NNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQ  139 (253)
Q Consensus        80 ~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVk  139 (253)
                      ...++..|++.||+|+..||+.|..||.+||... ..|.|..++|-.||+||..|++.++
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~-~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCT-TSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            4467889999999999999999999999999754 5689999999999999999998653

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

Probab=98.66  E-value=4.4e-09  Score=76.80  Aligned_cols=48  Identities=17%  Similarity=0.128  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHH
Q 039361           89 DIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNK  136 (253)
Q Consensus        89 ~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~  136 (253)
                      +.||+|+..||.-|..||.+||......|.|..++|--||+||..||+
T Consensus        20 erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           20 EEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            568999999999999999999998877799999999999999999984

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

Probab=98.60  E-value=2.7e-08  Score=91.56  Aligned_cols=59  Identities=22%  Similarity=0.398  Sum_probs=39.8

Q ss_pred             CCCcccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHH
Q 039361           77 DNNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKN  137 (253)
Q Consensus        77 ~~~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~r  137 (253)
                      +.....++..|+.+||+||.+||..|..|++|||..  ..|.+.++||..||.|||.|+..
T Consensus         6 ~~~~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~--~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A            6 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGN--ARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -------------CHHHHHHHHHHHHHHHHHTCCSS--SCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             ccccchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCC--CCCcCHHHHHHHHHHHHHHHHhh
Confidence            344568899999999999999999999999999932  24666677799999999999754

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

Probab=98.37  E-value=9.9e-08  Score=88.93  Aligned_cols=60  Identities=18%  Similarity=0.216  Sum_probs=47.3

Q ss_pred             CCcccccccchHHHHHHHHHHHhcHhhhhccCCCCC-cCCCCchhhhHHHHHHHHHHHHHH
Q 039361           78 NNNNKKMILRKDIERQRRQHLSMLHASLRSLLPLQS-ITGKRSISDHINEARNYINYLNKN  137 (253)
Q Consensus        78 ~~~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~-~k~K~Sis~il~eAI~YIKeLq~r  137 (253)
                      .....++.+|+.+||.||.+||..|..|++|||... ...|.+.++||..||.|||.|+..
T Consensus         8 ~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B            8 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             chhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            334578999999999999999999999999999421 123555566799999999999843

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

Probab=98.15  E-value=2.4e-06  Score=66.38  Aligned_cols=51  Identities=16%  Similarity=0.120  Sum_probs=45.8

Q ss_pred             HHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHH
Q 039361           90 IERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQE  140 (253)
Q Consensus        90 ~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVke  140 (253)
                      .||.|=..||+-|..||.+||......|.|..++|--||+||..|++-+++
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            358888899999999999999887777999999999999999999988754

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

Probab=97.52  E-value=0.00017  Score=54.38  Aligned_cols=50  Identities=16%  Similarity=0.171  Sum_probs=42.3

Q ss_pred             HHHHHhcHhhhhccCCCCC-cCCCCchhhhHHHHHHHHHHHHHHHHHHHHh
Q 039361           95 RQHLSMLHASLRSLLPLQS-ITGKRSISDHINEARNYINYLNKNIQELGLK  144 (253)
Q Consensus        95 R~kMn~lf~~LRSLLP~~~-~k~K~Sis~il~eAI~YIKeLq~rVkeLe~k  144 (253)
                      |-.+|..+..|..|||... ...|++..+||.-|++||++||+..+.+.+.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~   54 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   54 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6779999999999999743 4458899999999999999999887777543

>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=95.83  E-value=0.12  Score=37.42  Aligned_cols=64  Identities=17%  Similarity=0.154  Sum_probs=50.9

Q ss_pred             eEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          181 VEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       181 veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      +.|.+.|.  .+++.|.+|..+|-+.|+.|.+++....++.++..+.+   .+.+  ..+...|.++|.++
T Consensus         6 ~~l~v~~~--DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v---~~~~--~~~l~~l~~~L~~~   69 (91)
T 1zpv_A            6 AIITVVGK--DKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVV---SSDE--KQDFTYLRNEFEAF   69 (91)
T ss_dssp             EEEEEEES--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE---EESS--CCCHHHHHHHHHHH
T ss_pred             EEEEEEEC--CCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEE---EeCC--CCCHHHHHHHHHHH
Confidence            45666674  56889999999999999999999998888877777777   5544  34788888888764

>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=93.03  E-value=0.47  Score=39.22  Aligned_cols=64  Identities=11%  Similarity=0.083  Sum_probs=50.0

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .+.|.+.|.  .+++.+++|..+|.+.|+.|+.++.....+.++.++.+   ....   .+...|++.|.++
T Consensus         6 ~~~itv~~~--DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v---~~~~---~~~~~l~~~L~~~   69 (192)
T 1u8s_A            6 HLVITAVGT--DRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLI---SGSP---SNITRVETTLPLL   69 (192)
T ss_dssp             EEEEEEEEE--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE---EECH---HHHHHHHHHHHHH
T ss_pred             EEEEEEEcC--CCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEE---ecCC---CCHHHHHHHHHHH
Confidence            356777775  45789999999999999999999999888888888777   4321   3567777777654

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

Probab=91.81  E-value=0.75  Score=38.44  Aligned_cols=66  Identities=8%  Similarity=-0.031  Sum_probs=48.5

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCc-cccHHHHHHHHHh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLT-CVDLRVLQLKLDH  250 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~-~id~~~l~~kL~~  250 (253)
                      .+.|.|.|.  .+++.++.|...|.++|+.|+.++..+..+.++..+.+   ...... ......|++.|..
T Consensus         5 ~~~ltv~~~--DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v---~~~~~~~~~~~~~l~~~L~~   71 (195)
T 2nyi_A            5 SFVVSVAGS--DRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLV---SLNAKDGKLIQSALESALPG   71 (195)
T ss_dssp             EEEEEEEEE--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE---EESSSSSHHHHHHHHHHSTT
T ss_pred             EEEEEEEeC--CCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEE---EecCccchhHHHHHHHHHHH
Confidence            357778885  45789999999999999999999999888887777777   433210 0115667776654

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

Probab=90.83  E-value=0.64  Score=32.82  Aligned_cols=62  Identities=16%  Similarity=0.094  Sum_probs=42.1

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .|.+.+.  .+++.|.+|..+|.+.|+.+.+++....++.....+.+   .+.+  .....++.++|.+
T Consensus         7 ~l~v~~~--Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v---~~~~--~~~l~~l~~~L~~   68 (88)
T 2ko1_A            7 GIRIVGE--DKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMI---FVKN--TDKLTTLMDKLRK   68 (88)
T ss_dssp             EEEEEEE--CCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEE---EESS--HHHHHHHHHHHTT
T ss_pred             EEEEEEE--CCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEE---EECC--HHHHHHHHHHHhc
Confidence            4445453  45788999999999999999999988766644455555   4433  2244555555543

>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=90.21  E-value=1.4  Score=36.32  Aligned_cols=65  Identities=18%  Similarity=0.201  Sum_probs=47.1

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeC--------CeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTD--------EGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~--------~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      ...|.+.|.  .+++.+.+|...|.+.|++|..+...+.+        +.++-.+..   ...  ...+...|++.|..+
T Consensus        93 ~~~l~v~~~--D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~---~~~--~~~~~~~l~~~l~~~  165 (192)
T 1u8s_A           93 TVEVYVESD--DKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISA---RVD--SGCNLMQLQEEFDAL  165 (192)
T ss_dssp             EEEEEEEES--CCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEE---EEC--TTSCHHHHHHHHHHH
T ss_pred             eEEEEEEeC--CCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEE---eCC--CCCCHHHHHHHHHHH
Confidence            345666664  45788999999999999999999888664        244444555   332  356888999998764

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

Probab=87.56  E-value=2  Score=35.72  Aligned_cols=64  Identities=8%  Similarity=0.075  Sum_probs=47.2

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeC------CeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTD------EGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~------~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      ...|.|.|.  .+++.+.+|-..|-++|+.|.++...+.+      ++++-.+..   .+.  ...+ ..|++.|..+
T Consensus        93 ~~iltv~g~--DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~---~~~--~~~~-~~l~~~l~~~  162 (195)
T 2nyi_A           93 EYELYVEGP--DSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRV---AFP--FPLY-QEVVTALSRV  162 (195)
T ss_dssp             EEEEEEEEE--CCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEE---EEE--GGGH-HHHHHHHHHH
T ss_pred             EEEEEEEeC--CCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEE---EcC--CCcc-HHHHHHHHHH
Confidence            356777775  45789999999999999999999988775      455555555   332  2446 8888888754

---

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	253
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-10
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	2e-07
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	6e-06
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-05
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	2e-05
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-04

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 19/70 (27%), Positives = 28/70 (40%)

Query: 81  NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQE 140
           N K      +ERQRR  L     +LR  +P      K      + +A  YI  +    Q+
Sbjct: 4   NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQK 63

Query: 141 LGLKRDKLKN 150
           L  + D L+ 
Sbjct: 64  LISEEDLLRK 73

>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 = 45.3 bits (107), Expect = 2e-07
 Identities = 14/62 (22%), Positives = 33/62 (53%)

Query: 88  KDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDK 147
            ++E+ RR HL +    L+ L+PL   + + +    + +A+ +I  L  + ++   + D+
Sbjct: 6   NEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQ 65

Query: 148 LK 149
           L+
Sbjct: 66  LQ 67

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

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

 Score = 40.6 bits (95), Expect = 6e-06
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 90  IERQRRQHLSMLHASLRSLLP----LQSITGKRSISDHINEARNYINYLNKNIQ 139
            E+ RR  L++    L SL+P     Q+++   S +  +  A  YI +L +N  
Sbjct: 9   AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>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 = 39.5 bits (92), Expect = 2e-05
 Identities = 8/53 (15%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 88  KDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQE 140
              ER+R   ++    +L+      +   +    + +  A  YI  L   +++
Sbjct: 17  TMRERRRLSKVNEAFETLKRSTS-SNPNQRLPKVEILRNAIRYIEGLQALLRD 68

>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 = 39.9 bits (93), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 87  RKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRD 146
              +ER+RR H+     SLR  +P      K S +  +++A  YI Y+ +         D
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKNHTHQQDID 64

Query: 147 KLK 149
            LK
Sbjct: 65  DLK 67

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 82  KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQEL 141
           +K      IE++ R  ++     L+ L+       K + S  + +A +YI +L  + Q+L
Sbjct: 5   EKRTAHNAIEKRYRSSINDKIIELKDLVV--GTEAKLNKSAVLRKAIDYIRFLQHSNQKL 62

Query: 142 GLKRDKLKNLSE 153
             +   L+    
Sbjct: 63  KQENLSLRTAVH 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	253
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.59
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.58
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.47
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.46
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.36
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.16
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	95.4
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	95.04
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	94.27
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	85.68
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	84.83

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

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

Probab=99.59  E-value=9e-16  Score=112.94  Aligned_cols=66  Identities=21%  Similarity=0.335  Sum_probs=60.9

Q ss_pred             cccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhh
Q 039361           84 MILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLK  149 (253)
Q Consensus        84 k~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~  149 (253)
                      +..|+.+||+||.+||+.|..|++|||......|+|.++||..||+||++|++.++.|..+++.+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~   67 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            568999999999999999999999999887778899999999999999999999999998876654

>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=99.58  E-value=1.2e-15  Score=114.40  Aligned_cols=70  Identities=27%  Similarity=0.259  Sum_probs=63.0

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN  150 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~  150 (253)
                      ..++..|+++||+||..||+.|..|++|||......|.|.++||..||+||++|++.+++|+.+++.+..
T Consensus         4 ~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   73 (88)
T d1nkpa_           4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK   73 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3568899999999999999999999999998777778999999999999999999999999887765543

>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=99.52  E-value=5.5e-15  Score=109.16  Aligned_cols=67  Identities=22%  Similarity=0.284  Sum_probs=60.1

Q ss_pred             cccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q 039361           82 KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN  150 (253)
Q Consensus        82 ~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~  150 (253)
                      .++..|+++||+||..||+.|..|++|||...  +|.|.++||..||+||++|+++++.|..+...+..
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~--~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~   71 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56889999999999999999999999999754  47788889999999999999999999988766654

>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=99.50  E-value=1.2e-14  Score=107.74  Aligned_cols=67  Identities=28%  Similarity=0.410  Sum_probs=58.7

Q ss_pred             cccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhh
Q 039361           82 KKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLK  149 (253)
Q Consensus        82 ~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~  149 (253)
                      .++..|+.+||+||.+||+.|..|++|||... ..|+|.++||..||+||+.|++.++.|....+.+.
T Consensus         1 ~rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~-~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   67 (83)
T d1nkpb_           1 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36889999999999999999999999999643 34788899999999999999999999988765543

>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=99.47  E-value=7e-15  Score=104.11  Aligned_cols=56  Identities=29%  Similarity=0.386  Sum_probs=49.2

Q ss_pred             ccccchHHHHHHHHHHHhcHhhhhccCCCC----CcCCCCchhhhHHHHHHHHHHHHHHH
Q 039361           83 KMILRKDIERQRRQHLSMLHASLRSLLPLQ----SITGKRSISDHINEARNYINYLNKNI  138 (253)
Q Consensus        83 kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~----~~k~K~Sis~il~eAI~YIKeLq~rV  138 (253)
                      ++..|+.+||+||.+||+.|..|++|||..    ....|.|.++||..||+||++||++|
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            578999999999999999999999999953    23457788888999999999999865

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

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

Probab=99.46  E-value=1.1e-14  Score=104.77  Aligned_cols=59  Identities=15%  Similarity=0.146  Sum_probs=53.0

Q ss_pred             cccccccchHHHHHHHHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 039361           80 NNKKMILRKDIERQRRQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQ  139 (253)
Q Consensus        80 ~~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVk  139 (253)
                      ...++..|+..||+||..||+.|..|++|||.... +|.|.+++|..||+||++||+.|+
T Consensus         9 ~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~-~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPN-QRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTT-SCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHhh
Confidence            44678899999999999999999999999998753 588999999999999999998765

>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=1.1e-13  Score=98.38  Aligned_cols=57  Identities=23%  Similarity=0.425  Sum_probs=50.0

Q ss_pred             ccccccchHHHHHHHHHHHhcHhhhhccCCCCCcC---CCCchhhhHHHHHHHHHHHHHH
Q 039361           81 NKKMILRKDIERQRRQHLSMLHASLRSLLPLQSIT---GKRSISDHINEARNYINYLNKN  137 (253)
Q Consensus        81 ~~kk~~H~~~ERqRR~kMn~lf~~LRSLLP~~~~k---~K~Sis~il~eAI~YIKeLq~r  137 (253)
                      +.++..|+.+||+||..||..|..|++|||..+..   .|.|.++||..||+||++||++
T Consensus         3 ~~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            56789999999999999999999999999976532   3677788899999999999865

>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=99.16  E-value=6.7e-12  Score=88.02  Aligned_cols=54  Identities=24%  Similarity=0.241  Sum_probs=45.9

Q ss_pred             HHHHHhcHhhhhccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q 039361           95 RQHLSMLHASLRSLLPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKN  150 (253)
Q Consensus        95 R~kMn~lf~~LRSLLP~~~~k~K~Sis~il~eAI~YIKeLq~rVkeLe~kK~~l~~  150 (253)
                      |.+||+.|..||+|||+...  |+|.++||.+||+||+.||+++++|+.+...+..
T Consensus         1 R~~in~~f~~L~~lvP~~~~--K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   54 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDA--KMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKL   54 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSC--CCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCC--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56899999999999998652  4555666999999999999999999998776654

>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=95.40  E-value=0.099  Score=36.29  Aligned_cols=63  Identities=17%  Similarity=0.156  Sum_probs=51.3

Q ss_pred             EEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          182 EIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       182 eI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .|.+.|+  .+++.++.|-..|-+.|..+.+++-...++.++..+.+   .+..  ..+.+.|+++|..+
T Consensus         4 vitv~g~--DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v---~~~~--~~~~~~l~~~l~~l   66 (83)
T d1zpva1           4 IITVVGK--DKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVV---SSDE--KQDFTYLRNEFEAF   66 (83)
T ss_dssp             EEEEEES--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE---EESS--CCCHHHHHHHHHHH
T ss_pred             EEEEEcC--CCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEE---EEec--CCCHHHHHHHHHHH
Confidence            4667774  56889999999999999999999999999988877777   5443  45788899888764

>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=95.04  E-value=0.066  Score=37.67  Aligned_cols=64  Identities=11%  Similarity=0.078  Sum_probs=51.4

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .+.|.+.|.  .+++.+.+|...|-+.|..++.++....++.+...+.+   .....   ++++|+..|.++
T Consensus         5 ~~vitv~G~--DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v---~~~~~---~~~~l~~~L~~l   68 (86)
T d1u8sa1           5 HLVITAVGT--DRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLI---SGSPS---NITRVETTLPLL   68 (86)
T ss_dssp             EEEEEEEEE--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE---EECHH---HHHHHHHHHHHH
T ss_pred             EEEEEEEeC--CCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEE---EcCcc---cHHHHHHHHHHH
Confidence            456777774  46889999999999999999999999999999888888   54332   567788777654

>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=94.27  E-value=0.15  Score=36.30  Aligned_cols=67  Identities=15%  Similarity=0.072  Sum_probs=48.0

Q ss_pred             eeEEEEEeecCCCcchHHHHHHHHHHCCceEEEEEeeeeC------CeEEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          180 GVEIVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQTD------EGFFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       180 ~veI~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~~~------~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      .++|.|.|.  .+++.+.+|-..|-++|+.+.+.+..+..      +.-.+.+++   .+.-+..++...|+++|..+
T Consensus         6 tv~v~v~g~--DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~---~~~~p~~~~~~~l~~~l~~l   78 (93)
T d1u8sa2           6 TVEVYVESD--DKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAI---SARVDSGCNLMQLQEEFDAL   78 (93)
T ss_dssp             EEEEEEEES--CCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEE---EEEECTTSCHHHHHHHHHHH
T ss_pred             EEEEEEEEC--CCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEE---EEEcCccccHHHHHHHHHHH
Confidence            567888885  56889999999999999999999876532      122333444   33334467899999998765

>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=85.68  E-value=1.1  Score=30.61  Aligned_cols=61  Identities=11%  Similarity=0.016  Sum_probs=38.5

Q ss_pred             EEEEeecCCCcchHHHHHHHHHHCCceEEEEEeee-eCCe--EEEEEEeeccccCCCccccHHHHHHHHHhh
Q 039361          183 IVINSVHKEENLKLSKVMEAVLEEGLDVIRCASTQ-TDEG--FFHTIQAEESQVGDLTCVDLRVLQLKLDHS  251 (253)
Q Consensus       183 I~i~~~~~~~~~~Ls~Vm~~Lee~gLdVvsassS~-~~~~--~~~tI~a~~~kv~~~~~id~~~l~~kL~~~  251 (253)
                      |.+.|.  .+++.|.+|..++-++|+.+.+++... .+|.  +..+|..   +..   ..+..+|-++|..+
T Consensus         4 i~i~~~--Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v---~~~---~~~l~~ll~kL~~l   67 (77)
T d1y7pa2           4 LRIIAE--NKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYF---EIE---GGDFEKILERVKTF   67 (77)
T ss_dssp             EEEEEE--CCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEE---EEC---SSCHHHHHHHHHTC
T ss_pred             EEEEEe--cCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEE---EcC---cccHHHHHHHHHcC
Confidence            455563  457899999999999999999998775 4442  3344444   222   23788888888753

>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=84.83  E-value=3.9  Score=27.23  Aligned_cols=50  Identities=16%  Similarity=0.044  Sum_probs=39.0

Q ss_pred             CCcchHHHHHHHHHHCCceEEEEEeeeeCCeEEEEEEeeccccCCCccccHHHHHHHHHh
Q 039361          191 EENLKLSKVMEAVLEEGLDVIRCASTQTDEGFFHTIQAEESQVGDLTCVDLRVLQLKLDH  250 (253)
Q Consensus       191 ~~~~~Ls~Vm~~Lee~gLdVvsassS~~~~~~~~tI~a~~~kv~~~~~id~~~l~~kL~~  250 (253)
                      .+++.|.++++.|.+.|+.|........++.-+..|.+     .     |+....+.|.+
T Consensus         8 d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~v-----d-----d~~~a~~~L~~   57 (71)
T d2f06a1           8 NVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRP-----S-----NMDKCIEVLKE   57 (71)
T ss_dssp             SSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEE-----S-----CHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEE-----C-----CHHHHHHHHHH
Confidence            45788999999999999999999888878877666666     1     45566666654