Citrus Sinensis ID: 039443

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
AQRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESLERRRALLKEEDHYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHFRPTQAE
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcccccEEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEcccEEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEEccccccc
Coil and Loop (DISEMBL)
AQRNIKEKHRRTHMKDLISQLASlipsssklsmpeILDEATSYITHLQKNKESLERRRALLKeedhyeptvmnittsgsTLEVNLICGSNRNFMFHEIISVLEEGAAEVInvtqfnsgdrVIFSVLSkvhfrptqae
Flexible Loop (DISEMBL)
aqrnikekhrrtHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESLERRRALLkeedhyeptvmnittsgstLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSvlskvhfrptqae
Low Complexity Region (SEG)
AQRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESLERRRALLKEEDHYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHFRPTQAE
Disordered region (IsUnstruct)
******************************************************************YEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF******
Disordered Region (DISOPRED)
*QRNIKEKHRRTHMKDLISQLASL************LDEATSYITHLQ********************************LEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF******
Disordered Region (DISEMBL)
************HMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESLERRRALLKEEDHYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHFRPTQAE
Disordered Region (DISPRO)
**RNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESLERRRALLKEEDHYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHFRP****
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
AQRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEIxxxxxxxxxxxxxxxxxxxxxxxxxxxxDHYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHFRPTQAE
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

No hits with e-value below 0.001 by BLAST

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	137
225425500	370	PREDICTED: uncharacterized protein LOC10	0.897	0.332	0.426	9e-19
225425498	189	PREDICTED: uncharacterized protein LOC10	0.919	0.666	0.416	1e-17
147799004	905	hypothetical protein VITISV_014706 [Viti	0.890	0.134	0.352	2e-15
147863541	168	hypothetical protein VITISV_038226 [Viti	0.890	0.726	0.383	3e-15
5091553	188	T10O24.22 [Arabidopsis thaliana]	0.934	0.680	0.375	3e-15
79340924	181	basic helix-loop-helix domain-containing	0.992	0.751	0.355	7e-15
297849398	187	T10O24.22 [Arabidopsis lyrata subsp. lyr	0.934	0.684	0.352	7e-15
224079207	162	predicted protein [Populus trichocarpa]	0.963	0.814	0.384	7e-15
147770000	176	hypothetical protein VITISV_017511 [Viti	0.890	0.693	0.357	7e-15
359473250	168	PREDICTED: uncharacterized protein LOC10	0.890	0.726	0.375	2e-14

>gi|225425500|ref|XP_002263481.1| PREDICTED: uncharacterized protein LOC100263706 [Vitis vinifera]

 Score = 98.2 bits (243), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 58/136 (42%), Positives = 82/136 (60%), Gaps = 13/136 (9%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKNKESLERRRALL 61
           R+  E++RR HMKDL S+LA L+P+  SK S+   LD AT+YI  LQK  E+L++ + LL
Sbjct: 38  RSAVERNRRMHMKDLFSRLAFLVPTRPSKSSLHVSLDHATTYIKQLQKRIETLKQTKQLL 97

Query: 62  KEE------------DHYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEV 109
           +                    V+ +   GS+LE+ LI GSN+ F  HE+ISVLEE AA+V
Sbjct: 98  QGSTDETGGVRCQMSGASRSPVITVRDMGSSLELLLISGSNKKFRLHEVISVLEEEAAQV 157

Query: 110 INVTQFNSGDRVIFSV 125
           + V Q   GDR+ +S+
Sbjct: 158 VTVNQCIVGDRICYSI 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425498|ref|XP_002263440.1| PREDICTED: uncharacterized protein LOC100241449 [Vitis vinifera]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 55/132 (41%), Positives = 85/132 (64%), Gaps = 6/132 (4%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIPSS-SKLSMPEILDEATSYITHLQKNKESLERRRALL 61
           RN  EK+RR  MKDL ++LA  IP++ SK S+  +L+ AT+++  LQ+  + L++++ LL
Sbjct: 36  RNEIEKNRRMSMKDLYARLAFQIPTAPSKSSLHLLLEHATTHVKRLQQRLKMLKQKKQLL 95

Query: 62  KEEDHY-----EPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFN 116
           +   H+        V+ +   GSTLEV L  G N+NF  +E+ISVLEE AA+V+   Q  
Sbjct: 96  EGRTHHITGSSRSPVIIVREMGSTLEVFLTSGLNKNFFLYEVISVLEEEAAQVVTANQST 155

Query: 117 SGDRVIFSVLSK 128
            GDR+I+S+ S+
Sbjct: 156 VGDRIIYSICSQ 167

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147799004|emb|CAN70396.1| hypothetical protein VITISV_014706 [Vitis vinifera]

 Score = 87.0 bits (214), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 49/139 (35%), Positives = 82/139 (58%), Gaps = 17/139 (12%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIPSS-SKLSMPEILDEATSYITHLQKNKESLERRRALL 61
           RN  E+ RR ++ +L S+L  L+P   SK S+PE+LD+AT+++  L +  E L++++ LL
Sbjct: 743 RNALERDRRQYIXELSSRLGFLLPPPLSKRSLPELLDQATTHVKQLGQRVEMLKQKKQLL 802

Query: 62  KEED---------------HYEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGA 106
           +  D                + P V+ +   GS LEV +  GSN+ FM H++I VL E A
Sbjct: 803 EGSDTDDQITGIRDQMMSDSWSP-VLTVRDLGSMLEVCVKSGSNKKFMLHQVIQVLVEEA 861

Query: 107 AEVINVTQFNSGDRVIFSV 125
           A+V+ ++  N GDR+ +++
Sbjct: 862 AQVVALSYSNVGDRIFYTI 880

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147863541|emb|CAN79761.1| hypothetical protein VITISV_038226 [Vitis vinifera]

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/133 (38%), Positives = 81/133 (60%), Gaps = 11/133 (8%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIP--SSSKLSMPEILDEATSYITHLQKNKESLERRRAL 60
           RN  E++RR +MKDL S+LA LIP     + S+  +L++A +Y+  LQ+  E L++RR L
Sbjct: 12  RNALERNRRMYMKDLFSKLAYLIPIQPGPRSSLHXLLNQAIAYVKELQERIEMLKQRRQL 71

Query: 61  LKEEDHYEPT--------VMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINV 112
           L E  H++          V+++   G  LE+ LI G N NF  H++I+VL E AAEV++V
Sbjct: 72  L-EGTHHDAAGISGSMSPVVSLRDLGFILELCLITGLNENFTLHQVINVLLEEAAEVVDV 130

Query: 113 TQFNSGDRVIFSV 125
           +    G R+ +++
Sbjct: 131 SYSTVGHRIFYTI 143

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5091553|gb|AAD39582.1|AC007067_22 T10O24.22 [Arabidopsis thaliana]

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/136 (37%), Positives = 86/136 (63%), Gaps = 8/136 (5%)

Query: 2   QRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESL-ERRRAL 60
           QRN++EK RR  MK L S L+S +  + KL +P ++D+ATSY+  L++N   L E++R L
Sbjct: 18  QRNLREKDRRMRMKHLFSILSSHVSPTRKLPVPHLIDQATSYMIQLKENVNYLKEKKRTL 77

Query: 61  LKEE--DHYEPTV----MNITTSGSTLEVNLICGSN-RNFMFHEIISVLEEGAAEVINVT 113
           L+ E  + YE +     ++I +  ST+E+NLI   N +  M HE++S+ EE  A+V++  
Sbjct: 78  LQGELGNLYEGSFLLPKLSIRSRDSTIEMNLIMDLNMKRVMLHELVSIFEEEGAQVMSAN 137

Query: 114 QFNSGDRVIFSVLSKV 129
             N  DR  ++++++V
Sbjct: 138 LQNLNDRTTYTIIAQV 153

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79340924|ref|NP_563873.2| basic helix-loop-helix domain-containing protein [Arabidopsis thaliana] gi|332190477|gb|AEE28598.1| basic helix-loop-helix domain-containing protein [Arabidopsis thaliana]

 Score = 85.5 bits (210), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 53/149 (35%), Positives = 90/149 (60%), Gaps = 13/149 (8%)

Query: 2   QRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESL-ERRRAL 60
           QRN++EK RR  MK L S L+S +  + KL +P ++D+ATSY+  L++N   L E++R L
Sbjct: 18  QRNLREKDRRMRMKHLFSILSSHVSPTRKLPVPHLIDQATSYMIQLKENVNYLKEKKRTL 77

Query: 61  LKEE--DHYEPTV----MNITTSGSTLEVNLICGSN-RNFMFHEIISVLEEGAAEVINVT 113
           L+ E  + YE +     ++I +  ST+E+NLI   N +  M HE++S+ EE  A+V++  
Sbjct: 78  LQGELGNLYEGSFLLPKLSIRSRDSTIEMNLIMDLNMKRVMLHELVSIFEEEGAQVMSAN 137

Query: 114 QFNSGDRVIF-----SVLSKVHFRPTQAE 137
             N  DR  +     +++S++   P++ E
Sbjct: 138 LQNLNDRTTYTIIAQAIISRIGIDPSRIE 166

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849398|ref|XP_002892580.1| T10O24.22 [Arabidopsis lyrata subsp. lyrata] gi|297338422|gb|EFH68839.1| T10O24.22 [Arabidopsis lyrata subsp. lyrata]

 Score = 85.5 bits (210), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 88/136 (64%), Gaps = 8/136 (5%)

Query: 2   QRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESL-ERRRAL 60
           QRN++EK RR  MK L S+L+S +  + KL +P+++D+ATSY+  L++N   L E+++ L
Sbjct: 18  QRNLREKDRRMRMKHLFSELSSHVSPTRKLPVPQLIDQATSYMIQLKENVNYLKEKKKTL 77

Query: 61  LKEE--DHYEPTV----MNITTSGSTLEVNLICGSN-RNFMFHEIISVLEEGAAEVINVT 113
           ++ E  + YE +     ++I +  ST+E+NLI   N +  M HE++S+ EE  A++++  
Sbjct: 78  VQGELGNLYEGSSLLPKLSIRSRDSTIELNLIMDLNMKRVMLHELVSIFEEEGAQIMSAN 137

Query: 114 QFNSGDRVIFSVLSKV 129
             N  DR  ++++++V
Sbjct: 138 LQNLNDRTTYTIIAQV 153

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224079207|ref|XP_002305793.1| predicted protein [Populus trichocarpa] gi|222848757|gb|EEE86304.1| predicted protein [Populus trichocarpa]

 Score = 85.5 bits (210), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 58/151 (38%), Positives = 81/151 (53%), Gaps = 19/151 (12%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIPSSSK----LSMPEILDEATSYITHLQKNKESLERRR 58
           R + E++RR  MK+L SQL SL+P  S     LS+P+ LDEA SYI  LQ N E ++ ++
Sbjct: 12  RKLIERNRRNQMKELYSQLNSLVPHQSSREPVLSVPDQLDEAASYIKRLQTNLEKMKEKK 71

Query: 59  ALLKEEDHYEPTVMN---------------ITTSGSTLEVNLICGSNRNFMFHEIISVLE 103
             L   +  + T  N               ++  GSTLEV L+ G +  FMF EII VL 
Sbjct: 72  DSLMGMERADYTCKNSSGGKTAGLRSPQIEVSEMGSTLEVVLMNGLDSRFMFIEIIRVLH 131

Query: 104 EGAAEVINVTQFNSGDRVIFSVLSKVHFRPT 134
           E  AE+IN +     D V  ++ SKV+  P+
Sbjct: 132 EEGAEIINASLSVVQDTVFHTIHSKVYQLPS 162

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147770000|emb|CAN72144.1| hypothetical protein VITISV_017511 [Vitis vinifera]

 Score = 85.5 bits (210), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 50/140 (35%), Positives = 82/140 (58%), Gaps = 18/140 (12%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIPSS-SKLSMPEILDEATSYITHLQKNKESLERRRALL 61
           R   E+ RR   K+L S+L  L+P+  SK S+PE+LD+AT+++  L +  E L++++ LL
Sbjct: 13  RKALERDRRQCTKELFSRLGFLLPTPLSKRSLPEMLDQATTHVKQLGQRVEMLKQKKQLL 72

Query: 62  KE-----------EDH-----YEPTVMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEG 105
           +             DH     + P V+ ++  GS LEV +  GSN+ FM H++I VL E 
Sbjct: 73  EGSSSIDDQTTGIRDHMMGGAWLP-VLTVSDLGSMLEVCVKSGSNKKFMLHQVIQVLVEE 131

Query: 106 AAEVINVTQFNSGDRVIFSV 125
           AA+V+ ++  N GDR+ + +
Sbjct: 132 AAQVVALSYSNVGDRIFYKI 151

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473250|ref|XP_003631277.1| PREDICTED: uncharacterized protein LOC100854886 [Vitis vinifera]

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/133 (37%), Positives = 81/133 (60%), Gaps = 11/133 (8%)

Query: 3   RNIKEKHRRTHMKDLISQLASLIP--SSSKLSMPEILDEATSYITHLQKNKESLERRRAL 60
           RN  E++RR +MKDL S+LA LIP     + S+  +L++A +++  LQ+  E L++RR L
Sbjct: 12  RNALERNRRMYMKDLFSKLAYLIPIQPGPRSSLHALLNQAIAHVKELQERIEMLKQRRQL 71

Query: 61  LKEEDHYEPT--------VMNITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINV 112
           L E  H++          V+++   G  LE+ LI G N NF  H++I+VL E AAEV++V
Sbjct: 72  L-EGTHHDAAGISGSMSPVVSLRDLGFILELCLITGLNENFTLHQVINVLLEEAAEVVDV 130

Query: 113 TQFNSGDRVIFSV 125
           +    G R+ +++
Sbjct: 131 SYSTVGHRIFYTI 143

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	137
TAIR|locus:505006117	181	AT1G10585 [Arabidopsis thalian	0.927	0.701	0.370	5.8e-18
TAIR|locus:4515102513	174	AT1G10586 [Arabidopsis thalian	0.927	0.729	0.318	4.9e-14
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.430	0.310	0.476	6.8e-13
UNIPROTKB|Q6V3B1	94	MAX "MAX protein" [Homo sapien	0.496	0.723	0.363	7e-06
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.795	0.439	0.279	8e-06
UNIPROTKB|G3V2R5	125	MAX "Protein max" [Homo sapien	0.481	0.528	0.368	9e-06
UNIPROTKB|P52162	160	MAX "Protein max" [Gallus gall	0.467	0.4	0.369	1.1e-05
UNIPROTKB|E2QZS2	160	MAX "Uncharacterized protein"	0.467	0.4	0.369	1.1e-05
UNIPROTKB|G3V563	121	MAX "Protein max" [Homo sapien	0.467	0.528	0.369	1.1e-05
UNIPROTKB|P61244	160	MAX "Protein max" [Homo sapien	0.467	0.4	0.369	1.1e-05

TAIR|locus:505006117 AT1G10585 [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 50/135 (37%), Positives = 85/135 (62%)

Query:     2 QRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESL-ERRRAL 60
             QRN++EK RR  MK L S L+S +  + KL +P ++D+ATSY+  L++N   L E++R L
Sbjct:    18 QRNLREKDRRMRMKHLFSILSSHVSPTRKLPVPHLIDQATSYMIQLKENVNYLKEKKRTL 77

Query:    61 LKEE--DHYEPTVM----NITTSGSTLEVNLICGSN-RNFMFHEIISVLEEGAAEVINVT 113
             L+ E  + YE + +    +I +  ST+E+NLI   N +  M HE++S+ EE  A+V++  
Sbjct:    78 LQGELGNLYEGSFLLPKLSIRSRDSTIEMNLIMDLNMKRVMLHELVSIFEEEGAQVMSAN 137

Query:   114 QFNSGDRVIFSVLSK 128
               N  DR  ++++++
Sbjct:   138 LQNLNDRTTYTIIAQ 152

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0006865 "amino acid transport" evidence=RCA

TAIR|locus:4515102513 AT1G10586 [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 43/135 (31%), Positives = 80/135 (59%)

Query:     2 QRNIKEKHRRTHMKDLISQLASLIPSSSKLSMPEILDEATSYITHLQKNKESL-ERRRAL 60
             QRN++EK RR  MK L S L+S +  + +L +P+++D+A SY+  L++    L E +R +
Sbjct:    18 QRNLREKERRMRMKHLFSILSSHVSPTRRLPVPQLIDQAVSYMIQLKEKVNYLNEMKRRM 77

Query:    61 LKEE--DHYEPTVM----NITTSGSTLEVNLICGSN-RNFMFHEIISVLEEGAAEVINVT 113
             L  E  +  E + +    +I +  S +E+NL+   N +  M H+++SV EE  A+V++  
Sbjct:    78 LGGEVKNRSEGSSLLPKLSIRSLDSIIEMNLVMDLNMKGVMLHKLVSVFEEEGAQVMSAN 137

Query:   114 QFNSGDRVIFSVLSK 128
               N  DR  ++++++
Sbjct:   138 LQNLNDRTFYTIIAQ 152

GO:0005634 "nucleus" evidence=ISM

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

 Score = 119 (46.9 bits), Expect = 6.8e-13, Sum P(2) = 6.8e-13
 Identities = 30/63 (47%), Positives = 40/63 (63%)

Query:     3 RNIKEKHRRTHMKDLISQLASLIP---SSSKLSMPEILDEATSYITHLQKNKESL-ERRR 58
             R   EK+RR  MK L S+L SL+P   S+  L++P+ LDEA +YI  LQ N E   ER+R
Sbjct:    16 RKTVEKNRRMQMKSLYSELISLLPHHSSTEPLTLPDQLDEAANYIKKLQVNVEKKRERKR 75

Query:    59 ALL 61
              L+
Sbjct:    76 NLV 78

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

UNIPROTKB|Q6V3B1 MAX "MAX protein" [Homo sapiens (taxid:9606)]

 Score = 104 (41.7 bits), Expect = 7.0e-06, P = 7.0e-06
 Identities = 28/77 (36%), Positives = 42/77 (54%)

Query:     1 AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ-KNK------ 51
             A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +++ KN       
Sbjct:    17 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 76

Query:    52 ESLERRRALLKEEDHYE 68
             + L+R+ ALL+++   E
Sbjct:    77 DDLKRQNALLEQQGESE 93

GO:0046983 "protein dimerization activity" evidence=IEA

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

 Score = 108 (43.1 bits), Expect = 8.0e-06, P = 8.0e-06
 Identities = 33/118 (27%), Positives = 58/118 (49%)

Query:     4 NIKEKHRRTHMKDLISQLASLIPSSS---KLSMPEILDEATSYITHLQKNKESLERRRAL 60
             N  E+ RR  + +L S L +L+P +    KLS+P  +     YI  LQK  E+LER++  
Sbjct:    74 NAYERDRRKQLNELYSSLRALLPDADHTKKLSIPTTVSRVLKYIPELQKQVENLERKKKE 133

Query:    61 LKEED--HYEPTVMN--ITTSGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQ 114
             L      + +P V+   + + G    V+  C ++   M    +S+L   A  V+ +++
Sbjct:   134 LTTTSTTNCKPGVLGSQLMSEGMAPIVSATCINDMEIMVQ--VSLLSNVAGSVLPLSK 189

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|G3V2R5 MAX "Protein max" [Homo sapiens (taxid:9606)]

 Score = 103 (41.3 bits), Expect = 9.0e-06, P = 9.0e-06
 Identities = 28/76 (36%), Positives = 43/76 (56%)

Query:     1 AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ-KNK------ 51
             A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +++ KN       
Sbjct:    17 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 76

Query:    52 ESLERRRALLKEE-DH 66
             + L+R+ ALL+++ +H
Sbjct:    77 DDLKRQNALLEQQGEH 92

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|P52162 MAX "Protein max" [Gallus gallus (taxid:9031)]

 Score = 102 (41.0 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query:     1 AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ-KNK------ 51
             A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +++ KN       
Sbjct:    26 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 85

Query:    52 ESLERRRALLKEE 64
             + L+R+ ALL+++
Sbjct:    86 DDLKRQNALLEQQ 98

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0071339 "MLL1 complex" evidence=ISS

UNIPROTKB|E2QZS2 MAX "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 102 (41.0 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query:     1 AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ-KNK------ 51
             A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +++ KN       
Sbjct:    26 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 85

Query:    52 ESLERRRALLKEE 64
             + L+R+ ALL+++
Sbjct:    86 DDLKRQNALLEQQ 98

GO:0071339 "MLL1 complex" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|G3V563 MAX "Protein max" [Homo sapiens (taxid:9606)]

 Score = 102 (41.0 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query:     1 AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ-KNK------ 51
             A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +++ KN       
Sbjct:    17 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 76

Query:    52 ESLERRRALLKEE 64
             + L+R+ ALL+++
Sbjct:    77 DDLKRQNALLEQQ 89

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|P61244 MAX "Protein max" [Homo sapiens (taxid:9606)]

 Score = 102 (41.0 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query:     1 AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ-KNK------ 51
             A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +++ KN       
Sbjct:    26 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 85

Query:    52 ESLERRRALLKEE 64
             + L+R+ ALL+++
Sbjct:    86 DDLKRQNALLEQQ 98

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

GO:0006461 "protein complex assembly" evidence=IEA

GO:0009267 "cellular response to starvation" evidence=IEA

GO:0010629 "negative regulation of gene expression" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0030425 "dendrite" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0032868 "response to insulin stimulus" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0048678 "response to axon injury" evidence=IEA

GO:0051402 "neuron apoptotic process" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IEA

GO:0071375 "cellular response to peptide hormone stimulus" evidence=IEA

GO:0071339 "MLL1 complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0003712 "transcription cofactor activity" evidence=TAS

GO:0003713 "transcription coactivator activity" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	137
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	7e-09
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-08
smart00353	53	smart00353, HLH, helix loop helix domain	1e-07

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

 Score = 48.2 bits (116), Expect = 7e-09
 Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 4  NIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQ 48
          N +E+ RR  + D   +L  L+P+  + KLS  EIL  A  YI HLQ
Sbjct: 6  NERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

>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 = 46.8 bits (112), Expect = 3e-08
 Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 3  RNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKE 52
           N++E+ RR  + D   +L SL+P+   S KLS  EIL +A  YI  LQ+  +
Sbjct: 8  HNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 44.9 bits (107), Expect = 1e-07
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 4  NIKEKHRRTHMKDLISQLASLIP---SSSKLSMPEILDEATSYITHLQKNKES 53
          N +E+ RR  + +   +L SL+P    + KLS  EIL  A  YI  LQ+  + 
Sbjct: 1  NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
smart00353	53	HLH helix loop helix domain.	99.54
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.52
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.51
KOG1318	411	consensus Helix loop helix transcription factor EB	98.75
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.5
PLN03217	93	transcription factor ATBS1; Provisional	98.45
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.32
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.22
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.2
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.17
KOG0561	373	consensus bHLH transcription factor [Transcription	98.15
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.07
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.51
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.38
KOG3898	254	consensus Transcription factor NeuroD and related	97.28
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.18
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.17
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.08
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.04
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	96.98
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	96.91
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.72
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	96.66
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	96.53
KOG4395	285	consensus Transcription factor Atonal, contains HT	96.39
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.07
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	95.55
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.35
PRK05007	884	PII uridylyl-transferase; Provisional	95.11
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	95.03
PRK04374	869	PII uridylyl-transferase; Provisional	95.02
KOG3910	632	consensus Helix loop helix transcription factor [T	94.99
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	94.97
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	94.63
PRK03059	856	PII uridylyl-transferase; Provisional	94.47
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	94.37
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.3
PRK03381	774	PII uridylyl-transferase; Provisional	94.29
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	94.17
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	94.11
PRK05092	931	PII uridylyl-transferase; Provisional	93.94
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	93.85
PRK01759	854	glnD PII uridylyl-transferase; Provisional	93.8
PRK00194	90	hypothetical protein; Validated	93.7
PRK03381	774	PII uridylyl-transferase; Provisional	93.51
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	93.45
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	93.41
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	93.29
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	93.08
PRK01759	854	glnD PII uridylyl-transferase; Provisional	92.72
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	92.58
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	91.51
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	91.42
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	91.14
PRK00275	895	glnD PII uridylyl-transferase; Provisional	91.07
PRK05007	884	PII uridylyl-transferase; Provisional	91.05
PRK03059	856	PII uridylyl-transferase; Provisional	90.91
PRK05092	931	PII uridylyl-transferase; Provisional	90.75
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	90.57
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	89.63
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	89.55
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	89.48
PRK04435	147	hypothetical protein; Provisional	89.39
PRK04374	869	PII uridylyl-transferase; Provisional	89.21
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	88.32
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	87.33
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	87.03
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	85.39
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	85.3
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	84.75
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	84.64
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	83.87
cd02116	60	ACT ACT domains are commonly involved in specifica	83.18
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	83.15
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	81.54
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	81.19
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	80.68
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	80.62
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	80.16

>smart00353 HLH helix loop helix domain

Probab=99.54  E-value=2.2e-14  Score=88.78  Aligned_cols=49  Identities=39%  Similarity=0.625  Sum_probs=45.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHH
Q 039443            4 NIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKE   52 (137)
Q Consensus         4 ~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~   52 (137)
                      |..||+||..||+.|..|++++|.   ..|+||++||..|++||+.|+++++
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            578999999999999999999995   6799999999999999999999875

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

Probab=99.52  E-value=3.1e-14  Score=89.71  Aligned_cols=50  Identities=40%  Similarity=0.628  Sum_probs=47.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC---CCCCHHhHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPSS---SKLSMPEILDEATSYITHLQKNK   51 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~~---~k~~k~~il~~Ai~YIk~L~~~v   51 (137)
                      .|+..||.||..||+.|..|++++|..   .|+||++||..|++||+.|++.+
T Consensus         7 ~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           7 AHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            599999999999999999999999995   89999999999999999999875

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

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

Probab=99.51  E-value=2.9e-14  Score=89.28  Aligned_cols=47  Identities=40%  Similarity=0.662  Sum_probs=44.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC-----CCCCHHhHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPSS-----SKLSMPEILDEATSYITHLQ   48 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~~-----~k~~k~~il~~Ai~YIk~L~   48 (137)
                      .|+..||.||..||+.|..|+.+||..     .|+||++||..||+||++||
T Consensus         4 ~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    4 KHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            599999999999999999999999984     78999999999999999997

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

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

Probab=98.75  E-value=1.7e-08  Score=85.95  Aligned_cols=53  Identities=32%  Similarity=0.483  Sum_probs=48.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQKNKESL   54 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~~v~~L   54 (137)
                      +||++||+||..+|+++-.|..|||.    ..|+.|..||..+++||+.|++..++.
T Consensus       236 ~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~  292 (411)
T KOG1318|consen  236 NHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRA  292 (411)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999998    368889999999999999999877733

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

Probab=98.50  E-value=8.6e-08  Score=75.75  Aligned_cols=56  Identities=38%  Similarity=0.472  Sum_probs=50.5

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQKNKESLERR   57 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~   57 (137)
                      .+|++||+|-+.+|..|..||.++|.    ..|++|.++|..||.||+.|++-++.-+.-
T Consensus       112 ~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  112 ARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            57899999999999999999999997    468999999999999999999988775543

>PLN03217 transcription factor ATBS1; Provisional

Probab=98.45  E-value=7.5e-07  Score=60.91  Aligned_cols=53  Identities=30%  Similarity=0.557  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHHhcCCC------CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 039443           12 THMKDLISQLASLIPS------SSKLSMPEILDEATSYITHLQKNKESLERRRALLKEE   64 (137)
Q Consensus        12 ~~mn~~~~~Lrsl~P~------~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~~~   64 (137)
                      .+|+++.++|+.|+|.      .+|.+-+.+|.|+++||+.|+..++.|.++..+|...
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            6899999999999997      4678899999999999999999999999999888765

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

Probab=98.32  E-value=1.7e-06  Score=69.70  Aligned_cols=58  Identities=22%  Similarity=0.331  Sum_probs=50.6

Q ss_pred             cHHHHHHHHHHHHHHHHH-HhcCCC-CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039443            4 NIKEKHRRTHMKDLISQL-ASLIPS-SSKLSMPEILDEATSYITHLQKNKESLERRRALL   61 (137)
Q Consensus         4 ~~~ER~RR~~mn~~~~~L-rsl~P~-~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l   61 (137)
                      -++||+|=+|+|+.|..| |.-.|+ ..++.|++||..||.||..||.-++++.+....+
T Consensus       123 TMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  123 TMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            478999999999999999 555666 6789999999999999999999999998865544

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.22  E-value=2.7e-06  Score=66.12  Aligned_cols=60  Identities=32%  Similarity=0.451  Sum_probs=51.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC------CC-CCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS------SS-KLSMPEILDEATSYITHLQKNKESLERRRALL   61 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~------~~-k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l   61 (137)
                      .|--.||+||.-+|.-|..|..|||.      .+ |++|+-||-.+|+||..|.....+-+.+...|
T Consensus        65 aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L  131 (229)
T KOG1319|consen   65 AHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL  131 (229)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47789999999999999999999996      23 89999999999999999988877766655443

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

Probab=98.20  E-value=2e-06  Score=78.60  Aligned_cols=49  Identities=27%  Similarity=0.432  Sum_probs=46.3

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQKN   50 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~~   50 (137)
                      +|+.+||+||++||..+..|.++||.    ..|+||..||..||.+|+.+++.
T Consensus        23 ~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   23 NRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            68999999999999999999999998    48999999999999999999875

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

Probab=98.17  E-value=6.6e-06  Score=65.73  Aligned_cols=60  Identities=30%  Similarity=0.400  Sum_probs=51.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCC-HHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLS-MPEILDEATSYITHLQKNKESLERRRALL   61 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~-k~~il~~Ai~YIk~L~~~v~~L~~~k~~l   61 (137)
                      .||+-||+||.++++.|..|+-+||.  ..+.. ..+||..|..||+.|+.+..+.+...+.+
T Consensus        62 ~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l  124 (232)
T KOG2483|consen   62 HHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDL  124 (232)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHH
Confidence            59999999999999999999999998  23333 69999999999999998877777655544

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.15  E-value=1.9e-06  Score=71.04  Aligned_cols=51  Identities=31%  Similarity=0.512  Sum_probs=45.6

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHHHHH
Q 039443            4 NIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESL   54 (137)
Q Consensus         4 ~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v~~L   54 (137)
                      |--||+|.+-+|.-|.+||+|+|.  ..|++|+-||..+.+||.+|+..--+|
T Consensus        65 NsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   65 NSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             cchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            456999999999999999999998  689999999999999999998765443

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

Probab=98.07  E-value=3.3e-06  Score=68.16  Aligned_cols=51  Identities=29%  Similarity=0.549  Sum_probs=45.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--------CCCCCHHhHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--------SSKLSMPEILDEATSYITHLQKNKE   52 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--------~~k~~k~~il~~Ai~YIk~L~~~v~   52 (137)
                      .|-+.||+||.+||..+..|+.|||.        .+|+.|++||.-|++|++.|+..-.
T Consensus        35 ~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   35 RKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            46688999999999999999999996        3799999999999999999986543

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

Probab=97.51  E-value=0.00077  Score=44.72  Aligned_cols=43  Identities=9%  Similarity=0.047  Sum_probs=38.9

Q ss_pred             EecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEE
Q 039443           86 ICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSK  128 (137)
Q Consensus        86 ~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~ak  128 (137)
                      +.+.+++|+|.+|..+|.++||+|..|.+++.|+++.-+|.+.
T Consensus         6 v~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~   48 (72)
T cd04895           6 VDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVT   48 (72)
T ss_pred             EEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEE
Confidence            3466899999999999999999999999999999988877775

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

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

Probab=97.38  E-value=0.0014  Score=43.84  Aligned_cols=44  Identities=14%  Similarity=0.159  Sum_probs=39.4

Q ss_pred             EecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           86 ICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        86 ~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      +.+..+||+|.+|..+|-++|++|.+|.+++.|+++.-+|.+.=
T Consensus         6 V~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d   49 (75)
T cd04897           6 VQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRH   49 (75)
T ss_pred             EEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEc
Confidence            44678999999999999999999999999999999987777753

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.

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

Probab=97.28  E-value=0.00013  Score=58.98  Aligned_cols=49  Identities=33%  Similarity=0.463  Sum_probs=44.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHH
Q 039443            3 RNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNK   51 (137)
Q Consensus         3 h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v   51 (137)
                      =|..||+|...+|+.|..||.++|.   ..|++|..++.-|-+||..|.+-.
T Consensus        76 aNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~  127 (254)
T KOG3898|consen   76 ANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL  127 (254)
T ss_pred             ccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence            3789999999999999999999995   789999999999999999988643

>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=97.18  E-value=0.0034  Score=41.44  Aligned_cols=42  Identities=21%  Similarity=0.211  Sum_probs=37.9

Q ss_pred             ecCCCcchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEE
Q 039443           87 CGSNRNFMFHEIISVLEEGAAEVINVTQFN-SGDRVIFSVLSK  128 (137)
Q Consensus        87 ~~~~~~~~L~~il~~Le~~~L~V~~a~~s~-~~~~v~~ti~ak  128 (137)
                      ++.+++|+|.++..+|..+|++|++|.+++ .|+.++-+|.+.
T Consensus         6 ~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~   48 (76)
T cd04927           6 FCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFIT   48 (76)
T ss_pred             EECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEe
Confidence            355899999999999999999999999996 799999888885

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

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

Probab=97.17  E-value=0.0029  Score=41.10  Aligned_cols=46  Identities=15%  Similarity=0.260  Sum_probs=38.8

Q ss_pred             eEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEE
Q 039443           82 EVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNS-GDRVIFSVLSK  128 (137)
Q Consensus        82 ~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~v~~ti~ak  128 (137)
                      +|.+. +.+++|+|+++..+|..+|++|++|.+.+. ++.++-++.+.
T Consensus         3 ~i~v~-~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~   49 (73)
T cd04900           3 EVFIY-TPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVL   49 (73)
T ss_pred             EEEEE-ecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEE
Confidence            34444 448999999999999999999999999887 68888888875

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

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

Probab=97.08  E-value=0.0047  Score=40.38  Aligned_cols=43  Identities=16%  Similarity=0.397  Sum_probs=39.0

Q ss_pred             EecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEE
Q 039443           86 ICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSK  128 (137)
Q Consensus        86 ~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~ak  128 (137)
                      +.+.+++|+|.+|..+|..+|+.|++|.+++.|+.++-++.+.
T Consensus         5 v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~   47 (74)
T cd04925           5 LTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVR   47 (74)
T ss_pred             EEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEE
Confidence            3466899999999999999999999999999999998888875

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

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.04  E-value=0.00033  Score=65.03  Aligned_cols=58  Identities=34%  Similarity=0.520  Sum_probs=52.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC-CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKNKESLERRRA   59 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~-~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~   59 (137)
                      +||+.|++-|.-+|+....|+.++|. ..|+.|+..+.-||+||++|+..-+.|.....
T Consensus       279 AHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~  337 (953)
T KOG2588|consen  279 AHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENA  337 (953)
T ss_pred             hhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhh
Confidence            69999999999999999999999998 78999999999999999999887776665443

>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=96.98  E-value=0.0075  Score=39.14  Aligned_cols=46  Identities=15%  Similarity=0.211  Sum_probs=38.8

Q ss_pred             eEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEE
Q 039443           82 EVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSK  128 (137)
Q Consensus        82 ~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~ak  128 (137)
                      .+.+. ..+++|+|.+|..+|.++|++|+++.+.+.++.++.+|++.
T Consensus         3 ri~V~-~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~   48 (72)
T cd04926           3 RLELR-TEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVT   48 (72)
T ss_pred             EEEEE-ECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEE
Confidence            34443 34789999999999999999999999998888888888875

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.

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

Probab=96.91  E-value=0.0064  Score=40.61  Aligned_cols=42  Identities=7%  Similarity=0.017  Sum_probs=38.2

Q ss_pred             ecCCCcchHHHHHHHHHhCCcEEEEEEEe--eeCCeEEEEEEEE
Q 039443           87 CGSNRNFMFHEIISVLEEGAAEVINVTQF--NSGDRVIFSVLSK  128 (137)
Q Consensus        87 ~~~~~~~~L~~il~~Le~~~L~V~~a~~s--~~~~~v~~ti~ak  128 (137)
                      .+.+++|+|.+|..+|.++|++|.+|.++  +.|+++.-+|.+.
T Consensus         6 ~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~   49 (75)
T cd04896           6 RCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQ   49 (75)
T ss_pred             EeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEe
Confidence            35689999999999999999999999999  9999988877773

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.

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.72  E-value=0.00077  Score=50.92  Aligned_cols=50  Identities=30%  Similarity=0.475  Sum_probs=45.9

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNK   51 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v   51 (137)
                      -||..||+|-.-+|+.|..||..+|.  +.|.+|...|.-|..||..|-+-+
T Consensus        81 ~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   81 MANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            48999999999999999999999998  789999999999999999886544

>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=96.66  E-value=0.022  Score=35.81  Aligned_cols=45  Identities=13%  Similarity=0.059  Sum_probs=39.4

Q ss_pred             ecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           87 CGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        87 ~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      .+.+++|.|.++..+|.++|+.|.++.+.+.++.++.++++.-.+
T Consensus         6 ~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~   50 (70)
T cd04899           6 TALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDAD   50 (70)
T ss_pred             EEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCC
Confidence            455789999999999999999999999999888888888887544

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

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

Probab=96.53  E-value=0.02  Score=37.55  Aligned_cols=49  Identities=10%  Similarity=0.203  Sum_probs=40.0

Q ss_pred             eEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEecC
Q 039443           82 EVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNS-GDRVIFSVLSKVHF  131 (137)
Q Consensus        82 ~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~v~~ti~akv~~  131 (137)
                      +|.+++. .++++|.++..+|..+||+|++|.+.+. +|.++-++.+.=.+
T Consensus         3 eI~V~~~-Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~   52 (68)
T cd04928           3 EITFAAG-DKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWK   52 (68)
T ss_pred             EEEEEEC-CCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCC
Confidence            4555444 7999999999999999999999999765 77888888876433

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.

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

Probab=96.39  E-value=0.0062  Score=49.43  Aligned_cols=50  Identities=28%  Similarity=0.375  Sum_probs=44.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHH
Q 039443            3 RNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKE   52 (137)
Q Consensus         3 h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~   52 (137)
                      -|..||+|...+|..|..||-.+|.   ..|++|-..|--|-.||-.|-..++
T Consensus       178 anarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  178 ANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             cchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            4789999999999999999999998   5789999999999999988866553

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

Probab=96.07  E-value=0.055  Score=35.37  Aligned_cols=48  Identities=21%  Similarity=0.291  Sum_probs=39.8

Q ss_pred             EEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 039443           83 VNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVH  130 (137)
Q Consensus        83 V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~  130 (137)
                      |..+.|.+++|.+..+..+|.++|.++.+++.+..++.+...+.+.+.
T Consensus         4 vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~   51 (76)
T PF13740_consen    4 VITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP   51 (76)
T ss_dssp             EEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES
T ss_pred             EEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC
Confidence            344567789999999999999999999999999999999888888776

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

Probab=95.55  E-value=0.15  Score=31.61  Aligned_cols=45  Identities=13%  Similarity=0.152  Sum_probs=37.5

Q ss_pred             ecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           87 CGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        87 ~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      .+.+++|.|.++...|.++|+.+.++.+.+.++.....+++.-.+
T Consensus         6 ~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~   50 (70)
T cd04873           6 YAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSD   50 (70)
T ss_pred             EeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCC
Confidence            455789999999999999999999999988877666777776443

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

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.35  E-value=0.12  Score=48.36  Aligned_cols=62  Identities=19%  Similarity=0.141  Sum_probs=48.9

Q ss_pred             CCceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           68 EPTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        68 ~~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      ..|.|.+....+ +.-+..+++.+++|+|++|..+|..+|++|++|.+++.|+++.-+|.+.=
T Consensus       800 ~~~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d  862 (895)
T PRK00275        800 FPTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITD  862 (895)
T ss_pred             CCCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEEC
Confidence            356676665433 23344455668999999999999999999999999999999998888863

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.11  E-value=0.11  Score=48.65  Aligned_cols=60  Identities=8%  Similarity=0.063  Sum_probs=46.3

Q ss_pred             CceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEE
Q 039443           69 PTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSK  128 (137)
Q Consensus        69 ~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~ak  128 (137)
                      +|.|.+....| ..-+.-+.+.+++|+|.+|..+|.++|++|.+|-+++.|+++.-+|.+.
T Consensus       795 ~~~V~~d~~~s~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~  855 (884)
T PRK05007        795 PTEVSFLPTHTDRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILA  855 (884)
T ss_pred             CCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEE
Confidence            45566654333 2233334466899999999999999999999999999999988777774

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

Probab=95.03  E-value=0.33  Score=31.48  Aligned_cols=43  Identities=14%  Similarity=0.225  Sum_probs=36.1

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeee--CCeEEEEEEEEecC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNS--GDRVIFSVLSKVHF  131 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~--~~~v~~ti~akv~~  131 (137)
                      .+++|+|.+|..++.+.|+.+.+.++...  ++....+|.++|.+
T Consensus        14 ~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d   58 (80)
T PF13291_consen   14 EDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKD   58 (80)
T ss_dssp             E--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESS
T ss_pred             EcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECC
Confidence            47899999999999999999999999985  66777899988876

>PRK04374 PII uridylyl-transferase; Provisional

Probab=95.02  E-value=0.18  Score=47.29  Aligned_cols=60  Identities=12%  Similarity=0.081  Sum_probs=47.6

Q ss_pred             CceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEE
Q 039443           69 PTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSK  128 (137)
Q Consensus        69 ~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~ak  128 (137)
                      +|.|.+....+ ..-+..+++..++|+|.+|-.+|..+|++|++|.+++.|+++.-+|.+.
T Consensus       783 ~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~  843 (869)
T PRK04374        783 APRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQIT  843 (869)
T ss_pred             CCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEE
Confidence            45666664333 3333444566899999999999999999999999999999999888886

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=94.99  E-value=0.026  Score=49.79  Aligned_cols=54  Identities=19%  Similarity=0.255  Sum_probs=45.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQKNKESLE   55 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~~v~~L~   55 (137)
                      +.|++||-|-+-+|+.|..|-.+.-.    ...-.|--||..|+.-|-.||++|++-.
T Consensus       529 aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN  586 (632)
T KOG3910|consen  529 ANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN  586 (632)
T ss_pred             hhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence            57899999999999999999766543    3446788999999999999999998744

>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=94.97  E-value=0.27  Score=29.99  Aligned_cols=32  Identities=13%  Similarity=0.269  Sum_probs=29.4

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeeeCC
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNSGD  119 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~  119 (137)
                      ..+++|.|.++...|.++|+.|.++.+.+.++
T Consensus         7 ~~drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    7 VPDRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             EETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             cCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            34889999999999999999999999999876

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 ....

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

Probab=94.63  E-value=0.27  Score=32.19  Aligned_cols=47  Identities=13%  Similarity=0.273  Sum_probs=41.4

Q ss_pred             EEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           85 LICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        85 ~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      .+.|.+++|...+|-..|.++|..+++++....++.+++.+...+..
T Consensus         5 tv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~~   51 (77)
T cd04893           5 SALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSW   51 (77)
T ss_pred             EEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEecc
Confidence            44566899999999999999999999999999999998888877653

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

>PRK03059 PII uridylyl-transferase; Provisional

Probab=94.47  E-value=0.27  Score=46.00  Aligned_cols=59  Identities=17%  Similarity=0.166  Sum_probs=45.4

Q ss_pred             CceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEE
Q 039443           69 PTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLS  127 (137)
Q Consensus        69 ~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~a  127 (137)
                      +|.+.+....+ ..-+..+.+.+++|+|.+|..+|..+|++|++|.+++.|+++.-+|.+
T Consensus       773 ~~~V~~~~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V  832 (856)
T PRK03059        773 TPRVDLRPDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI  832 (856)
T ss_pred             CceEEEEEcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            34555544322 222333445589999999999999999999999999999999988887

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=94.37  E-value=0.042  Score=47.71  Aligned_cols=41  Identities=29%  Similarity=0.423  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHH
Q 039443            6 KEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITH   46 (137)
Q Consensus         6 ~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~   46 (137)
                      +-|.||++-|--|+.|..++|-    .+.+||++|+.-|..|||-
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            4589999999999999999997    5779999999999999985

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.30  E-value=2.1  Score=39.94  Aligned_cols=62  Identities=11%  Similarity=0.088  Sum_probs=45.5

Q ss_pred             CceeEEEe--eCCeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEe-eeCCeEEEEEEEEecC
Q 039443           69 PTVMNITT--SGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQF-NSGDRVIFSVLSKVHF  131 (137)
Q Consensus        69 ~p~v~v~~--~~s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s-~~~~~v~~ti~akv~~  131 (137)
                      .|.+.+..  .+...+|.+ .+.+++|+|.+|..+|..+|++|++|.++ +.|+.++-+|.++-.+
T Consensus       655 ~~~v~~~~~~~~~~t~i~V-~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~  719 (850)
T TIGR01693       655 GPLALIDGTRPSGGTEVFI-YAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLF  719 (850)
T ss_pred             CCEEEEeccCCCCeEEEEE-EeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCC
Confidence            34455432  122334444 44589999999999999999999999998 6688888888876443

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

>PRK03381 PII uridylyl-transferase; Provisional

Probab=94.29  E-value=0.32  Score=44.96  Aligned_cols=61  Identities=15%  Similarity=0.094  Sum_probs=47.0

Q ss_pred             CceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           69 PTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        69 ~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      +|.+.+....+ ..-+..+.+..++|+|.+|..+|.++|++|.+|.+++.|+.++-+|.+.=
T Consensus       694 ~~~v~~~~~~~~~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d  755 (774)
T PRK03381        694 PPRVLWLDGASPDATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTG  755 (774)
T ss_pred             CcEEEEEECCCCCeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEEC
Confidence            34555554332 23344445668999999999999999999999999999999998888763

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

Probab=94.17  E-value=0.039  Score=50.29  Aligned_cols=40  Identities=30%  Similarity=0.474  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHH
Q 039443            6 KEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYIT   45 (137)
Q Consensus         6 ~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk   45 (137)
                      +=|.||.|-|+-|+.|.-+||-    .+-+||++|+.-||.|.+
T Consensus        53 AARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   53 AARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH
Confidence            4588999999999999999997    578999999999999986

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

Probab=94.11  E-value=0.25  Score=31.91  Aligned_cols=46  Identities=11%  Similarity=0.144  Sum_probs=38.0

Q ss_pred             EecCCCcchHHHHHHHHHhCCcEEEEEEEeeeC------CeEEEEEEEEecC
Q 039443           86 ICGSNRNFMFHEIISVLEEGAAEVINVTQFNSG------DRVIFSVLSKVHF  131 (137)
Q Consensus        86 ~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~------~~v~~ti~akv~~  131 (137)
                      +.+..++|.+.+|-..|.++|+.+.+.+..+.+      +.++..+.+.+.+
T Consensus         4 v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p~   55 (81)
T cd04869           4 VVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPA   55 (81)
T ss_pred             EEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecCC
Confidence            446679999999999999999999999998887      5566677766654

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

>PRK05092 PII uridylyl-transferase; Provisional

Probab=93.94  E-value=0.48  Score=44.61  Aligned_cols=61  Identities=15%  Similarity=0.209  Sum_probs=47.6

Q ss_pred             CceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           69 PTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        69 ~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      .|.|.+....+ ..-+..+.+.+++|+|.+|..+|.++|++|.+|.+++.++++.-+|.+.-
T Consensus       830 ~~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d  891 (931)
T PRK05092        830 PPRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTD  891 (931)
T ss_pred             CCEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeC
Confidence            45666664333 22233445568999999999999999999999999999999998888864

>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=93.85  E-value=0.51  Score=29.80  Aligned_cols=45  Identities=11%  Similarity=0.141  Sum_probs=37.2

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEecCC
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNS-GDRVIFSVLSKVHFR  132 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~v~~ti~akv~~~  132 (137)
                      ..+++|.|.+|...+.+.|..+.+.++... ++.....|.+++.+.
T Consensus         6 ~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~   51 (74)
T cd04887           6 LPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSE   51 (74)
T ss_pred             eCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCH
Confidence            347899999999999999999999998876 466667788877653

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.

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=93.80  E-value=0.31  Score=45.52  Aligned_cols=60  Identities=10%  Similarity=0.071  Sum_probs=46.0

Q ss_pred             CceeEEEeeCC-eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEE
Q 039443           69 PTVMNITTSGS-TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSK  128 (137)
Q Consensus        69 ~p~v~v~~~~s-~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~ak  128 (137)
                      +|.|.+....+ ..-+.-+...+++|+|.+|..+|.++|++|.+|-+++.|+++.-+|.+.
T Consensus       770 ~~~V~~dn~~s~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~  830 (854)
T PRK01759        770 KTEVRFLNEEKQEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILT  830 (854)
T ss_pred             CCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEE
Confidence            45566654333 2233334466899999999999999999999999999999988777765

>PRK00194 hypothetical protein; Validated

Probab=93.70  E-value=0.28  Score=32.65  Aligned_cols=48  Identities=13%  Similarity=0.175  Sum_probs=39.9

Q ss_pred             EEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           84 NLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        84 ~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      ..+.|.+++|.+.++...|-++|+.+++.+..+.++.++..+.+.+..
T Consensus         6 ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~~   53 (90)
T PRK00194          6 ITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDISE   53 (90)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEecC
Confidence            344566799999999999999999999999988888777777777654

>PRK03381 PII uridylyl-transferase; Provisional

Probab=93.51  E-value=0.59  Score=43.25  Aligned_cols=60  Identities=12%  Similarity=0.158  Sum_probs=46.1

Q ss_pred             CceeEEEee-CCeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           69 PTVMNITTS-GSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        69 ~p~v~v~~~-~s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      .|.+.+... +...+|.++ +.+++|+|++|..+|..+|++|++|++.+.+|.++-+|.+.-
T Consensus       587 ~~~v~~~~~~~~~~~V~V~-~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~  647 (774)
T PRK03381        587 GVHVEIAPADPHMVEVTVV-APDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSP  647 (774)
T ss_pred             CCEEEEeeCCCCeEEEEEE-ecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEEC
Confidence            344554422 344566554 458999999999999999999999999998888888888763

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

Probab=93.45  E-value=0.52  Score=30.42  Aligned_cols=47  Identities=17%  Similarity=0.261  Sum_probs=39.0

Q ss_pred             EEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           85 LICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        85 ~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      .+.|..++|...++-..|.++|+++.+.+.+..++.+...+.+.+..
T Consensus         3 tv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p~   49 (75)
T cd04870           3 TVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIPD   49 (75)
T ss_pred             EEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcCC
Confidence            34577899999999999999999999999998888766666665543

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.

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

Probab=93.41  E-value=0.65  Score=28.36  Aligned_cols=43  Identities=16%  Similarity=0.207  Sum_probs=33.8

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeee-----CCeEEEEEEEEecC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNS-----GDRVIFSVLSKVHF  131 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~-----~~~v~~ti~akv~~  131 (137)
                      .+++|.|.+|+..+.+.|+++.+.+....     ++...+.+...+.+
T Consensus         6 ~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~   53 (73)
T cd04886           6 PDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRG   53 (73)
T ss_pred             CCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCC
Confidence            47899999999999999999999887764     35555666666643

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.

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

Probab=93.29  E-value=0.27  Score=45.82  Aligned_cols=61  Identities=15%  Similarity=0.128  Sum_probs=45.3

Q ss_pred             CceeEEEeeCCe-eeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           69 PTVMNITTSGST-LEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        69 ~p~v~v~~~~s~-~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      +|.|++...-+. ..+.-+.+..++|+|..+-.+|.+++|++.+|.++++|.++.-+|.+..
T Consensus       778 ~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~  839 (867)
T COG2844         778 PPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTD  839 (867)
T ss_pred             CCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEec
Confidence            466776533221 2233334778999999999999999999999999999998876555443

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

Probab=93.08  E-value=0.31  Score=32.41  Aligned_cols=47  Identities=11%  Similarity=0.169  Sum_probs=40.2

Q ss_pred             EEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           85 LICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        85 ~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      .+.|.+++|.+.+|...|-++|+++++++..+.++.++..+.+.+.+
T Consensus         5 ~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~~   51 (88)
T cd04872           5 TVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDISE   51 (88)
T ss_pred             EEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeCC
Confidence            34566899999999999999999999999999888877777777664

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.

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=92.72  E-value=0.92  Score=42.46  Aligned_cols=59  Identities=10%  Similarity=0.168  Sum_probs=45.1

Q ss_pred             CceeEEEeeC--CeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEE
Q 039443           69 PTVMNITTSG--STLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFN-SGDRVIFSVLSK  128 (137)
Q Consensus        69 ~p~v~v~~~~--s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~-~~~~v~~ti~ak  128 (137)
                      .|.+.+....  ...+|.++ +.+++|+|++|..+|..+||+|++|.+.+ .+|.++-+|.+.
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~-~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~  725 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIY-CQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVT  725 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEE-ecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEe
Confidence            4555555332  33345544 45799999999999999999999999976 799988888775

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=92.58  E-value=0.71  Score=42.96  Aligned_cols=62  Identities=13%  Similarity=0.084  Sum_probs=48.0

Q ss_pred             CceeEEEeeCCe-eeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 039443           69 PTVMNITTSGST-LEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVH  130 (137)
Q Consensus        69 ~p~v~v~~~~s~-~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~  130 (137)
                      +|.|.+....+. .-+.-+.+.+++|+|.+|..+|.++|++|.++.+++.++++.-+|.+.-.
T Consensus       766 ~~~V~~d~~~s~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~  828 (850)
T TIGR01693       766 PPRVTILNTASRKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDL  828 (850)
T ss_pred             CCeEEEccCCCCCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECC
Confidence            455666544432 33444556689999999999999999999999999999988877777643

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.

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

Probab=91.51  E-value=1.3  Score=28.24  Aligned_cols=43  Identities=9%  Similarity=0.083  Sum_probs=35.1

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeCC-eEEEEEEEEecC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSGD-RVIFSVLSKVHF  131 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~-~v~~ti~akv~~  131 (137)
                      .+++|.|.++++.|.++|+.+.+..+.+..+ .--|.+.+.+.+
T Consensus         7 ~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~   50 (75)
T cd04880           7 KNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEG   50 (75)
T ss_pred             CCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEEC
Confidence            3689999999999999999999998888755 444676666665

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

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

Probab=91.42  E-value=1  Score=28.74  Aligned_cols=33  Identities=15%  Similarity=0.270  Sum_probs=28.9

Q ss_pred             EEecCCCcchHHHHHHHHHhCCcEEEEEEEeee
Q 039443           85 LICGSNRNFMFHEIISVLEEGAAEVINVTQFNS  117 (137)
Q Consensus        85 ~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~  117 (137)
                      .+.|..++|.+.+|-..|-++|+.+++.+..+.
T Consensus         3 ~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~   35 (74)
T cd04875           3 TLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVD   35 (74)
T ss_pred             EEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeec
Confidence            345668999999999999999999999998863

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.

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

Probab=91.14  E-value=1.7  Score=27.30  Aligned_cols=44  Identities=9%  Similarity=0.144  Sum_probs=34.8

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEecCC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNS-GDRVIFSVLSKVHFR  132 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~v~~ti~akv~~~  132 (137)
                      .+++|.|.+|+..|.+.|+++...+.+.. ++..-..|.+.+.+.
T Consensus         8 ~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~   52 (76)
T cd04888           8 EHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTM   52 (76)
T ss_pred             cCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCch
Confidence            36789999999999999999999987654 455566777766554

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.

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=91.07  E-value=1.1  Score=42.30  Aligned_cols=51  Identities=4%  Similarity=0.094  Sum_probs=40.9

Q ss_pred             CeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEe-eeCCeEEEEEEEEec
Q 039443           79 STLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQF-NSGDRVIFSVLSKVH  130 (137)
Q Consensus        79 s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s-~~~~~v~~ti~akv~  130 (137)
                      ...+|.++|. +++|+|.++..+|..+|++|++|.+. +-+|.++-+|.+.=.
T Consensus       703 ~~t~V~V~~~-DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~  754 (895)
T PRK00275        703 GGTQIFIYAP-DQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDD  754 (895)
T ss_pred             CeEEEEEEeC-CCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCC
Confidence            4556666555 79999999999999999999999984 457787778877643

>PRK05007 PII uridylyl-transferase; Provisional

Probab=91.05  E-value=1.8  Score=40.64  Aligned_cols=59  Identities=12%  Similarity=0.245  Sum_probs=43.8

Q ss_pred             CceeEEEee--CCeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEE
Q 039443           69 PTVMNITTS--GSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNS-GDRVIFSVLSK  128 (137)
Q Consensus        69 ~p~v~v~~~--~s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~v~~ti~ak  128 (137)
                      .|.+.+...  +...+|.+ ++.+++|+|.+|..+|..+|++|++|.+.+. +|.++-++.+.
T Consensus       688 ~p~V~i~~~~~~~~t~V~V-~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~  749 (884)
T PRK05007        688 KPLVLLSKQATRGGTEIFI-WSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVL  749 (884)
T ss_pred             CCeEEEEecCCCCeEEEEE-EecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEE
Confidence            455555542  23445555 4558999999999999999999999998776 55887677665

>PRK03059 PII uridylyl-transferase; Provisional

Probab=90.91  E-value=1.2  Score=41.83  Aligned_cols=50  Identities=8%  Similarity=0.101  Sum_probs=41.6

Q ss_pred             CeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEe-eeCCeEEEEEEEEe
Q 039443           79 STLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQF-NSGDRVIFSVLSKV  129 (137)
Q Consensus        79 s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s-~~~~~v~~ti~akv  129 (137)
                      ...+|.++|. +++|+|+++..+|..+||+|++|.+. +.+|.++-++.+.=
T Consensus       677 ~~~~v~i~~~-d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~  727 (856)
T PRK03059        677 EGLQVMVYTP-DQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLD  727 (856)
T ss_pred             CeEEEEEEec-CCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeC
Confidence            4557766555 79999999999999999999999995 45888888888764

>PRK05092 PII uridylyl-transferase; Provisional

Probab=90.75  E-value=1.9  Score=40.68  Aligned_cols=60  Identities=13%  Similarity=0.285  Sum_probs=45.4

Q ss_pred             CceeEEEee--CCeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEe
Q 039443           69 PTVMNITTS--GSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFN-SGDRVIFSVLSKV  129 (137)
Q Consensus        69 ~p~v~v~~~--~s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~-~~~~v~~ti~akv  129 (137)
                      .|.+.++..  +...+|.++|. +++|+|.+|..+|..+|++|++|.+.+ .|+.++-+|.+.-
T Consensus       719 ~~~v~~~~~~~~~~t~v~I~~~-Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~  781 (931)
T PRK05092        719 PLATEVRPDPARGVTEVTVLAA-DHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQD  781 (931)
T ss_pred             CcEEEEEecCCCCeEEEEEEeC-CCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEEC
Confidence            355655543  23556666555 789999999999999999999999877 4777777777653

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

Probab=90.57  E-value=2.2  Score=24.85  Aligned_cols=43  Identities=14%  Similarity=0.236  Sum_probs=32.9

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeeeC-CeEEEEEEEEec
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNSG-DRVIFSVLSKVH  130 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~-~~v~~ti~akv~  130 (137)
                      +.++++.+.+++..|.++++++.+..+...+ +...+.+..++.
T Consensus         5 ~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~   48 (71)
T cd04876           5 AIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVR   48 (71)
T ss_pred             EeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEEC
Confidence            3467889999999999999999999887765 545455555543

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

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=89.63  E-value=0.33  Score=43.57  Aligned_cols=37  Identities=32%  Similarity=0.487  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHH
Q 039443            9 HRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYIT   45 (137)
Q Consensus         9 ~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk   45 (137)
                      +-|.++|.-+..|.||+|.    ++|+||-|+|.-++.|++
T Consensus        35 RHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   35 RHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            3467889999999999997    799999999999999985

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

Probab=89.55  E-value=1.4  Score=28.29  Aligned_cols=38  Identities=13%  Similarity=0.174  Sum_probs=30.1

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEE
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVL  126 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~  126 (137)
                      +.+++|.|.+|+..+.+.|..+.+.++.+. +.+.+++.
T Consensus         7 ~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~l~i~   44 (74)
T cd04877           7 CEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GRIYLNFP   44 (74)
T ss_pred             EEccchHHHHHHHHHHHCCCceEEEEEecC-CeEEEEeE
Confidence            347899999999999999999999999775 54333433

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

>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=89.48  E-value=3.3  Score=26.81  Aligned_cols=44  Identities=9%  Similarity=0.101  Sum_probs=35.9

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeC-CeEEEEEEEEecCC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSG-DRVIFSVLSKVHFR  132 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~-~~v~~ti~akv~~~  132 (137)
                      .+++|.|.+++..|.++|+.+.+..+.+.. +.-.|++.+.+...
T Consensus         9 ~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~   53 (80)
T cd04905           9 PNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGH   53 (80)
T ss_pred             CCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECC
Confidence            367999999999999999999999887763 45557888777654

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

>PRK04435 hypothetical protein; Provisional

Probab=89.39  E-value=3.2  Score=30.63  Aligned_cols=55  Identities=13%  Similarity=0.276  Sum_probs=41.4

Q ss_pred             eCCeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEecCC
Q 039443           77 SGSTLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNS-GDRVIFSVLSKVHFR  132 (137)
Q Consensus        77 ~~s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~v~~ti~akv~~~  132 (137)
                      .|..+.+.+.+. +++|.|.+|+..|.+.|+.|.+.+.+.. ++....+|.+.+.+.
T Consensus        66 ~~r~vtL~i~l~-Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~  121 (147)
T PRK04435         66 KGKIITLSLLLE-DRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSM  121 (147)
T ss_pred             CCcEEEEEEEEe-cCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCCh
Confidence            344444444444 6799999999999999999999987653 677777888887654

>PRK04374 PII uridylyl-transferase; Provisional

Probab=89.21  E-value=2.1  Score=40.23  Aligned_cols=50  Identities=16%  Similarity=0.209  Sum_probs=41.9

Q ss_pred             CeeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEe
Q 039443           79 STLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFN-SGDRVIFSVLSKV  129 (137)
Q Consensus        79 s~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~-~~~~v~~ti~akv  129 (137)
                      ...+|.++|. +++|+|++|..+|..+|++|++|.+.+ .+|.++-+|.+.=
T Consensus       689 ~~~~v~v~~~-d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~  739 (869)
T PRK04374        689 DALEVFVYSP-DRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLP  739 (869)
T ss_pred             CeEEEEEEeC-CCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeC
Confidence            4567766555 799999999999999999999999977 5888888888753

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

Probab=88.32  E-value=4  Score=24.73  Aligned_cols=38  Identities=11%  Similarity=0.245  Sum_probs=29.4

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeeeC-CeEEEEE
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNSG-DRVIFSV  125 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~-~~v~~ti  125 (137)
                      ..+++|.|.+++..|.++++.+.+.+....+ +...+++
T Consensus         7 ~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i   45 (72)
T cd04874           7 AEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYM   45 (72)
T ss_pred             eCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEE
Confidence            3478999999999999999999998887653 3433333

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.

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

Probab=87.33  E-value=2  Score=26.02  Aligned_cols=39  Identities=15%  Similarity=0.281  Sum_probs=30.0

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeC--CeEEEEEEE
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSG--DRVIFSVLS  127 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~--~~v~~ti~a  127 (137)
                      .+++|.|.++++.|.++|+.+.+...+...  +...+.++.
T Consensus         7 ~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~v   47 (65)
T cd04882           7 PDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRT   47 (65)
T ss_pred             CCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEe
Confidence            368999999999999999999887765543  455555554

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.

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

Probab=87.03  E-value=3.4  Score=24.81  Aligned_cols=40  Identities=5%  Similarity=-0.036  Sum_probs=32.4

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeeeC--CeEEEEEEE
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNSG--DRVIFSVLS  127 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~--~~v~~ti~a  127 (137)
                      ..+++|.+.++...|.+.|+.+.+..+...+  +...+++.+
T Consensus         6 ~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v   47 (71)
T cd04879           6 HKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV   47 (71)
T ss_pred             ecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc
Confidence            3467899999999999999999999987754  565556655

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

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

Probab=85.39  E-value=2.8  Score=25.94  Aligned_cols=43  Identities=9%  Similarity=0.159  Sum_probs=34.0

Q ss_pred             ecCCCcchHHHHHHHHHhCCcEEEEEEEee--eCCeEEEEEEEEe
Q 039443           87 CGSNRNFMFHEIISVLEEGAAEVINVTQFN--SGDRVIFSVLSKV  129 (137)
Q Consensus        87 ~~~~~~~~L~~il~~Le~~~L~V~~a~~s~--~~~~v~~ti~akv  129 (137)
                      ...+++|.+.++...|.++|+.+.+..++.  .++...+.+.+.-
T Consensus         5 ~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~   49 (73)
T cd04902           5 RNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDE   49 (73)
T ss_pred             EeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCC
Confidence            455789999999999999999998887765  3567766776543

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

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

Probab=85.30  E-value=3.5  Score=26.58  Aligned_cols=43  Identities=7%  Similarity=0.067  Sum_probs=34.9

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeE-EEEEEEEecC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSGDRV-IFSVLSKVHF  131 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v-~~ti~akv~~  131 (137)
                      .+++|.|.++|..+...|+.+.+..+-+..+.- -|.+.+.+.+
T Consensus         8 ~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~   51 (74)
T cd04904           8 KEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEV   51 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEc
Confidence            467999999999999999999999998875543 3676666654

ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy

>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate

Probab=84.75  E-value=4.1  Score=24.30  Aligned_cols=41  Identities=12%  Similarity=0.178  Sum_probs=32.7

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeC-CeEEEEEEEEe
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSG-DRVIFSVLSKV  129 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~-~~v~~ti~akv  129 (137)
                      .+++|.|.++.+.|.+.|..+.+..+...+ +..++.|....
T Consensus         6 ~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~~   47 (56)
T cd04889           6 ENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFSD   47 (56)
T ss_pred             CCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEECC
Confidence            368999999999999999999888877754 66666665543

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

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=84.64  E-value=0.73  Score=35.03  Aligned_cols=46  Identities=24%  Similarity=0.290  Sum_probs=35.6

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHH
Q 039443            4 NIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQK   49 (137)
Q Consensus         4 ~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~   49 (137)
                      .-.||.|-+.+++.|.-|++|+|.  ..++.+-..+.-+.+||..|.|
T Consensus        27 ~~~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~dE   74 (173)
T KOG4447|consen   27 QRKERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSLDE   74 (173)
T ss_pred             hHHHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhHHH
Confidence            345899999999999999999998  4555555557777777776654

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

Probab=83.87  E-value=4.2  Score=25.29  Aligned_cols=38  Identities=11%  Similarity=0.086  Sum_probs=30.3

Q ss_pred             CCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           90 NRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        90 ~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      +++|.|.+++..|.+.|+.|.+..+...++.  ..++..+
T Consensus        10 d~pG~La~v~~~l~~~~inI~~i~~~~~~~~--~~~rl~~   47 (66)
T cd04908          10 NKPGRLAAVTEILSEAGINIRALSIADTSEF--GILRLIV   47 (66)
T ss_pred             CCCChHHHHHHHHHHCCCCEEEEEEEecCCC--CEEEEEE
Confidence            6899999999999999999999888776564  3444444

Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.

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

Probab=83.18  E-value=5.6  Score=21.62  Aligned_cols=30  Identities=27%  Similarity=0.465  Sum_probs=25.9

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSG  118 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~  118 (137)
                      .++++.+.+++..|...|+.+...+....+
T Consensus         6 ~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           6 PDRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             cCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            356889999999999999999999887653

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

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

Probab=83.15  E-value=7.3  Score=23.40  Aligned_cols=39  Identities=13%  Similarity=0.216  Sum_probs=29.8

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeee--CCeEEEEEE
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNS--GDRVIFSVL  126 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~--~~~v~~ti~  126 (137)
                      ..+++|.|.++...|.++|+.+.+......  ++...+.|.
T Consensus         6 ~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~   46 (71)
T cd04903           6 HKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIE   46 (71)
T ss_pred             eCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEE
Confidence            447899999999999999999998887663  344444443

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.

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

Probab=81.54  E-value=7.4  Score=26.52  Aligned_cols=44  Identities=7%  Similarity=0.097  Sum_probs=34.9

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeCCe-EEEEEEEEecCC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSGDR-VIFSVLSKVHFR  132 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~-v~~ti~akv~~~  132 (137)
                      .+++|.|.++|..|...|+.+.+..+-+..+. --|.|.+.+.+.
T Consensus        22 ~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg~   66 (90)
T cd04931          22 KEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDKK   66 (90)
T ss_pred             CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcC
Confidence            46799999999999999999999999887443 336766666653

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

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

Probab=81.19  E-value=1.3  Score=27.37  Aligned_cols=44  Identities=11%  Similarity=0.005  Sum_probs=32.8

Q ss_pred             EecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           86 ICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        86 ~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      +...+++|.|.+++..|.+.|..+.+.+....++..+..+...+
T Consensus         4 ~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~~   47 (69)
T cd04901           4 HIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDIDS   47 (69)
T ss_pred             EEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcCC
Confidence            34557899999999999999999977766554566555555444

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

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

Probab=80.68  E-value=9.1  Score=25.00  Aligned_cols=43  Identities=12%  Similarity=0.157  Sum_probs=33.9

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeCC-eEEEEEEEEecC
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSGD-RVIFSVLSKVHF  131 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~-~v~~ti~akv~~  131 (137)
                      .+++|.|.+++..|...|+.+.+..+-+..+ .--|.+.+.+.+
T Consensus         8 ~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e~   51 (74)
T cd04929           8 KNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCEC   51 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEc
Confidence            4679999999999999999999999988633 333666666554

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

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

Probab=80.62  E-value=8.2  Score=24.25  Aligned_cols=28  Identities=14%  Similarity=0.203  Sum_probs=25.5

Q ss_pred             CCcchHHHHHHHHHhCCcEEEEEEEeee
Q 039443           90 NRNFMFHEIISVLEEGAAEVINVTQFNS  117 (137)
Q Consensus        90 ~~~~~L~~il~~Le~~~L~V~~a~~s~~  117 (137)
                      +++|.|.++++.|.++|+.+++......
T Consensus         8 d~pG~L~~l~~~i~~~g~nI~~i~~~~~   35 (72)
T cd04884           8 DKPGTLKPVVDTLREFNARIISILTAFE   35 (72)
T ss_pred             CCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence            6899999999999999999999987765

This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=80.16  E-value=10  Score=22.69  Aligned_cols=42  Identities=7%  Similarity=0.015  Sum_probs=32.7

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeee--CCeEEEEEEEEe
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNS--GDRVIFSVLSKV  129 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~--~~~v~~ti~akv  129 (137)
                      ..+++|.|.++...|.++|..+.+.+....  ++...+.+...+
T Consensus         7 ~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~   50 (72)
T cd04878           7 VENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEG   50 (72)
T ss_pred             EcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEEC
Confidence            346789999999999999999999988764  455555665554

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

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	137
1r05_A	87	Solution Structure Of Max B-Hlh-Lz Length = 87		1e-04
1nkp_B	83	Crystal Structure Of Myc-Max Recognizing Dna Length		2e-04
1nlw_B	76	Crystal Structure Of Mad-Max Recognizing Dna Length		3e-04
1an2_A	86	Recognition By Max Of Its Cognate Dna Through A Dim		4e-04

>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz Length = 87

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 9/73 (12%)
Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITH-------LQKNK 51
          A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI +       LQ++ 
Sbjct: 6  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDI 65
Query: 52 ESLERRRALLKEE 64
          + L+R+ ALL+++
Sbjct: 66 DDLKRQNALLEQQ 78

>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna Length = 83

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 9/73 (12%)
Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHL-------QKNK 51
          A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI ++       Q++ 
Sbjct: 4  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 63
Query: 52 ESLERRRALLKEE 64
          + L+R+ ALL+++
Sbjct: 64 DDLKRQNALLEQQ 76

>pdb|1NLW|B Chain B, Crystal Structure Of Mad-Max Recognizing Dna Length = 76

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 9/73 (12%)
Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHL-------QKNK 51
          A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI ++       Q++ 
Sbjct: 3  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 62
Query: 52 ESLERRRALLKEE 64
          + L+R+ ALL+++
Sbjct: 63 DDLKRQNALLEQQ 75

>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric BHLHZ DOMAIN Length = 86

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 9/73 (12%)
Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHL-------QKNK 51
          A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI ++       Q++ 
Sbjct: 5  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 64
Query: 52 ESLERRRALLKEE 64
          + L+R+ ALL+++
Sbjct: 65 DDLKRQNALLEQQ 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	137
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	7e-12
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	1e-10
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-10
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	5e-10
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	2e-08
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	4e-08

>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 = 56.6 bits (137), Expect = 7e-12
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 4  NIKEKHRRTHMKDLISQLASLIP---SSSKLSMPEILDEATSYITHLQKNKESLERRRAL 60
          N+ E+ RR  +K     L   IP   ++ K     IL +AT+YI  +Q  ++ L     L
Sbjct: 11 NVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL 70

Query: 61 LKEE 64
          L++ 
Sbjct: 71 LRKR 74

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

 Score = 53.2 bits (128), Expect = 1e-10
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 4  NIKEKHRRTHMKDLISQLASLIPSS-SKLSMPEILDEATSYITHLQKNKESLERRRALLK 62
          N  EK  R+ + D I +L  L+  + +KL+   +L +A  YI  LQ + + L++    L+
Sbjct: 11 NAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR 70

Query: 63 EE 64
            
Sbjct: 71 TA 72

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

 Score = 52.4 bits (126), Expect = 2e-10
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 4  NIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESLERRRALL 61
          N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI ++++   + ++    L
Sbjct: 7  NALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL 66

Query: 62 KEE 64
          K +
Sbjct: 67 KRQ 69

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

 Score = 51.6 bits (124), Expect = 5e-10
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 4  NIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESLERRRALL 61
          N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI ++++   + ++    L
Sbjct: 17 NALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL 76

Query: 62 KEE 64
          K +
Sbjct: 77 KRQ 79

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

 Score = 47.1 bits (112), Expect = 2e-08
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 1  AQRNIKEKHRRTHMKDLISQLASLIP---SSSKLSMPEILDEATSYITHLQKNKESLERR 57
          +  N  EK+RR H++  + +L  L+P    SS+ +   +L +A  +I  L+ +      +
Sbjct: 3  STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

Query: 58 RALLKEE 64
             L+ E
Sbjct: 63 IDQLQRE 69

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

 Score = 46.2 bits (110), Expect = 4e-08
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 6/55 (10%)

Query: 4  NIKEKHRRTHMKDLISQLASLIPSSS------KLSMPEILDEATSYITHLQKNKE 52
          N  E+ RR  + + I QL+ +IP SS        S   IL +A+ YI  L+++  
Sbjct: 10 NEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.73
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.71
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.71
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.68
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.66
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.6
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.59
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.58
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.55
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.54
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.52
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.5
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.47
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.24
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.05
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.93
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.88
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.36
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	95.24
2nyi_A	195	Unknown protein; protein structure initiative, PSI	94.15
1u8s_A	192	Glycine cleavage system transcriptional repressor,	94.03
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	92.59
2nyi_A	195	Unknown protein; protein structure initiative, PSI	86.32

>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=99.73  E-value=7.7e-18  Score=113.42  Aligned_cols=62  Identities=29%  Similarity=0.461  Sum_probs=58.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC-CCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPSS-SKLSMPEILDEATSYITHLQKNKESLERRRALLKE   63 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~~-~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~~   63 (137)
                      .|+.+||+||..||+.|..|+++||.. .|+||++||.+||+||++|+++++.|+.+.+.|..
T Consensus         9 ~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   71 (82)
T 1am9_A            9 AHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999994 89999999999999999999999999998877654

>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=99.71  E-value=2.7e-17  Score=110.61  Aligned_cols=62  Identities=34%  Similarity=0.512  Sum_probs=57.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESLERRRALLKE   63 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~~   63 (137)
                      .||..||+||..||+.|..|+++||.  ..|+||++||..||+||+.|+++++.|+.+++.+..
T Consensus         5 ~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~   68 (83)
T 1nkp_B            5 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999998  589999999999999999999999999988876643

>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=99.71  E-value=2.2e-17  Score=110.52  Aligned_cols=61  Identities=34%  Similarity=0.518  Sum_probs=57.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .||.+||+||..||+.|..|+++||.  ..|+||++||..||+||+.|++.+++|+.+.+.|.
T Consensus        15 ~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A           15 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999998  47999999999999999999999999999988764

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

Probab=99.68  E-value=1.5e-16  Score=106.81  Aligned_cols=61  Identities=26%  Similarity=0.373  Sum_probs=57.1

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .||..||+||..||+.|..|+++||.   ..|++|++||..|++||+.|+++.+.|..+++.+.
T Consensus         4 ~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~   67 (80)
T 1nlw_A            4 THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999996   47899999999999999999999999999887664

>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=99.66  E-value=2.2e-16  Score=107.70  Aligned_cols=61  Identities=31%  Similarity=0.458  Sum_probs=55.6

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .||+.||+||..||+.|..|+++||.   ..|+||++||..||+||+.|+++.+.+..+++.+.
T Consensus         9 ~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A            9 THNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999999999999999998   36999999999999999999999998887665543

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

Probab=99.60  E-value=1.4e-15  Score=99.95  Aligned_cols=54  Identities=28%  Similarity=0.504  Sum_probs=50.2

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC-CCCCCHHhHHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKNKESLE   55 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~-~~k~~k~~il~~Ai~YIk~L~~~v~~L~   55 (137)
                      +|+.+||+||.+||+.|..|++|||. ..|+||++||..||+||+.|++.+.=|+
T Consensus        11 ~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B           11 SRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            69999999999999999999999998 5799999999999999999999886553

>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=99.59  E-value=5.8e-16  Score=99.60  Aligned_cols=51  Identities=35%  Similarity=0.507  Sum_probs=47.1

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC-------CCCCCHHhHHHHHHHHHHHHHHHH
Q 039443            1 AQRNIKEKHRRTHMKDLISQLASLIPS-------SSKLSMPEILDEATSYITHLQKNK   51 (137)
Q Consensus         1 ~~h~~~ER~RR~~mn~~~~~Lrsl~P~-------~~k~~k~~il~~Ai~YIk~L~~~v   51 (137)
                      .+|+.+||.||..||+.|..|++|||.       .+|.+|+++|+.||+||++|++++
T Consensus         4 ~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            4 ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            379999999999999999999999996       368999999999999999999765

>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=99.58  E-value=5.6e-16  Score=99.72  Aligned_cols=51  Identities=39%  Similarity=0.574  Sum_probs=46.7

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC------CCCCHHhHHHHHHHHHHHHHHHH
Q 039443            1 AQRNIKEKHRRTHMKDLISQLASLIPSS------SKLSMPEILDEATSYITHLQKNK   51 (137)
Q Consensus         1 ~~h~~~ER~RR~~mn~~~~~Lrsl~P~~------~k~~k~~il~~Ai~YIk~L~~~v   51 (137)
                      ..|+.+||+||..||+.|..|+++||..      .|+||++||..||+||++|+++.
T Consensus         7 ~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            7 AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            3699999999999999999999999983      38999999999999999999764

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

Probab=99.55  E-value=9.2e-15  Score=104.49  Aligned_cols=57  Identities=30%  Similarity=0.518  Sum_probs=52.5

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC----CCCCHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPSS----SKLSMPEILDEATSYITHLQKNKESLERRR   58 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~~----~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k   58 (137)
                      .|+.+||+||..||+.|..|+++||..    .|+||++||..||+||+.|++.++.|++..
T Consensus        30 ~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           30 NHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999972    589999999999999999999999998753

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

Probab=99.54  E-value=2.9e-15  Score=99.62  Aligned_cols=54  Identities=22%  Similarity=0.307  Sum_probs=49.3

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCC-CHHhHHHHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS---SSKL-SMPEILDEATSYITHLQKNKESLE   55 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~-~k~~il~~Ai~YIk~L~~~v~~L~   55 (137)
                      .||+.||+||..+|+.|..|+.+||.   ..|. +|++||..||+||+.|++++++++
T Consensus         8 ~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            8 HHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            69999999999999999999999994   4565 899999999999999999999875

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

Probab=99.52  E-value=1.8e-14  Score=91.84  Aligned_cols=51  Identities=27%  Similarity=0.396  Sum_probs=47.5

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKE   52 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~   52 (137)
                      .||+.||+|++.||+.|..||++||.   ..|+||.+||..||+||..|++.++
T Consensus         5 ~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            5 KANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            58999999999999999999999997   4689999999999999999998764

>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=99.50  E-value=1.6e-14  Score=94.23  Aligned_cols=51  Identities=25%  Similarity=0.364  Sum_probs=47.5

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKE   52 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v~   52 (137)
                      .||+.||+|++.||+.|..||.+||.  ..|+||++||..||+||..|++.++
T Consensus        15 ~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           15 AATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            58999999999999999999999997  4799999999999999999998653

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

Probab=99.47  E-value=1.9e-14  Score=95.07  Aligned_cols=48  Identities=35%  Similarity=0.495  Sum_probs=45.1

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQK   49 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~   49 (137)
                      .|+.+||+||.+||+.|..|++|||.    .+|+||++||..||+||+.|+.
T Consensus        12 ~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           12 AHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             hcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            59999999999999999999999997    3799999999999999999874

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

Probab=99.24  E-value=2.3e-12  Score=83.71  Aligned_cols=46  Identities=30%  Similarity=0.383  Sum_probs=42.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHH
Q 039443            4 NIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQK   49 (137)
Q Consensus         4 ~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~   49 (137)
                      +..||+|+..||+.|..||.+||.   ..|+||.+||..||+||..||+
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            467999999999999999999998   4789999999999999999984

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

Probab=99.05  E-value=2e-10  Score=93.83  Aligned_cols=49  Identities=27%  Similarity=0.548  Sum_probs=42.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC-CCCCCHHhHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKN   50 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~-~~k~~k~~il~~Ai~YIk~L~~~   50 (137)
                      .|+.+||+||.+||..|..|++|||. .+|+||++||..||.||+.++..
T Consensus        15 ~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           15 SRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            69999999999999999999999995 78999999999999999999764

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

Probab=98.93  E-value=1.9e-09  Score=74.48  Aligned_cols=48  Identities=35%  Similarity=0.422  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHHH
Q 039443            6 KEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKES   53 (137)
Q Consensus         6 ~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~~   53 (137)
                      .||.|...||+.|..||.+||.   ..|++|.++|.-||+||..|++-+++
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            3689999999999999999997   46899999999999999999998765

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

Probab=98.88  E-value=1.5e-09  Score=89.71  Aligned_cols=49  Identities=35%  Similarity=0.482  Sum_probs=45.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQKN   50 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~~   50 (137)
                      +|+.+||+||.+||+.|..|++|||.    ..|+||++||..||.|||.|+..
T Consensus        16 ~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           16 AHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            59999999999999999999999994    78999999999999999999743

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

Probab=98.36  E-value=1.4e-06  Score=58.47  Aligned_cols=47  Identities=28%  Similarity=0.490  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHhcCCC----CCCCCHHhHHHHHHHHHHHHHHHHHHHHHH
Q 039443           11 RTHMKDLISQLASLIPS----SSKLSMPEILDEATSYITHLQKNKESLERR   57 (137)
Q Consensus        11 R~~mn~~~~~Lrsl~P~----~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~   57 (137)
                      |-.+|+.+..|..|||.    ..|++|.+||..|++||+.|++..+.+.+.
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            66799999999999996    368999999999999999998877776653

>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=95.24  E-value=0.18  Score=32.27  Aligned_cols=45  Identities=7%  Similarity=0.076  Sum_probs=38.9

Q ss_pred             ecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           87 CGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        87 ~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      .+.+++|.+.+|...|-+.|..+.+.+....++..+..+.+.+.+
T Consensus        11 ~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~~   55 (91)
T 1zpv_A           11 VGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE   55 (91)
T ss_dssp             EESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS
T ss_pred             EECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeCC
Confidence            445899999999999999999999999988888777778777765

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

Probab=94.15  E-value=0.25  Score=36.57  Aligned_cols=46  Identities=22%  Similarity=0.229  Sum_probs=39.3

Q ss_pred             EEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 039443           85 LICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVH  130 (137)
Q Consensus        85 ~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~  130 (137)
                      .++|..++|.+..|...|.++|+.|++++..+.++.++..+.+...
T Consensus         9 tv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~~~   54 (195)
T 2nyi_A            9 SVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVSLN   54 (195)
T ss_dssp             EEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES
T ss_pred             EEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEEec
Confidence            3445589999999999999999999999999998888777777654

>1u8s_A Glycine cleavage system transcriptional repressor, putative; structural genomics, protein structure initiative (PSI), domain swapping; 2.45A {Vibrio cholerae} SCOP: d.58.18.5 d.58.18.5

Probab=94.03  E-value=0.27  Score=35.96  Aligned_cols=47  Identities=13%  Similarity=0.278  Sum_probs=39.5

Q ss_pred             eEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 039443           82 EVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKV  129 (137)
Q Consensus        82 ~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv  129 (137)
                      .+.++ |.+++|.+.+|...|.++|+.+++++....++.++.++.+..
T Consensus         8 ~itv~-~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~   54 (192)
T 1u8s_A            8 VITAV-GTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG   54 (192)
T ss_dssp             EEEEE-EECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEE-cCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEec
Confidence            34444 458999999999999999999999999998888887777654

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

Probab=92.59  E-value=0.93  Score=28.26  Aligned_cols=44  Identities=14%  Similarity=0.153  Sum_probs=35.4

Q ss_pred             cCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           88 GSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        88 ~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      ..+++|.|.+|...|.+.|+.+.+.+....++.....+...+.+
T Consensus        12 ~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~~~~   55 (88)
T 2ko1_A           12 GEDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIFVKN   55 (88)
T ss_dssp             EECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEEESS
T ss_pred             EECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEEECC
Confidence            44789999999999999999999999988766444566666543

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

Probab=86.32  E-value=2.5  Score=31.09  Aligned_cols=47  Identities=9%  Similarity=0.114  Sum_probs=36.2

Q ss_pred             EEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeC------CeEEEEEEEEec
Q 039443           83 VNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSG------DRVIFSVLSKVH  130 (137)
Q Consensus        83 V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~------~~v~~ti~akv~  130 (137)
                      +.+. |..++|.+.+|-..|-++|+.+.+++..+.+      +.++..+...+.
T Consensus        96 ltv~-g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~~  148 (195)
T 2nyi_A           96 LYVE-GPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAFP  148 (195)
T ss_dssp             EEEE-EECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEEE
T ss_pred             EEEE-eCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEcC
Confidence            3444 4579999999999999999999999999876      445445555443

---

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	137
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	4e-11
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	2e-09
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	7e-09
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-08
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-08
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	2e-07
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	2e-07
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	3e-06

>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 = 53.4 bits (128), Expect = 4e-11
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 1  AQRNIKEKHRRTHMKDLISQLASLIP---SSSKLSMPEILDEATSYITHLQKNKESLERR 57
             N+ E+ RR  +K     L   IP   ++ K     IL +AT+YI  +Q  ++ L   
Sbjct: 8  RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE 67

Query: 58 RALLKEE 64
            LL++ 
Sbjct: 68 EDLLRKR 74

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

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

 Score = 48.7 bits (116), Expect = 2e-09
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESLERRR 58
          A  N  E+ RR H+KD    L   +PS    K S  +ILD+AT YI ++++   + ++  
Sbjct: 4  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 63

Query: 59 ALLKEE 64
            LK +
Sbjct: 64 DDLKRQ 69

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

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

 Score = 47.2 bits (112), Expect = 7e-09
 Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPSSS---KLSMPEILDEATSYITHLQKNKESLERR 57
          +  N  EK+RR H++  + +L  L+P      + +   +L +A  +I  L+ +      +
Sbjct: 3  STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

Query: 58 RALLKEE 64
             L+ E
Sbjct: 63 IDQLQRE 69

>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 = 46.4 bits (110), Expect = 1e-08
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 7/57 (12%)

Query: 4  NIKEKHRRTHMKDLISQLASLIP-------SSSKLSMPEILDEATSYITHLQKNKES 53
             E+ RR  +   + +LASLIP        S+  S    ++ A  YI HLQ+N  +
Sbjct: 7  KHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST 63

>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 = 46.5 bits (110), Expect = 1e-08
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 3  RNIKEKHRRTHMKDLISQLASLIPSS-SKLSMPEILDEATSYITHLQKNKESLERRRALL 61
           N  EK  R+ + D I +L  L+  + +KL+   +L +A  YI  LQ + + L++    L
Sbjct: 10 HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL 69

Query: 62 KEE 64
          +  
Sbjct: 70 RTA 72

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (102), Expect = 2e-07
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 11 RTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKNKESLERRRALLKEEDH 66
          R+ + D I +L  L+    +K+    +L +A  YI +LQ+    L +   +LK  + 
Sbjct: 1  RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQ 57

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

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

 Score = 43.2 bits (102), Expect = 2e-07
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 6/58 (10%)

Query: 1  AQRNIKEKHRRTHMKDLISQLASLIPSS------SKLSMPEILDEATSYITHLQKNKE 52
          AQ N  E+ RR  + + I QL+ +IP S      S  S   IL +A+ YI  L+++  
Sbjct: 7  AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

>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 = 40.2 bits (94), Expect = 3e-06
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 4  NIKEKHRRTHMKDLISQLASLIPSSS--KLSMPEILDEATSYITHLQK 49
           ++E+ R + + +    L     S+   +L   EIL  A  YI  LQ 
Sbjct: 17 TMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQA 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.67
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.63
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.63
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.5
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	95.54
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	95.24
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	90.74
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	88.16
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	87.29
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	86.75
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	81.87

>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=99.70  E-value=2.3e-17  Score=108.31  Aligned_cols=61  Identities=26%  Similarity=0.373  Sum_probs=56.9

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .||..||+||..||+.|..|+++||.   ..|+||++||..||+||+.|++.++.|..+++.+.
T Consensus         4 ~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~   67 (79)
T d1nlwa_           4 THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999997   46899999999999999999999999998887664

>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=99.70  E-value=1.8e-17  Score=109.32  Aligned_cols=61  Identities=30%  Similarity=0.462  Sum_probs=57.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC-CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~-~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .|+++||+||..||+.|..|+++||. .+|+||++||..||+||+.|+++++.|..+...+.
T Consensus         9 ~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk   70 (80)
T d1am9a_           9 AHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999998 67999999999999999999999999998877654

>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=99.67  E-value=6e-17  Score=108.31  Aligned_cols=61  Identities=31%  Similarity=0.458  Sum_probs=56.5

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS---SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~---~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .||++||+||..||+.|..|+++||+   ..|+||++||..|++||+.|++.++.|..+++.+.
T Consensus         9 ~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   72 (88)
T d1nkpa_           9 THNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999999999999999997   46899999999999999999999999998776654

>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=99.67  E-value=7.8e-17  Score=106.68  Aligned_cols=61  Identities=34%  Similarity=0.518  Sum_probs=56.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKESLERRRALLK   62 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   62 (137)
                      .||.+||+||.+||+.|..|+++||.  ..|+||++||..||+||+.|++.+..|..+.+.+.
T Consensus         5 ~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   67 (83)
T d1nkpb_           5 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999997  57899999999999999999999999998776543

>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=99.63  E-value=8.9e-17  Score=103.18  Aligned_cols=51  Identities=25%  Similarity=0.364  Sum_probs=47.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCCHHhHHHHHHHHHHHHHHHHH
Q 039443            2 QRNIKEKHRRTHMKDLISQLASLIPS--SSKLSMPEILDEATSYITHLQKNKE   52 (137)
Q Consensus         2 ~h~~~ER~RR~~mn~~~~~Lrsl~P~--~~k~~k~~il~~Ai~YIk~L~~~v~   52 (137)
                      .||..||+||..||+.|..|+++||.  ..|+||++||..||+||++|++.|+
T Consensus        15 ~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          15 AATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            59999999999999999999999998  4689999999999999999998764

>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=99.63  E-value=1.1e-16  Score=101.13  Aligned_cols=51  Identities=35%  Similarity=0.507  Sum_probs=47.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC-------CCCCCHHhHHHHHHHHHHHHHHHH
Q 039443            1 AQRNIKEKHRRTHMKDLISQLASLIPS-------SSKLSMPEILDEATSYITHLQKNK   51 (137)
Q Consensus         1 ~~h~~~ER~RR~~mn~~~~~Lrsl~P~-------~~k~~k~~il~~Ai~YIk~L~~~v   51 (137)
                      ..|+.+||+||..||+.|..|+++||.       ..|+||++||..|++||++|++++
T Consensus         4 ~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           4 ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            379999999999999999999999994       578999999999999999999865

>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=99.50  E-value=2.8e-15  Score=95.10  Aligned_cols=50  Identities=38%  Similarity=0.566  Sum_probs=46.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC------CCCCCHHhHHHHHHHHHHHHHHH
Q 039443            1 AQRNIKEKHRRTHMKDLISQLASLIPS------SSKLSMPEILDEATSYITHLQKN   50 (137)
Q Consensus         1 ~~h~~~ER~RR~~mn~~~~~Lrsl~P~------~~k~~k~~il~~Ai~YIk~L~~~   50 (137)
                      ..|+.+||+||..||+.|..|+++||.      ..|+||++||..|++||+.|+++
T Consensus         7 ~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           7 AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            379999999999999999999999996      35899999999999999999865

>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=99.50  E-value=5.6e-15  Score=92.71  Aligned_cols=53  Identities=28%  Similarity=0.441  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHHhcCCC-CCCCCHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 039443           11 RTHMKDLISQLASLIPS-SSKLSMPEILDEATSYITHLQKNKESLERRRALLKE   63 (137)
Q Consensus        11 R~~mn~~~~~Lrsl~P~-~~k~~k~~il~~Ai~YIk~L~~~v~~L~~~k~~l~~   63 (137)
                      |..||+.|..|+++||+ .+|+||++||.+||+||+.|+++++.|+++...+..
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   54 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKL   54 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56799999999999998 579999999999999999999999999998876654

>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=95.54  E-value=0.07  Score=32.81  Aligned_cols=49  Identities=6%  Similarity=0.082  Sum_probs=42.0

Q ss_pred             EEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 039443           84 NLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHFR  132 (137)
Q Consensus        84 ~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~~  132 (137)
                      ..+.|..++|.+.+|-..|-++|..+.+++..+.++.++..+.+.+.+.
T Consensus         5 itv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~~~~   53 (83)
T d1zpva1           5 ITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDEK   53 (83)
T ss_dssp             EEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESSC
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEEecC
Confidence            3345678999999999999999999999999999998888888877654

>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=95.24  E-value=0.064  Score=33.39  Aligned_cols=48  Identities=13%  Similarity=0.186  Sum_probs=41.3

Q ss_pred             EEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 039443           84 NLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLSKVHF  131 (137)
Q Consensus        84 ~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~akv~~  131 (137)
                      ..+.|.+++|.+.++...|-+.|..+++++...+++.+.+.+.+.+.+
T Consensus         8 itv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~~   55 (86)
T d1u8sa1           8 ITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP   55 (86)
T ss_dssp             EEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH
T ss_pred             EEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcCc
Confidence            334566899999999999999999999999999999888888777643

>d2f06a1 d.58.18.11 (A:71-141) Hypothetical protein BT0572 {Bacteroides thetaiotaomicron [TaxId: 818]}

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

Probab=90.74  E-value=0.64  Score=27.76  Aligned_cols=39  Identities=8%  Similarity=0.080  Sum_probs=32.6

Q ss_pred             CCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEE
Q 039443           89 SNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVLS  127 (137)
Q Consensus        89 ~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~a  127 (137)
                      .+++|.|.++++.|.+.|+.+........++.-+..|.+
T Consensus         7 ~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~v   45 (71)
T d2f06a1           7 PNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRP   45 (71)
T ss_dssp             ESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEE
T ss_pred             cCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEE
Confidence            378999999999999999999999988888876544443

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

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

Probab=88.16  E-value=1.5  Score=26.18  Aligned_cols=37  Identities=16%  Similarity=0.170  Sum_probs=32.2

Q ss_pred             CCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEE
Q 039443           90 NRNFMFHEIISVLEEGAAEVINVTQFNSGDRVIFSVL  126 (137)
Q Consensus        90 ~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~~ti~  126 (137)
                      +++|.|.++...|.+.|+.+.+.+++...+.-++-|.
T Consensus        12 NkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Rii   48 (70)
T d2f06a2          12 NKSGRLTEVTEVLAKENINLSALCIAENADFGILRGI   48 (70)
T ss_dssp             SSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEE
T ss_pred             CCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEEE
Confidence            7899999999999999999999999888776665553

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

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

Probab=87.29  E-value=1.2  Score=27.07  Aligned_cols=48  Identities=0%  Similarity=-0.034  Sum_probs=37.5

Q ss_pred             EEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeCCeEE-EEEEEEecCC
Q 039443           85 LICGSNRNFMFHEIISVLEEGAAEVINVTQFNSGDRVI-FSVLSKVHFR  132 (137)
Q Consensus        85 ~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~~~v~-~ti~akv~~~  132 (137)
                      ++.-.+++|.|.+++..+.++|+...+..+-+..+... |.+.+.+.+.
T Consensus         6 i~~~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~~g~   54 (80)
T d2qmwa2           6 ITPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQADSA   54 (80)
T ss_dssp             EEESSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEESCC
T ss_pred             EEeCCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEecC
Confidence            33445789999999999999999999999988765543 6666776553

>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=86.75  E-value=2.2  Score=26.15  Aligned_cols=52  Identities=8%  Similarity=0.127  Sum_probs=37.3

Q ss_pred             eeeEEEEecCCCcchHHHHHHHHHhCCcEEEEEEEeeeC--------CeEEEEEEEEecCC
Q 039443           80 TLEVNLICGSNRNFMFHEIISVLEEGAAEVINVTQFNSG--------DRVIFSVLSKVHFR  132 (137)
Q Consensus        80 ~~~V~~~~~~~~~~~L~~il~~Le~~~L~V~~a~~s~~~--------~~v~~ti~akv~~~  132 (137)
                      .++|.+.|. .++|.+.+|-..|-++|+.+.+.+..+..        +.++-.+.+.+...
T Consensus         6 tv~v~v~g~-DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~p~~   65 (93)
T d1u8sa2           6 TVEVYVESD-DKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVDSG   65 (93)
T ss_dssp             EEEEEEEES-CCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEECTT
T ss_pred             EEEEEEEEC-CCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEcCcc
Confidence            455665555 79999999999999999999999876532        13444555555543

>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=81.87  E-value=0.47  Score=28.78  Aligned_cols=40  Identities=8%  Similarity=0.130  Sum_probs=26.7

Q ss_pred             CCcchHHHHHHHHHhCCcEEEEEEEeee-CCe--EEEEEEEEe
Q 039443           90 NRNFMFHEIISVLEEGAAEVINVTQFNS-GDR--VIFSVLSKV  129 (137)
Q Consensus        90 ~~~~~L~~il~~Le~~~L~V~~a~~s~~-~~~--v~~ti~akv  129 (137)
                      +++|.|.+|...+-++|..+.+.+.... +|.  +..+|..+.
T Consensus        10 Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~   52 (77)
T d1y7pa2          10 NKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEI   52 (77)
T ss_dssp             CCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEE
T ss_pred             cCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEc
Confidence            7899999999999999999999997763 432  334444443