Citrus Sinensis ID: 046429

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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
SMLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEEEEEcccEEEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEEcccccccHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccEEEEEEcccEEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEccccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
SMLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMksikpnssnnimdetnnicsnfpvvelkdlgsSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD
Flexible Loop (DISEMBL)
SMLSQEDRLDLACCYIKQLRERIDKLNRMKEQamksikpnssnnimDETNNICSNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAkisrlgvetsracqrlhdlvd
Low Complexity Region (SEG)
SMLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD
Disordered region (IsUnstruct)
********LDLACCYIKQLRERI*************************TNNICSNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET************
Disordered Region (DISOPRED)
***SQ*DRLDLACCYIKQLR****************************************LKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLV*
Disordered Region (DISEMBL)
SMLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD
Disordered Region (DISPRO)
***SQEDRLDLACCYIKQLRERIDKLNRMKEQA********************SNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
SMLSQEDRLDLACCYxxxxxxxxxxxxxxxxxxxxxIKPNSSNNIMDETNNICSNFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD
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
255540707	173	DNA binding protein, putative [Ricinus c	0.912	0.722	0.656	3e-43
224135791	178	predicted protein [Populus trichocarpa]	0.963	0.741	0.585	5e-41
224121682	179	predicted protein [Populus trichocarpa]	0.963	0.737	0.588	9e-40
356513596	191	PREDICTED: uncharacterized protein LOC10	0.970	0.696	0.6	4e-39
356508667	190	PREDICTED: uncharacterized protein LOC10	0.948	0.684	0.6	9e-39
356516682	193	PREDICTED: uncharacterized protein LOC10	0.963	0.683	0.577	3e-38
225457062	178	PREDICTED: uncharacterized protein LOC10	0.963	0.741	0.6	2e-37
358248500	161	uncharacterized protein LOC100787505 [Gl	0.773	0.658	0.601	1e-25
242056735	232	hypothetical protein SORBIDRAFT_03g00856	0.956	0.564	0.427	4e-22
226531322	229	putative HLH DNA-binding domain superfam	0.978	0.585	0.437	1e-21

>gi|255540707|ref|XP_002511418.1| DNA binding protein, putative [Ricinus communis] gi|223550533|gb|EEF52020.1| DNA binding protein, putative [Ricinus communis]

 Score =  179 bits (454), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 82/125 (65%), Positives = 106/125 (84%)

Query: 3   LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELK 62
           LSQ+D+LD A  YIK L+ERI+KL +MKEQAM+S+  NS+NN   +   + S  P++EL+
Sbjct: 48  LSQQDQLDHAAAYIKHLKERIEKLKKMKEQAMRSLATNSTNNNALDATTMGSRLPMIELR 107

Query: 63  DLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLG 122
           DLGSSIEV+LISG+++NFMLYEVI+I+EEEGA+VVSASFST+GDK+FH + AQ KISR+G
Sbjct: 108 DLGSSIEVILISGLKKNFMLYEVITIVEEEGAEVVSASFSTVGDKVFHIIHAQVKISRVG 167

Query: 123 VETSR 127
           VETSR
Sbjct: 168 VETSR 172

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135791|ref|XP_002322161.1| predicted protein [Populus trichocarpa] gi|222869157|gb|EEF06288.1| predicted protein [Populus trichocarpa]

 Score =  172 bits (435), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 79/135 (58%), Positives = 109/135 (80%), Gaps = 3/135 (2%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVEL 61
           MLSQ+D+L+LA CYIKQ+RER++KL R+KEQA+ +I+ + S      +  I    PV+EL
Sbjct: 46  MLSQQDQLELAACYIKQMRERVEKLKRVKEQAITTIQTSRSGMT---SMMIGLRLPVIEL 102

Query: 62  KDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 121
           +D GSSIEVVL+SG+ +NFM YEVI++L +EGA+VVSAS+ST+GDK+FHT+ AQ +ISR+
Sbjct: 103 RDFGSSIEVVLVSGLNKNFMFYEVITVLSDEGAEVVSASYSTVGDKVFHTIHAQVRISRV 162

Query: 122 GVETSRACQRLHDLV 136
           GVETSR  +RL +L+
Sbjct: 163 GVETSRVWERLQELI 177

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224121682|ref|XP_002318646.1| predicted protein [Populus trichocarpa] gi|222859319|gb|EEE96866.1| predicted protein [Populus trichocarpa]

 Score =  167 bits (424), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 80/136 (58%), Positives = 109/136 (80%), Gaps = 4/136 (2%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKE-QAMKSIKPNSSNNIMDETNNICSNFPVVE 60
           MLSQ+D+L+LA CYIKQLRER++ L R+KE QA+ + + +SS      +  I    PVVE
Sbjct: 46  MLSQQDQLELAACYIKQLRERVEGLKRVKEEQAITTTRTSSSAKT---SMMIGLRLPVVE 102

Query: 61  LKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISR 120
           L+D GS+IEVVLISG+ +NFM YEVI++L +EGA+V+SAS+ST+GDK+FHT+ AQ +ISR
Sbjct: 103 LRDFGSTIEVVLISGLNKNFMFYEVINVLSDEGAEVISASYSTVGDKVFHTIHAQVRISR 162

Query: 121 LGVETSRACQRLHDLV 136
           +GVETSR C+RL +L+
Sbjct: 163 VGVETSRVCERLQELI 178

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513596|ref|XP_003525498.1| PREDICTED: uncharacterized protein LOC100811485 [Glycine max]

 Score =  166 bits (419), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 81/135 (60%), Positives = 107/135 (79%), Gaps = 2/135 (1%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVEL 61
           MLSQ+D+LDLA  YIK+L+ERI+KL   KE+ M  +  ++ NN  +   NI S  P++E+
Sbjct: 49  MLSQQDQLDLATTYIKRLKERIEKLKGEKEKIMNMMMSSNQNN--NSIFNIGSQLPLLEI 106

Query: 62  KDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 121
           KDLGS IEV+LISG+ +NFMLYEVIS+LEEEGA+VV+A+FST+ DKIF+TV AQ KISR+
Sbjct: 107 KDLGSGIEVMLISGLNKNFMLYEVISVLEEEGAEVVTANFSTVADKIFYTVHAQVKISRV 166

Query: 122 GVETSRACQRLHDLV 136
           GVE +R  QRL +L+
Sbjct: 167 GVEPTRVYQRLQELI 181

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508667|ref|XP_003523076.1| PREDICTED: uncharacterized protein LOC100790403 [Glycine max]

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 81/135 (60%), Positives = 103/135 (76%), Gaps = 5/135 (3%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVEL 61
           ML Q D+LDLA  YIK + ERI+KL R KEQ M +   N    + +  NN+ S  P+VEL
Sbjct: 51  MLGQRDQLDLAARYIKHMNERIEKLKRQKEQVMSN---NDDRKMFN--NNVESKLPIVEL 105

Query: 62  KDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 121
           +DLGSSIEV+L+SG+ + FMLYEVIS+LEEEGA+VV+ASFST+GDKIF+ V AQ KISR+
Sbjct: 106 RDLGSSIEVMLVSGLNKAFMLYEVISVLEEEGAEVVTASFSTVGDKIFYVVHAQVKISRV 165

Query: 122 GVETSRACQRLHDLV 136
           GVET+RA  RL + +
Sbjct: 166 GVETTRAYNRLQEFI 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516682|ref|XP_003527022.1| PREDICTED: uncharacterized protein LOC100809363 [Glycine max]

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 78/135 (57%), Positives = 105/135 (77%), Gaps = 3/135 (2%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVEL 61
           ML  +D+LDLA  YI+Q+ ER++KL R KEQAM S + N    + +  NN+ S  P++EL
Sbjct: 52  MLGLQDQLDLAARYIRQMTERVEKLKRQKEQAM-SNQSNDGRKMFN--NNVESKLPILEL 108

Query: 62  KDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 121
           +DLGS IEV+L++G+ + FMLYEVIS+LEEEGA+VV+ASFST+GDKIF+ V AQAKISR+
Sbjct: 109 RDLGSGIEVILVTGLNKTFMLYEVISVLEEEGAEVVTASFSTVGDKIFYVVHAQAKISRV 168

Query: 122 GVETSRACQRLHDLV 136
           GVET+R   RL + +
Sbjct: 169 GVETTRVYNRLQEFI 183

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457062|ref|XP_002279841.1| PREDICTED: uncharacterized protein LOC100253569 [Vitis vinifera] gi|297733800|emb|CBI15047.3| unnamed protein product [Vitis vinifera]

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 81/135 (60%), Positives = 106/135 (78%), Gaps = 3/135 (2%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVEL 61
           MLSQ+D+L+ A  YIKQL+ERI++L   KE A +    N  NN++D    I    PV++L
Sbjct: 46  MLSQQDQLEQAANYIKQLKERIEELKGRKELATRVAGTN--NNLIDAVM-IGLRLPVIDL 102

Query: 62  KDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 121
           +DLGSS+EV+LISG+ +NFMLYEVIS+LEEEGA+VVSAS ST+GDK+FH++ AQ KISR+
Sbjct: 103 RDLGSSLEVMLISGLNKNFMLYEVISVLEEEGAEVVSASVSTVGDKVFHSLHAQVKISRV 162

Query: 122 GVETSRACQRLHDLV 136
           GVETSR  QRL +L+
Sbjct: 163 GVETSRVWQRLQELI 177

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248500|ref|NP_001239892.1| uncharacterized protein LOC100787505 [Glycine max] gi|255639839|gb|ACU20212.1| unknown [Glycine max]

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 65/108 (60%), Positives = 82/108 (75%), Gaps = 2/108 (1%)

Query: 2   MLSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVEL 61
           MLSQ+D+L LA  YIK LRERI+KL   KE+AM  +    SN   +   N  S  P++E+
Sbjct: 49  MLSQQDQLHLAATYIKHLRERIEKLKGEKEKAMNMMM--MSNQSNNRIFNTGSELPLLEI 106

Query: 62  KDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIF 109
           KDLGS IEV+LISG+ +NFMLYEVIS+LEEEGA+VV+A+FST+ DKIF
Sbjct: 107 KDLGSGIEVMLISGLNKNFMLYEVISVLEEEGAEVVAANFSTVADKIF 154

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242056735|ref|XP_002457513.1| hypothetical protein SORBIDRAFT_03g008560 [Sorghum bicolor] gi|241929488|gb|EES02633.1| hypothetical protein SORBIDRAFT_03g008560 [Sorghum bicolor]

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 62/145 (42%), Positives = 88/145 (60%), Gaps = 14/145 (9%)

Query: 3   LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICS-------- 54
           ++Q D+LD A  YIKQLRERI+ L   K++      P +  N         S        
Sbjct: 84  VTQLDQLDSAAAYIKQLRERIEAL---KQRKAGGPGPAAGCNGGGAVTASASASSASGGG 140

Query: 55  ---NFPVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHT 111
                PV+E++    +++VVLIS   R F L+EVI++LE+EGA+VVSASFS IGD+IF+T
Sbjct: 141 AGVRMPVIEVRYQDGTLDVVLISDAGRPFKLHEVITVLEQEGAEVVSASFSVIGDRIFYT 200

Query: 112 VRAQAKISRLGVETSRACQRLHDLV 136
           V +QA    +G++ +R  QRLHDL+
Sbjct: 201 VHSQALSPWVGLDAARVSQRLHDLL 225

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226531322|ref|NP_001140429.1| putative HLH DNA-binding domain superfamily protein [Zea mays] gi|194699478|gb|ACF83823.1| unknown [Zea mays] gi|414876676|tpg|DAA53807.1| TPA: putative HLH DNA-binding domain superfamily protein [Zea mays]

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 60/137 (43%), Positives = 86/137 (62%), Gaps = 3/137 (2%)

Query: 3   LSQEDRLDLACCYIKQLRERIDKLNRMKE---QAMKSIKPNSSNNIMDETNNICSNFPVV 59
           ++Q D+LD A  YIKQL+ERI+ L + K        +    ++              PV+
Sbjct: 86  VTQLDQLDSAAAYIKQLKERIEALKQRKAGCCNGGGAATEAATAAAGSTGGGGGVRMPVI 145

Query: 60  ELKDLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKIS 119
           E++    +++VVLIS   R F L+EVI++LE+EGA+VVSASFS IGDKIF+TV +QA   
Sbjct: 146 EVRCQDGTLDVVLISEAARPFKLHEVITVLEQEGAEVVSASFSVIGDKIFYTVHSQALSP 205

Query: 120 RLGVETSRACQRLHDLV 136
           R+GV+ +R  QRLH L+
Sbjct: 206 RIGVDAARVSQRLHALL 222

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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:4515102513	174	AT1G10586 [Arabidopsis thalian	0.875	0.689	0.348	6e-16
TAIR|locus:505006117	181	AT1G10585 [Arabidopsis thalian	0.875	0.662	0.325	5.6e-13
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.978	0.705	0.281	1.9e-12
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.890	0.491	0.236	1.3e-06
TAIR|locus:2080615	258	bHLH39 "basic helix-loop-helix	0.861	0.457	0.276	1.1e-05
TAIR|locus:2080600	253	bHLH38 "basic helix-loop-helix	0.839	0.454	0.235	0.00017

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

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 45/129 (34%), Positives = 77/129 (59%)

Query:     9 LDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELKDLGSSI 68
             +D A  Y+ QL+E+++ LN MK + +     N S           S  P + ++ L S I
Sbjct:    53 IDQAVSYMIQLKEKVNYLNEMKRRMLGGEVKNRSEG--------SSLLPKLSIRSLDSII 104

Query:    69 EVVLISGMQ-RNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSR 127
             E+ L+  +  +  ML++++S+ EEEGAQV+SA+   + D+ F+T+ AQA I R+G++ SR
Sbjct:   105 EMNLVMDLNMKGVMLHKLVSVFEEEGAQVMSANLQNLNDRTFYTIIAQAIICRIGIDPSR 164

Query:   128 ACQRLHDLV 136
               +RL D++
Sbjct:   165 IEERLRDII 173

GO:0005634 "nucleus" evidence=ISM

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

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 42/129 (32%), Positives = 78/129 (60%)

Query:     9 LDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELKDLGSSI 68
             +D A  Y+ QL+E +   N +KE+  +++      N+ + +  +    P + ++   S+I
Sbjct:    53 IDQATSYMIQLKENV---NYLKEKK-RTLLQGELGNLYEGSFLL----PKLSIRSRDSTI 104

Query:    69 EVVLISGMQ-RNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSR 127
             E+ LI  +  +  ML+E++SI EEEGAQV+SA+   + D+  +T+ AQA ISR+G++ SR
Sbjct:   105 EMNLIMDLNMKRVMLHELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQAIISRIGIDPSR 164

Query:   128 ACQRLHDLV 136
               +R+  ++
Sbjct:   165 IEERVRKII 173

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

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 40/142 (28%), Positives = 77/142 (54%)

Query:     3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSI---KPNS--SNNIMDETN-NICSNF 56
             L+  D+LD A  YIK+L+  ++K    K   + +    K NS  S+++    + ++    
Sbjct:    47 LTLPDQLDEAANYIKKLQVNVEKKRERKRNLVATTTLEKLNSVGSSSVSSSVDVSVPRKL 106

Query:    57 PVVELKDLGSSIEVVLISGMQRNFMLYEVISILEEE-GAQVVSASFSTIGDKIFHTVRAQ 115
             P +E+++ GS   + L++ ++  FM  E+I +L EE GA++  A +S + D +FHT+  +
Sbjct:   107 PKIEIQETGSIFHIFLVTSLEHKFMFCEIIRVLTEELGAEITHAGYSIVDDAVFHTLHCK 166

Query:   116 AKISRLGVETSRACQRLHDLVD 137
              +    G   S+  +RL  +V+
Sbjct:   167 VEEHDYGAR-SQIPERLEKIVN 187

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

 Score = 115 (45.5 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 30/127 (23%), Positives = 63/127 (49%)

Query:    15 YIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVE---LKDLGSSIEVV 71
             YI +L+++++ L R K++   +   N    ++          P+V    + D+   ++V 
Sbjct:   116 YIPELQKQVENLERKKKELTTTSTTNCKPGVLGSQLMSEGMAPIVSATCINDMEIMVQVS 175

Query:    72 LISGMQRNFM-LYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSRAC 129
             L+S +  + + L + I +LE EG   +S+S S+  G++ F+++  Q     +  E    C
Sbjct:   176 LLSNVAGSVLPLSKCIKVLENEGLHFISSSTSSGFGNRTFYSIHLQRSEGTINEECPAFC 235

Query:   130 QRLHDLV 136
             +RL  +V
Sbjct:   236 ERLEKVV 242

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2080615 bHLH39 "basic helix-loop-helix 39" [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 34/123 (27%), Positives = 61/123 (49%)

Query:    15 YIKQLRERIDKLNRMKEQAMKSI--KPNSSNNIMDETNNICSNFPVVELKDLGSSIEVVL 72
             YI +L+E++ KL + KE+ +  I  + N+   +      + +    V    LG +  +V 
Sbjct:   124 YIPELQEQVKKLIKKKEELLVQISGQRNTECYVKQPPKAVANYISTVSATRLGDNEVMVQ 183

Query:    73 ISGMQ-RNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQA-KISRLGVETSRAC 129
             IS  +  NF +  V+S LEE+   +V  S S + G+++F+T+  Q  KI    +      
Sbjct:   184 ISSSKIHNFSISNVLSGLEEDRFVLVDMSSSRSQGERLFYTLHLQVEKIENYKLNCEELS 243

Query:   130 QRL 132
             QR+
Sbjct:   244 QRM 246

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010106 "cellular response to iron ion starvation" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0055072 "iron ion homeostasis" evidence=IGI

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

 Score = 99 (39.9 bits), Expect = 0.00017, P = 0.00017
 Identities = 28/119 (23%), Positives = 60/119 (50%)

Query:     3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKSIKPNSSNNIMD--ETNNICSNFPVVE 60
             LS  + +  +  YI +L++++ +L + KE+ +  +       + D  +   + S    V 
Sbjct:   107 LSIPETVSKSLKYIPELQQQVKRLIQKKEEILVRVSGQRDFELYDKQQPKAVASYLSTVS 166

Query:    61 LKDLGSSIEVVLISGMQ-RNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAK 117
                LG +  +V +S  +  NF +  V+  +EE+G  +V  S S + G+++F+T+  Q +
Sbjct:   167 ATRLGDNEVMVQVSSSKIHNFSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQVE 225


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.132   0.359    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      137       137   0.00091  102 3  10 22  0.40    31
                                                     30  0.45    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  580 (62 KB)
  Total size of DFA:  157 KB (2095 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.03u 0.12s 22.15t   Elapsed:  00:00:01
  Total cpu time:  22.03u 0.12s 22.15t   Elapsed:  00:00:01
  Start:  Sat May 11 11:36:58 2013   End:  Sat May 11 11:36:59 2013

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010106 "cellular response to iron ion starvation" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0055072 "iron ion homeostasis" evidence=IGI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00150536 hypothetical protein (178 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.7
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.53
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.45
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.4
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.33
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.22
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.1
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.06
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	96.97
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	96.86
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.78
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.74
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	96.37
PRK00194	90	hypothetical protein; Validated	96.33
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	96.22
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	96.21
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.19
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	96.13
PRK03059	856	PII uridylyl-transferase; Provisional	96.1
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	95.96
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.94
PRK03381	774	PII uridylyl-transferase; Provisional	95.85
PRK05092	931	PII uridylyl-transferase; Provisional	95.72
PRK04374	869	PII uridylyl-transferase; Provisional	95.71
PRK05007	884	PII uridylyl-transferase; Provisional	95.57
smart00353	53	HLH helix loop helix domain.	94.85
PRK03381	774	PII uridylyl-transferase; Provisional	94.7
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	94.23
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.23
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	94.15
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.05
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	93.93
PRK01759	854	glnD PII uridylyl-transferase; Provisional	93.88
PRK05007	884	PII uridylyl-transferase; Provisional	93.77
PRK05092	931	PII uridylyl-transferase; Provisional	93.54
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	93.47
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	93.25
PRK04374	869	PII uridylyl-transferase; Provisional	93.18
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	92.21
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	92.18
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	92.07
PRK00275	895	glnD PII uridylyl-transferase; Provisional	91.95
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	91.68
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	91.41
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	91.39
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	91.36
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	91.1
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	91.07
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	91.05
cd02116	60	ACT ACT domains are commonly involved in specifica	90.98
PRK03059	856	PII uridylyl-transferase; Provisional	90.93
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	90.74
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	90.7
PRK08577	136	hypothetical protein; Provisional	90.7
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	90.37
PLN03217	93	transcription factor ATBS1; Provisional	90.1
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	89.34
PRK04435	147	hypothetical protein; Provisional	88.77
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	87.32
PRK11589	190	gcvR glycine cleavage system transcriptional repre	87.25
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	85.51
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	85.39
PRK07334	403	threonine dehydratase; Provisional	85.08
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	84.17
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	83.94
PRK11589	190	gcvR glycine cleavage system transcriptional repre	83.91
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	82.76
PF13710	63	ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.	82.59
COG3830	90	ACT domain-containing protein [Signal transduction	80.51

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

Probab=97.70  E-value=0.00052  Score=45.65  Aligned_cols=63  Identities=11%  Similarity=0.193  Sum_probs=49.9

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      +-+.+.++++.|++|.++|.+.|++|.+|..++.|+++.-+++-.=..+. .++-....++|++
T Consensus         4 iev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~-kl~d~~~~~~l~~   66 (72)
T cd04895           4 VKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGN-KLTDDSLIAYIEK   66 (72)
T ss_pred             EEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCC-CCCCHHHHHHHHH
Confidence            34567789999999999999999999999999999999999988754432 4544444555544

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=97.53  E-value=0.0013  Score=44.10  Aligned_cols=66  Identities=24%  Similarity=0.313  Sum_probs=51.8

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccch----HHHHHHHhhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET----SRACQRLHDLV  136 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~----~~l~~rL~~~i  136 (137)
                      |+-+.+.++|++|++|.++|-+.|++|.+|..++.|+++.=+++-.=.++. .+..    .++.++|.+.+
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~-kl~~~~~~~~l~~~L~~al   72 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGR-TLSTEGERQRVIKCLEAAI   72 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCC-ccCCHHHHHHHHHHHHHHH
Confidence            334567889999999999999999999999999999999999998766543 4433    44555555543

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.

>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=97.45  E-value=0.0026  Score=41.40  Aligned_cols=64  Identities=14%  Similarity=0.155  Sum_probs=45.9

Q ss_pred             EEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEee-CCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           69 EVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        69 eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      +|.+ ++.+++++|+++-.+|...|++|++|...+. +++++=+++-.=... ..++.+.-.++|++
T Consensus         3 ~i~v-~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~~~-~~~~~~~~~~~l~~   67 (73)
T cd04900           3 EVFI-YTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDPDG-EPIGERERLARIRE   67 (73)
T ss_pred             EEEE-EecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECCCC-CCCChHHHHHHHHH
Confidence            4544 4558999999999999999999999997655 789999988763332 23443444444443

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.

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

Probab=97.40  E-value=0.0029  Score=40.06  Aligned_cols=62  Identities=18%  Similarity=0.272  Sum_probs=47.5

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccch---HHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET---SRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~---~~l~~rL~~~  135 (137)
                      +.+.++++.|.++..+|.+.|++++++.....+++.+-+++.+-.... ..+.   .+++++|.+.
T Consensus         5 v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~-~~~~~~~~~i~~~l~~~   69 (70)
T cd04899           5 LTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQ-PLDPERQEALRAALGEA   69 (70)
T ss_pred             EEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCC-cCCHHHHHHHHHHHHhh
Confidence            355678999999999999999999999998888899999998875543 2332   2355555543

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.

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

Probab=97.33  E-value=0.0041  Score=40.80  Aligned_cols=63  Identities=19%  Similarity=0.285  Sum_probs=47.3

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeec-cCcccc----hHHHHHHHhhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKI-SRLGVE----TSRACQRLHDLV  136 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~-~~~~~d----~~~l~~rL~~~i  136 (137)
                      +.+.+++++|++|-.+|.+.|++|++|..++.|++++-+++-.-.+ .. .++    ..++.+.|.+.+
T Consensus         5 v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~-~~~~~~~~~~i~~~L~~~l   72 (74)
T cd04925           5 LTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGA-PIDDPIRLASIEDRLDNVL   72 (74)
T ss_pred             EEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCC-CCCCHHHHHHHHHHHHHHh
Confidence            4566899999999999999999999999988899999999865322 21 232    345555555543

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.

>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.22  E-value=0.0055  Score=40.51  Aligned_cols=44  Identities=16%  Similarity=0.135  Sum_probs=39.3

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEE-eeCCeEEEEEEEEe
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQA  116 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtIh~qv  116 (137)
                      +.+.++++.|+++..+|.+.|++|.+|..+ +.|++++-+++-+=
T Consensus         5 i~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d   49 (76)
T cd04927           5 LFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITD   49 (76)
T ss_pred             EEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeC
Confidence            455689999999999999999999999987 49999999998864

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

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

Probab=97.10  E-value=0.0067  Score=40.65  Aligned_cols=63  Identities=17%  Similarity=0.321  Sum_probs=49.7

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEE--eeCCeEEEEEEEEeeccCccc-c---hHHHHHHHhhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFS--TIGDKIFHTVRAQAKISRLGV-E---TSRACQRLHDLV  136 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s--~~~~r~fhtIh~qv~~~~~~~-d---~~~l~~rL~~~i  136 (137)
                      -+.+.++++.|++|.++|.+.|++|.+|..+  +.|+++.=+|+-.-.+ . .+ |   ...|.++|.+.+
T Consensus         4 ev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~~~g-~-kl~d~~~~~~L~~~L~~~l   72 (75)
T cd04896           4 QIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQSDG-K-KIMDPKKQAALCARLREEM   72 (75)
T ss_pred             EEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEeCCC-C-ccCCHHHHHHHHHHHHHHh
Confidence            3567789999999999999999999999999  9999999998884332 2 23 3   356677776654

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.

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

Probab=97.06  E-value=0.01  Score=38.56  Aligned_cols=65  Identities=20%  Similarity=0.257  Sum_probs=47.1

Q ss_pred             eEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           68 IEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        68 ~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .+|.+. ..+++++|+++..+|.+.|++|++|.....+++.+-+++.+=.+.. .++. ...+++++.
T Consensus         2 tri~V~-~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~~~~~-~~~~-~~~~~l~~~   66 (72)
T cd04926           2 VRLELR-TEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTDANGN-PVDP-KTIEAVRQE   66 (72)
T ss_pred             eEEEEE-ECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEECCCCC-cCCH-HHHHHHHHH
Confidence            355553 3478999999999999999999999987778888888887643322 2443 445566554

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.

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

Probab=96.97  E-value=0.011  Score=39.08  Aligned_cols=61  Identities=16%  Similarity=0.257  Sum_probs=52.6

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.++|.++++..++|-..|.+.|+++++++....+++.|..+...+..    .+.+.|.++|..+
T Consensus         4 ltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~~----~~~~~l~~~l~~~   64 (77)
T cd04893           4 ISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSW----DAIAKLEAALPGL   64 (77)
T ss_pred             EEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEecc----ccHHHHHHHHHHH
Confidence            345777899999999999999999999999999999999999998762    3678888888765

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

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

Probab=96.86  E-value=0.02  Score=37.67  Aligned_cols=65  Identities=18%  Similarity=0.169  Sum_probs=53.4

Q ss_pred             EEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EeeCCeEEEEEEEEeeccCcccchHHHHHHHhhhhC
Q 046429           69 EVVLISGMQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD  137 (137)
Q Consensus        69 eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~i~  137 (137)
                      +|.+.+ .+++.+|+++-.+|...|++|++|.. +..++.++-+++-+=.+   +=|...+.++|.+.++
T Consensus         3 eI~V~~-~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~---~~~~~~~~~~~~~~~~   68 (68)
T cd04928           3 EITFAA-GDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWK---RGETAALGHALQKEID   68 (68)
T ss_pred             EEEEEE-CCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCC---ccchHHHHHHHHHhhC
Confidence            565544 48899999999999999999999986 57889999998777433   6788999999988764

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.

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

Probab=96.78  E-value=0.014  Score=38.31  Aligned_cols=59  Identities=17%  Similarity=0.242  Sum_probs=48.6

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.|.++++.++++..+|.+.|+++++++.++.+++.--.++.++..    -+.++|...|.++
T Consensus         7 v~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~----~~~~~l~~~L~~l   65 (76)
T PF13740_consen    7 VVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPE----DSLERLESALEEL   65 (76)
T ss_dssp             EEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESH----HHHHHHHHHHHHH
T ss_pred             EEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCc----ccHHHHHHHHHHH
Confidence            4677899999999999999999999999999999988888888863    2668888888765

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

Probab=96.74  E-value=0.015  Score=37.88  Aligned_cols=61  Identities=11%  Similarity=0.196  Sum_probs=51.1

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      -+.|.++++...++-++|.+.|+++.+.+.++.++.  +++...+.-+. +.+.++|.+.|..+
T Consensus         3 tv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~--f~~~~~v~~p~-~~~~~~l~~~l~~l   63 (75)
T cd04870           3 TVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGR--LSLGILVQIPD-SADSEALLKDLLFK   63 (75)
T ss_pred             EEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCe--eEEEEEEEcCC-CCCHHHHHHHHHHH
Confidence            356888999999999999999999999998888765  56677777665 57789999988775

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.

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

Probab=96.37  E-value=0.045  Score=35.55  Aligned_cols=63  Identities=17%  Similarity=0.237  Sum_probs=48.4

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEeeC----CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFSTIG----DKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~----~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      -+.+.++++.+++|-+.|.+.|+++.+.+....+    +.-.+.+.+++..+. +.+..++.+.|..+
T Consensus         3 ~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p~-~~~~~~l~~~l~~l   69 (81)
T cd04869           3 EVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPA-GTDLDALREELEEL   69 (81)
T ss_pred             EEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecCC-CCCHHHHHHHHHHH
Confidence            3567789999999999999999999999998776    223444445555544 67889999888765

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

>PRK00194 hypothetical protein; Validated

Probab=96.33  E-value=0.024  Score=38.01  Aligned_cols=64  Identities=11%  Similarity=0.148  Sum_probs=50.0

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ++.+.+.++++.+++|.++|-+.|+++++.+....++..+-.+-+....  ...+.+.+.+.|.++
T Consensus         5 ~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~~--~~~~~~~l~~~l~~l   68 (90)
T PRK00194          5 IITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDISE--SKKDFAELKEELEEL   68 (90)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEecC--CCCCHHHHHHHHHHH
Confidence            3446777899999999999999999999999887777666656666543  246678888888765

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

Probab=96.22  E-value=0.027  Score=37.76  Aligned_cols=63  Identities=13%  Similarity=0.143  Sum_probs=50.4

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.+.|.++++.+++|-+.|-+.|+++++.+..+.+++.+-.+.+....  .+.+.++|.+.|.++
T Consensus         4 l~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~~--~~~~~~~L~~~l~~l   66 (88)
T cd04872           4 ITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDISE--SNLDFAELQEELEEL   66 (88)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeCC--CCCCHHHHHHHHHHH
Confidence            345677899999999999999999999999887777766666666542  256778999888765

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.

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

Probab=96.21  E-value=0.06  Score=33.09  Aligned_cols=59  Identities=20%  Similarity=0.107  Sum_probs=43.5

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLV  136 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~i  136 (137)
                      ..++++.|+++..+|.++|++|.++.....++.....+-+...+   .-+...+.++|+++.
T Consensus         7 ~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~   65 (66)
T PF01842_consen    7 VPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIVVD---EEDLEKLLEELEALP   65 (66)
T ss_dssp             EETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEEE---GHGHHHHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEECC---CCCHHHHHHHHHccc
Confidence            34789999999999999999999999887766322222223322   356688889888764

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

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

Probab=96.19  E-value=0.1  Score=32.40  Aligned_cols=46  Identities=17%  Similarity=0.280  Sum_probs=36.9

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeec
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKI  118 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~  118 (137)
                      +.+.++++.|+++..+|.+.|+.+.++.....+++..-.++..-..
T Consensus         5 i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~   50 (70)
T cd04873           5 VYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSD   50 (70)
T ss_pred             EEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCC
Confidence            3556789999999999999999999999877666666666665543

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

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

Probab=96.13  E-value=0.066  Score=34.56  Aligned_cols=64  Identities=14%  Similarity=0.176  Sum_probs=46.9

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEe-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.+.|.++++.+++|-+.|-+.|+++++.+..+ .++..|+. .+++..+....+...+.+.|.++
T Consensus         2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~-~~~~~~~~~~~~~~~l~~~l~~l   66 (74)
T cd04875           2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFM-RVEFELEGFDLSREALEAAFAPV   66 (74)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEE-EEEEEeCCCCCCHHHHHHHHHHH
Confidence            345677899999999999999999999998875 34444444 55555442125678888888765

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.

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.10  E-value=0.059  Score=50.35  Aligned_cols=82  Identities=20%  Similarity=0.211  Sum_probs=58.0

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHh
Q 046429           55 NFPVVELKDLG-SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLH  133 (137)
Q Consensus        55 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~  133 (137)
                      ..|.|.+.... .+.-++.+.+.+++++|++|-.+|.+.|++|.+|..++.|++++=+++-+-.+..-.-...++.++|.
T Consensus       772 ~~~~V~~~~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~~~~~~~~~~~~l~~~L~  851 (856)
T PRK03059        772 ITPRVDLRPDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDGSGLSDNRLQIQLETELL  851 (856)
T ss_pred             CCceEEEEEcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcCCCCCCHHHHHHHHHHHH
Confidence            45677776543 34445556677899999999999999999999999988899999999874222110112356666666


Q ss_pred             hhh
Q 046429          134 DLV  136 (137)
Q Consensus       134 ~~i  136 (137)
                      +.+
T Consensus       852 ~~L  854 (856)
T PRK03059        852 DAL  854 (856)
T ss_pred             HHh
Confidence            554

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

Probab=95.96  E-value=0.085  Score=34.42  Aligned_cols=66  Identities=21%  Similarity=0.242  Sum_probs=50.4

Q ss_pred             eeEEEE-EecCCCcccHHHHHHHHHHcCceEEEeEEEe--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           67 SIEVVL-ISGMQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        67 ~~eV~l-~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .+.+.+ +.+.+.++.|.+|..++.++|+.+.+.+...  .++...-+|..+|.+.   -++..+-++|+++
T Consensus         4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~---~~L~~ii~~L~~i   72 (80)
T PF13291_consen    4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDL---EHLNQIIRKLRQI   72 (80)
T ss_dssp             -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSH---HHHHHHHHHHCTS
T ss_pred             EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCH---HHHHHHHHHHHCC
Confidence            344444 4556789999999999999999999999876  4788888999999764   4567777777754

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.94  E-value=0.096  Score=49.21  Aligned_cols=82  Identities=15%  Similarity=0.140  Sum_probs=62.0

Q ss_pred             CCCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccch----HHH
Q 046429           54 SNFPVVELKDLGS-SIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET----SRA  128 (137)
Q Consensus        54 ~~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~----~~l  128 (137)
                      ...|.|.+....+ +.-++.+++.++++.|++|-.+|.+.|++|++|..++.|++++=+++-.-.++. .++.    .++
T Consensus       799 ~~~~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~-~l~~~~~~~~l  877 (895)
T PRK00275        799 AFPTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQ-PLSDPQLCSRL  877 (895)
T ss_pred             CCCCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCC-CCCCHHHHHHH
Confidence            3457888876543 555556778899999999999999999999999998889999999988754433 2322    446


Q ss_pred             HHHHhhhh
Q 046429          129 CQRLHDLV  136 (137)
Q Consensus       129 ~~rL~~~i  136 (137)
                      .++|.+.+
T Consensus       878 ~~~L~~~L  885 (895)
T PRK00275        878 QDAICEQL  885 (895)
T ss_pred             HHHHHHHH
Confidence            66666544

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.85  E-value=0.12  Score=47.80  Aligned_cols=80  Identities=16%  Similarity=0.101  Sum_probs=61.5

Q ss_pred             CCCeEEEEEc-CCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHh
Q 046429           55 NFPVVELKDL-GSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLH  133 (137)
Q Consensus        55 ~~p~V~V~~~-~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~  133 (137)
                      ..|.|.++.. .++.+|.+ .+.++++.|++|..+|...|++|++|...+.|+.++=++...-.... ..+.+++.+.|.
T Consensus       586 ~~~~v~~~~~~~~~~~V~V-~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~~~~-~~~~~~l~~~L~  663 (774)
T PRK03381        586 GGVHVEIAPADPHMVEVTV-VAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPRFGS-PPDAALLRQDLR  663 (774)
T ss_pred             CCCEEEEeeCCCCeEEEEE-EecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCC-cchHHHHHHHHH
Confidence            3567777543 46777755 56689999999999999999999999987788898888888754432 355678888887


Q ss_pred             hhh
Q 046429          134 DLV  136 (137)
Q Consensus       134 ~~i  136 (137)
                      +++
T Consensus       664 ~~L  666 (774)
T PRK03381        664 RAL  666 (774)
T ss_pred             HHH
Confidence            664

>PRK05092 PII uridylyl-transferase; Provisional

Probab=95.72  E-value=0.13  Score=48.45  Aligned_cols=82  Identities=17%  Similarity=0.264  Sum_probs=62.9

Q ss_pred             CCCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCccc-c---hHHH
Q 046429           54 SNFPVVELKDLGS-SIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGV-E---TSRA  128 (137)
Q Consensus        54 ~~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~-d---~~~l  128 (137)
                      ...|.|.+....+ +.-++.+.+.++++.|++|..+|.+.|++|.+|..++.|+++.=+++..-.++. .+ +   ..+|
T Consensus       828 ~~~~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~-~i~~~~~~~~l  906 (931)
T PRK05092        828 HVPPRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGL-KITNEARQAAI  906 (931)
T ss_pred             CCCCEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCC-cCCCHHHHHHH
Confidence            3457888876543 444555678889999999999999999999999999999999999998764433 22 2   3457


Q ss_pred             HHHHhhhh
Q 046429          129 CQRLHDLV  136 (137)
Q Consensus       129 ~~rL~~~i  136 (137)
                      +++|.+++
T Consensus       907 ~~~L~~~L  914 (931)
T PRK05092        907 RRALLAAL  914 (931)
T ss_pred             HHHHHHHh
Confidence            77777665

>PRK04374 PII uridylyl-transferase; Provisional

Probab=95.71  E-value=0.13  Score=48.25  Aligned_cols=82  Identities=16%  Similarity=0.179  Sum_probs=61.4

Q ss_pred             CCCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccc---hHHHH
Q 046429           54 SNFPVVELKDLG-SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSRAC  129 (137)
Q Consensus        54 ~~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d---~~~l~  129 (137)
                      ..+|.|.+.... .+.-++-+.+.++++.|++|-.+|.+.|++|.+|..++.|+++.-+++-+=.++. .++   ...|.
T Consensus       781 ~~~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~-~~~~~~~~~l~  859 (869)
T PRK04374        781 RFAPRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDR-PLSESARQALR  859 (869)
T ss_pred             CCCCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCC-cCChHHHHHHH
Confidence            345778887644 3556666778889999999999999999999999999889999999998754433 232   24555


Q ss_pred             HHHhhhh
Q 046429          130 QRLHDLV  136 (137)
Q Consensus       130 ~rL~~~i  136 (137)
                      ++|.+.+
T Consensus       860 ~~L~~~l  866 (869)
T PRK04374        860 DALCACL  866 (869)
T ss_pred             HHHHHHh
Confidence            5555443

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.57  E-value=0.1  Score=49.02  Aligned_cols=80  Identities=16%  Similarity=0.154  Sum_probs=59.2

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 046429           55 NFPVVELKDLG-SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSRACQ  130 (137)
Q Consensus        55 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d---~~~l~~  130 (137)
                      ..|.|.+..-. +..-|+-+.+.+.++.|++|.++|.+.|++|.+|..++.|+|+.=+++-+=..+. -++   ...|.+
T Consensus       794 ~~~~V~~d~~~s~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~~g~-~l~~~~~~~l~~  872 (884)
T PRK05007        794 VPTEVSFLPTHTDRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATADRR-ALNEELQQELRQ  872 (884)
T ss_pred             CCCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcCCCC-cCCHHHHHHHHH
Confidence            45678876543 3445555778899999999999999999999999999999999999888644322 355   234555


Q ss_pred             HHhhh
Q 046429          131 RLHDL  135 (137)
Q Consensus       131 rL~~~  135 (137)
                      +|.+.
T Consensus       873 ~L~~~  877 (884)
T PRK05007        873 RLTEA  877 (884)
T ss_pred             HHHHH
Confidence            55444

>smart00353 HLH helix loop helix domain

Probab=94.85  E-value=0.026  Score=34.22  Aligned_cols=22  Identities=45%  Similarity=0.643  Sum_probs=19.3

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLRERID   24 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve   24 (137)
                      ++-.+.|.+|++||++|+++++
T Consensus        31 ~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353       31 LSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Confidence            4667889999999999999876

>PRK03381 PII uridylyl-transferase; Provisional

Probab=94.70  E-value=0.36  Score=44.70  Aligned_cols=78  Identities=18%  Similarity=0.180  Sum_probs=57.9

Q ss_pred             CCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHh
Q 046429           55 NFPVVELKDLGS-SIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLH  133 (137)
Q Consensus        55 ~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~  133 (137)
                      ..|.|.+....+ +.-++-+.+.++++.|++|-.+|.+.|++|.+|..++.|++++=+++-+=.+.. .+.-.  .+.|+
T Consensus       693 ~~~~v~~~~~~~~~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g~-~~~~~--~~~l~  769 (774)
T PRK03381        693 APPRVLWLDGASPDATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAGG-PLADA--RAAVE  769 (774)
T ss_pred             CCcEEEEEECCCCCeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCCC-cCchH--HHHHH
Confidence            346777765543 455556677889999999999999999999999999889999999988754432 33222  55555


Q ss_pred             hh
Q 046429          134 DL  135 (137)
Q Consensus       134 ~~  135 (137)
                      +.
T Consensus       770 ~~  771 (774)
T PRK03381        770 QA  771 (774)
T ss_pred             HH
Confidence            43

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

Probab=94.23  E-value=0.25  Score=46.23  Aligned_cols=79  Identities=16%  Similarity=0.211  Sum_probs=60.7

Q ss_pred             CCCCCeEEEEEcCCe-eEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHH
Q 046429           53 CSNFPVVELKDLGSS-IEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQR  131 (137)
Q Consensus        53 ~~~~p~V~V~~~~~~-~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~r  131 (137)
                      ....|.|++.+..+. .-++-+.+++.++.|+++-.+|.+.|+++.+|..+++|.|+--++.-+..... .+ ...+++.
T Consensus       775 f~i~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~~-~l-~~~~~q~  852 (867)
T COG2844         775 FPIPPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADGQ-AL-NAELRQS  852 (867)
T ss_pred             eccCCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEeccccc-cC-CHHHHHH
Confidence            345688999876543 44445678899999999999999999999999999999998888887776543 44 3445554


Q ss_pred             Hh
Q 046429          132 LH  133 (137)
Q Consensus       132 L~  133 (137)
                      |.
T Consensus       853 l~  854 (867)
T COG2844         853 LL  854 (867)
T ss_pred             HH
Confidence            44

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.23  E-value=0.57  Score=43.63  Aligned_cols=80  Identities=18%  Similarity=0.123  Sum_probs=56.7

Q ss_pred             CCCeEEEEE-c-CCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEE-eeCCeEEEEEEEEeeccCcccchH----H
Q 046429           55 NFPVVELKD-L-GSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKISRLGVETS----R  127 (137)
Q Consensus        55 ~~p~V~V~~-~-~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtIh~qv~~~~~~~d~~----~  127 (137)
                      ..|.|.+.. . .++.+| .+.+.++++.|++|..+|...|++|++|..+ +.|++++=+++.+-.... .++.+    +
T Consensus       654 ~~~~v~~~~~~~~~~t~i-~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~-~~~~~~~~~~  731 (850)
T TIGR01693       654 GGPLALIDGTRPSGGTEV-FIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGS-PPAAERVFQE  731 (850)
T ss_pred             CCCEEEEeccCCCCeEEE-EEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCC-CCCcHHHHHH
Confidence            356676643 2 344445 4556688999999999999999999999875 789999998888765543 34333    3


Q ss_pred             HHHHHhhhh
Q 046429          128 ACQRLHDLV  136 (137)
Q Consensus       128 l~~rL~~~i  136 (137)
                      +.+.|.+.+
T Consensus       732 i~~~L~~~L  740 (850)
T TIGR01693       732 LLQGLVDVL  740 (850)
T ss_pred             HHHHHHHHH
Confidence            555555543

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.

>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=94.15  E-value=0.74  Score=29.10  Aligned_cols=59  Identities=15%  Similarity=0.135  Sum_probs=43.7

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEee-CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           74 SGMQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        74 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ...++++.|.++..++.++|+++.+.+.... ++.....+..++.+.   -.+.++-.+|+++
T Consensus         5 ~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~---~~l~~i~~~L~~i   64 (74)
T cd04887           5 ELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSE---EHAETIVAAVRAL   64 (74)
T ss_pred             EeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCH---HHHHHHHHHHhcC
Confidence            3457889999999999999999999887654 355555566666553   3457777777754

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=94.05  E-value=0.39  Score=45.01  Aligned_cols=80  Identities=15%  Similarity=0.137  Sum_probs=59.2

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 046429           55 NFPVVELKDLG-SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSRACQ  130 (137)
Q Consensus        55 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d---~~~l~~  130 (137)
                      .+|.|.+..-. +..-|+-+.+.+.++.|++|.++|.+.|++|.+|..++.|+|+.=+++-.=..+. -++   ...|.+
T Consensus       769 ~~~~V~~dn~~s~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g~-~l~~~~~~~l~~  847 (854)
T PRK01759        769 VKTEVRFLNEEKQEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQGQ-ALDEEERKALKS  847 (854)
T ss_pred             CCCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCCC-cCChHHHHHHHH
Confidence            45677776543 4555655778899999999999999999999999999999999988887644322 233   245555


Q ss_pred             HHhhh
Q 046429          131 RLHDL  135 (137)
Q Consensus       131 rL~~~  135 (137)
                      +|.+.
T Consensus       848 ~L~~~  852 (854)
T PRK01759        848 RLLSN  852 (854)
T ss_pred             HHHHH
Confidence            55543

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=93.93  E-value=0.53  Score=43.85  Aligned_cols=81  Identities=22%  Similarity=0.222  Sum_probs=61.4

Q ss_pred             CCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 046429           55 NFPVVELKDLGS-SIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSRACQ  130 (137)
Q Consensus        55 ~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d---~~~l~~  130 (137)
                      ..|.|.+....+ ..-++-+.+.++++.|++|.++|.+.|++|.+|++++.+++..-+++.+-.... -++   ...|.+
T Consensus       765 ~~~~V~~d~~~s~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~-~~~~~~~~~l~~  843 (850)
T TIGR01693       765 VPPRVTILNTASRKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGL-KLTDEEEQRLLE  843 (850)
T ss_pred             CCCeEEEccCCCCCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCC-CCCHHHHHHHHH
Confidence            456788876554 456666788899999999999999999999999999999999999988765432 222   345555


Q ss_pred             HHhhhh
Q 046429          131 RLHDLV  136 (137)
Q Consensus       131 rL~~~i  136 (137)
                      +|.+.+
T Consensus       844 ~L~~~l  849 (850)
T TIGR01693       844 VLAASV  849 (850)
T ss_pred             HHHHHh
Confidence            555443

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

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=93.88  E-value=0.9  Score=42.61  Aligned_cols=80  Identities=11%  Similarity=0.123  Sum_probs=56.9

Q ss_pred             CCCeEEEEEcC--CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EeeCCeEEEEEEEEeeccCcccchH---HH
Q 046429           55 NFPVVELKDLG--SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGVETS---RA  128 (137)
Q Consensus        55 ~~p~V~V~~~~--~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtIh~qv~~~~~~~d~~---~l  128 (137)
                      ..|.|.+....  ++.+|. +.+.++++.|++|..+|...|++|++|.. |..++.++=+++..=.++. .++.+   +|
T Consensus       663 ~~~~V~i~~~~~~~~t~V~-V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~-~~~~~~~~~l  740 (854)
T PRK01759        663 GDLLVKISNRFSRGGTEIF-IYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGK-LLEFDRRRQL  740 (854)
T ss_pred             CCCEEEEEecCCCCeEEEE-EEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCC-CCCHHHHHHH
Confidence            35777776543  455554 45568899999999999999999999996 5599999999988754432 34432   34


Q ss_pred             HHHHhhhh
Q 046429          129 CQRLHDLV  136 (137)
Q Consensus       129 ~~rL~~~i  136 (137)
                      .+.|.+.+
T Consensus       741 ~~~L~~aL  748 (854)
T PRK01759        741 EQALTKAL  748 (854)
T ss_pred             HHHHHHHH
Confidence            55555543

>PRK05007 PII uridylyl-transferase; Provisional

Probab=93.77  E-value=0.94  Score=42.63  Aligned_cols=80  Identities=14%  Similarity=0.150  Sum_probs=55.7

Q ss_pred             CCCeEEEEEcC--CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEE-eeCCeEEEEEEEEeeccCcccch---HHH
Q 046429           55 NFPVVELKDLG--SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKISRLGVET---SRA  128 (137)
Q Consensus        55 ~~p~V~V~~~~--~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtIh~qv~~~~~~~d~---~~l  128 (137)
                      ..|.|.+....  ++.+|.+ ++.++++.|++|..+|...|++|++|... ..+|+++=+++..-.++. .++.   .++
T Consensus       687 ~~p~V~i~~~~~~~~t~V~V-~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~-~~~~~~~~~I  764 (884)
T PRK05007        687 DKPLVLLSKQATRGGTEIFI-WSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGS-PLSQDRHQVI  764 (884)
T ss_pred             CCCeEEEEecCCCCeEEEEE-EecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCC-CCCHHHHHHH
Confidence            45777787543  4566644 56688999999999999999999999865 566699777776654432 2332   335


Q ss_pred             HHHHhhhh
Q 046429          129 CQRLHDLV  136 (137)
Q Consensus       129 ~~rL~~~i  136 (137)
                      .+.|.+.+
T Consensus       765 ~~~L~~aL  772 (884)
T PRK05007        765 RKALEQAL  772 (884)
T ss_pred             HHHHHHHH
Confidence            66665543

>PRK05092 PII uridylyl-transferase; Provisional

Probab=93.54  E-value=1  Score=42.45  Aligned_cols=80  Identities=18%  Similarity=0.190  Sum_probs=56.1

Q ss_pred             CCCeEEEEEcC--CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEE-eeCCeEEEEEEEEeeccCcccc---hHHH
Q 046429           55 NFPVVELKDLG--SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKISRLGVE---TSRA  128 (137)
Q Consensus        55 ~~p~V~V~~~~--~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtIh~qv~~~~~~~d---~~~l  128 (137)
                      ..|.|.++...  ++.+|.+++ .++++.|+++..+|...|++|++|... ..|++++=++..+-......-+   ..+|
T Consensus       718 ~~~~v~~~~~~~~~~t~v~I~~-~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~~~~l  796 (931)
T PRK05092        718 RPLATEVRPDPARGVTEVTVLA-ADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRRLARL  796 (931)
T ss_pred             CCcEEEEEecCCCCeEEEEEEe-CCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHHHHHH
Confidence            45778777643  577776654 488999999999999999999999965 5788888878765433221112   3455


Q ss_pred             HHHHhhh
Q 046429          129 CQRLHDL  135 (137)
Q Consensus       129 ~~rL~~~  135 (137)
                      .+.|.++
T Consensus       797 ~~~L~~~  803 (931)
T PRK05092        797 AKAIEDA  803 (931)
T ss_pred             HHHHHHH
Confidence            5566554

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

Probab=93.47  E-value=0.67  Score=29.33  Aligned_cols=60  Identities=12%  Similarity=0.106  Sum_probs=41.3

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEee-CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           74 SGMQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        74 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ...++++.|.+++.+|.++|+++...+.+.. ++  ..++.+.+.-....-...++-++|+++
T Consensus         6 ~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~--~~~i~~~v~v~~~~~~l~~l~~~L~~i   66 (76)
T cd04888           6 LLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHG--RANVTISIDTSTMNGDIDELLEELREI   66 (76)
T ss_pred             EecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCC--eEEEEEEEEcCchHHHHHHHHHHHhcC
Confidence            3456789999999999999999999877543 34  344444443333223568888888764

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.

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

Probab=93.25  E-value=1.1  Score=27.34  Aligned_cols=56  Identities=13%  Similarity=0.184  Sum_probs=38.9

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEee-----CCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTI-----GDKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-----~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      .++++.|.+++.+|.++|+++.+..+...     ++...-.+..++.+   .-+...+-++|++
T Consensus         6 ~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~---~~~l~~l~~~l~~   66 (73)
T cd04886           6 PDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRG---AEHIEEIIAALRE   66 (73)
T ss_pred             CCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCC---HHHHHHHHHHHHH
Confidence            46899999999999999999998887643     24444445555532   2344577777654

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.

>PRK04374 PII uridylyl-transferase; Provisional

Probab=93.18  E-value=1.1  Score=42.19  Aligned_cols=80  Identities=16%  Similarity=0.255  Sum_probs=56.3

Q ss_pred             CCeEEEE---EcCCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EeeCCeEEEEEEEEeeccCcccchHHHHHH
Q 046429           56 FPVVELK---DLGSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGVETSRACQR  131 (137)
Q Consensus        56 ~p~V~V~---~~~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtIh~qv~~~~~~~d~~~l~~r  131 (137)
                      .|.|.+.   +..++.+|.+.+ .+++++|+++--+|...|++|++|.. |..+|.++=|++..-......-...++.+.
T Consensus       676 ~~~v~~~~~~~~~~~~~v~v~~-~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~~  754 (869)
T PRK04374        676 QTLVKARRAVPDNDALEVFVYS-PDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAAA  754 (869)
T ss_pred             CCeEEEeeeccCCCeEEEEEEe-CCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHHH
Confidence            4555553   345778886654 47899999999999999999999986 568999999998864433211223445555


Q ss_pred             Hhhhh
Q 046429          132 LHDLV  136 (137)
Q Consensus       132 L~~~i  136 (137)
                      |.+.+
T Consensus       755 l~~~l  759 (869)
T PRK04374        755 LRQVL  759 (869)
T ss_pred             HHHHH
Confidence            55543

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

Probab=92.21  E-value=0.13  Score=31.67  Aligned_cols=22  Identities=41%  Similarity=0.525  Sum_probs=18.4

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLRERID   24 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve   24 (137)
                      ++-...|..|++||+.||+.++
T Consensus        39 ~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083          39 LSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhC
Confidence            4567789999999999998763

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=92.18  E-value=0.14  Score=31.42  Aligned_cols=18  Identities=50%  Similarity=0.554  Sum_probs=15.8

Q ss_pred             CChhhhHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLR   20 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq   20 (137)
                      +|-.+.|..|+.||++||
T Consensus        38 ~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen   38 LSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             SSHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhC
Confidence            466788999999999998

; 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 ....

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

Probab=92.07  E-value=2.1  Score=27.36  Aligned_cols=59  Identities=8%  Similarity=-0.013  Sum_probs=40.2

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEeeCC-eEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTIGD-KIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~-r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      .++++.|++|+.+|.+.|+.+.+--+.-..+ .--|.+..++....-..+...+-++|++
T Consensus         7 ~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~   66 (75)
T cd04880           7 KNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKR   66 (75)
T ss_pred             CCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence            3579999999999999999999997664443 5557766666542112333455555554

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

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=91.95  E-value=2.2  Score=40.27  Aligned_cols=79  Identities=8%  Similarity=0.089  Sum_probs=56.5

Q ss_pred             CCeEEEEEcC-----CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EeeCCeEEEEEEEEeeccCccc-ch---
Q 046429           56 FPVVELKDLG-----SSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGV-ET---  125 (137)
Q Consensus        56 ~p~V~V~~~~-----~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtIh~qv~~~~~~~-d~---  125 (137)
                      .|.|.+++..     ++.+|.+. +.++++.|+++..+|...|++|++|.. |..+|.++=+++.+-.++.... +.   
T Consensus       688 ~~~v~~~~~~~~~~~~~t~V~V~-~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~~~~~~~~r~  766 (895)
T PRK00275        688 GPLVLIKETTQREFEGGTQIFIY-APDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGEPIGDNPARI  766 (895)
T ss_pred             CCeEEEEecCccCCCCeEEEEEE-eCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCCCccchHHHH
Confidence            4666676543     56777554 558899999999999999999999985 7788899999888765543212 22   


Q ss_pred             HHHHHHHhhh
Q 046429          126 SRACQRLHDL  135 (137)
Q Consensus       126 ~~l~~rL~~~  135 (137)
                      .++.+.|.+.
T Consensus       767 ~~i~~~L~~~  776 (895)
T PRK00275        767 EQIREGLTEA  776 (895)
T ss_pred             HHHHHHHHHH
Confidence            2355555554

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

Probab=91.68  E-value=0.24  Score=30.88  Aligned_cols=58  Identities=14%  Similarity=0.165  Sum_probs=40.6

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ++...++++.|.++..+|.++|+.+.+.+....++..+-.+...+.      +...+-++|+++
T Consensus         3 ~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~~~------~l~~li~~l~~~   60 (69)
T cd04901           3 LHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDIDSE------VSEELLEALRAI   60 (69)
T ss_pred             EEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcCCC------CCHHHHHHHHcC
Confidence            3455678999999999999999999776544334454444444443      567888888763

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-

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

Probab=91.41  E-value=1.1  Score=27.93  Aligned_cols=57  Identities=16%  Similarity=0.266  Sum_probs=41.8

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEe--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +...+.++.+.++.++|.++|+.+.+...+.  -+++.+..++.+...      ...+-++|++.
T Consensus         4 v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~~~------~~~~~~~l~~~   62 (73)
T cd04902           4 VRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPV------PDEVLEELRAL   62 (73)
T ss_pred             EEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCCCC------CHHHHHHHHcC
Confidence            3456789999999999999999998887654  457777777665522      24666777653

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

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

Probab=91.39  E-value=1.8  Score=25.24  Aligned_cols=58  Identities=14%  Similarity=0.193  Sum_probs=39.6

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEeeC-CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTIG-DKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~-~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..++++.+.++.+.|.++|+++.+......+ +.....+...+..   ..+...+.++|..+
T Consensus         5 ~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~   63 (71)
T cd04876           5 AIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRD---LEHLARIMRKLRQI   63 (71)
T ss_pred             EeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECC---HHHHHHHHHHHhCC
Confidence            3457889999999999999999998876554 3333333333322   34567777777653

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

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

Probab=91.36  E-value=1.9  Score=26.06  Aligned_cols=57  Identities=12%  Similarity=0.056  Sum_probs=39.6

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..+.+++|.++..+|.++|+.+.+..+...+..-++.+...+.. .   ....+-++|+++
T Consensus         6 ~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~~-~---~~~~l~~~l~~~   62 (71)
T cd04879           6 HKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDS-P---VPEEVLEELKAL   62 (71)
T ss_pred             ecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcCC-C---CCHHHHHHHHcC
Confidence            34578999999999999999999998765431123334444533 2   356888888764

ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active

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

Probab=91.10  E-value=1.4  Score=26.82  Aligned_cols=51  Identities=22%  Similarity=0.193  Sum_probs=34.7

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEeeC--CeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTIG--DKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      .++++.|.+++.+|.++|+.+.+.......  +.....++.+  .      ..++.+.|++
T Consensus         7 ~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve--~------~~~~~~~L~~   59 (65)
T cd04882           7 PDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE--D------IEKAIEVLQE   59 (65)
T ss_pred             CCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC--C------HHHHHHHHHH
Confidence            358999999999999999999877654332  4444444433  2      3566666654

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.

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=91.07  E-value=2  Score=35.26  Aligned_cols=63  Identities=16%  Similarity=0.314  Sum_probs=47.5

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeC--CeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIG--DKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      |+.+.|.++++..+.|=..|-+.|+++++.+.+.-.  ++.|  +..++..+...++.+.+.+.|.+
T Consensus         2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~--mr~~v~~~~~~~~~~~l~~~l~~   66 (280)
T TIGR00655         2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFF--MRVEFQLEGFRLEESSLLAAFKS   66 (280)
T ss_pred             EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEE--EEEEEEeCCCCCCHHHHHHHHHH
Confidence            344567789999999999999999999999988754  4444  44555543334677888888876

This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=91.05  E-value=1.8  Score=35.64  Aligned_cols=61  Identities=13%  Similarity=0.126  Sum_probs=49.7

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEe-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.|.++++...+|-+.|-+.|+++.+.+..+ .++..|+ +.+++..+. +.+.+.|++.|.++
T Consensus        12 v~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~-m~~~~~~p~-~~~~~~L~~~L~~l   73 (286)
T PRK13011         12 LSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFF-MRVEFHSEE-GLDEDALRAGFAPI   73 (286)
T ss_pred             EEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEE-EEEEEecCC-CCCHHHHHHHHHHH
Confidence            4577899999999999999999999999874 4556666 577886544 67789999998875

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

Probab=90.98  E-value=1.6  Score=23.99  Aligned_cols=54  Identities=22%  Similarity=0.199  Sum_probs=34.6

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHH
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRL  132 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL  132 (137)
                      .+++..|.+++.+|.++|+.+........++.-...+...+....   +..++.++|
T Consensus         6 ~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l   59 (60)
T cd02116           6 PDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGDG---DLEKLLEAL   59 (60)
T ss_pred             cCCCchHHHHHHHHHHCCCcEEEEEeEEcCCCCeEEEEEEEechH---HHHHHHHHh
Confidence            346789999999999999999999876544221222233333211   455666555

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

>PRK03059 PII uridylyl-transferase; Provisional

Probab=90.93  E-value=3.2  Score=39.05  Aligned_cols=62  Identities=13%  Similarity=0.230  Sum_probs=50.1

Q ss_pred             CCeEEEEEc--CCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EeeCCeEEEEEEEEeec
Q 046429           56 FPVVELKDL--GSSIEVVLISGMQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKI  118 (137)
Q Consensus        56 ~p~V~V~~~--~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtIh~qv~~  118 (137)
                      .|.|.++..  .++.+|.+.| .+++++|+++--+|...|++|++|.. +..+|.++=|++.+-..
T Consensus       665 ~~~v~~~~~~~~~~~~v~i~~-~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~  729 (856)
T PRK03059        665 TPIVRARLSPAGEGLQVMVYT-PDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPE  729 (856)
T ss_pred             CCeEEEEecCCCCeEEEEEEe-cCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCC
Confidence            465557653  4677886654 48899999999999999999999986 67899999999887544

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=90.74  E-value=2.2  Score=35.06  Aligned_cols=61  Identities=18%  Similarity=0.123  Sum_probs=46.5

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEe--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.|.++++...+|-++|-+.|+++.+.+.++  .++.  .++..++.-..-..+.++|.+.|.++
T Consensus        11 v~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~--F~m~i~v~~~~~~~~~~~L~~~L~~l   73 (286)
T PRK06027         11 LSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGR--FFMRVEFEGDGLIFNLETLRADFAAL   73 (286)
T ss_pred             EECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCe--EEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence            4577899999999999999999999999998  7773  44445554311135578888888765

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

Probab=90.70  E-value=1.2  Score=28.65  Aligned_cols=56  Identities=11%  Similarity=0.105  Sum_probs=39.7

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           74 SGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        74 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .+.++++.|.+|..++.++|+.+.+..+..- +.++  +..++.+   --+++.+-.||+++
T Consensus         6 ~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~--l~i~v~~---~~~L~~li~~L~~i   61 (74)
T cd04877           6 TCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GRIY--LNFPTIE---FEKLQTLMPEIRRI   61 (74)
T ss_pred             EEEccchHHHHHHHHHHHCCCceEEEEEecC-CeEE--EEeEecC---HHHHHHHHHHHhCC
Confidence            4457889999999999999999999998653 3322  3334443   23567788887754

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

>PRK08577 hypothetical protein; Provisional

Probab=90.70  E-value=2.4  Score=30.68  Aligned_cols=59  Identities=14%  Similarity=0.245  Sum_probs=42.2

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEeeC-CeEEE-EEEEEeeccCcccchHHHHHHHhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTIG-DKIFH-TVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~-~r~fh-tIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..+.++.|.++..+|.++|+++.+.++.... +..++ .+...+.+.  ..+.+.+.++|+++
T Consensus        63 ~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~~--~~~l~~l~~~L~~l  123 (136)
T PRK08577         63 VEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSKS--DIDLEELEEELKKL  123 (136)
T ss_pred             EcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCCc--hhhHHHHHHHHHcC
Confidence            4567899999999999999999998876544 44333 234455442  24668888888764

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

Probab=90.37  E-value=2.7  Score=25.47  Aligned_cols=55  Identities=11%  Similarity=0.172  Sum_probs=38.9

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEee--CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTI--GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~--~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..+.++.|.++...|.++|+.+.+......  ++..+..  ..+...    +...+-++|+++
T Consensus         6 ~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~--i~v~~~----~~~~~i~~l~~~   62 (71)
T cd04903           6 HKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMV--IEVDQP----IDEEVIEEIKKI   62 (71)
T ss_pred             eCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEE--EEeCCC----CCHHHHHHHHcC
Confidence            346788999999999999999998876542  2333322  455442    667888888764

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.

>PLN03217 transcription factor ATBS1; Provisional

Probab=90.10  E-value=0.77  Score=31.76  Aligned_cols=33  Identities=24%  Similarity=0.459  Sum_probs=28.4

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 046429            4 SQEDRLDLACCYIKQLRERIDKLNRMKEQAMKS   36 (137)
Q Consensus         4 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~~   36 (137)
                      |-+-.+-|+.+||+.|+..|+.|.++=-+|+..
T Consensus        46 saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         46 SAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            556678899999999999999999987787754

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

Probab=89.34  E-value=3.4  Score=25.14  Aligned_cols=57  Identities=7%  Similarity=0.070  Sum_probs=38.0

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           74 SGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        74 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      ...+.++.|++++..|.++|+.+.+......++..+ .+...+...   -....+.++|++
T Consensus         6 ~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~-~~~i~~~~~---~~~~~~~~~L~~   62 (72)
T cd04874           6 IAEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKA-RIYMELEGV---GDIEELVEELRS   62 (72)
T ss_pred             EeCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeE-EEEEEEecc---ccHHHHHHHHhC
Confidence            345678999999999999999999887654432222 233455432   244577777765

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.

>PRK04435 hypothetical protein; Provisional

Probab=88.77  E-value=3.7  Score=30.41  Aligned_cols=73  Identities=14%  Similarity=0.204  Sum_probs=50.3

Q ss_pred             EEEcCCeeEEEEE-ecCCCcccHHHHHHHHHHcCceEEEeEEEe-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           61 LKDLGSSIEVVLI-SGMQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        61 V~~~~~~~eV~l~-s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .+....|=.+.+. ...+.++.|++|+.+|.++|++|..-+.+. .++...-+|-.++.+.  ..+...+-++|+++
T Consensus        61 ~~~~~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~--~~~L~~Li~~L~~i  135 (147)
T PRK04435         61 FDEMVKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSM--EGDIDELLEKLRNL  135 (147)
T ss_pred             ccccCCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCCh--HHHHHHHHHHHHcC
Confidence            3333334444442 234578999999999999999999988764 4566666666666543  35678888888764

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=87.32  E-value=3.8  Score=33.78  Aligned_cols=65  Identities=15%  Similarity=0.179  Sum_probs=48.3

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEE--eeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFS--TIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s--~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      |+.+.|.++++....|=..|-|.|+++++.+..  ...+..|=.+........ .++.+.+.+.|.++
T Consensus        11 iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~~~~-~~~~~~l~~~l~~l   77 (289)
T PRK13010         11 VLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQSAE-AASVDTFRQEFQPV   77 (289)
T ss_pred             EEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcCCCC-CCCHHHHHHHHHHH
Confidence            344567789999999999999999999999985  455566644443332222 67889999888765

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=87.25  E-value=3.9  Score=31.77  Aligned_cols=63  Identities=6%  Similarity=0.068  Sum_probs=53.7

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEee----CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFSTI----GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~----~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      -+.|.++++.+++|-++|-+.|+++.+-++.+.    .+.-.|.+++++.-+. +.+...|++.|.++
T Consensus        99 ~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~lP~-~~~~~~L~~~l~~l  165 (190)
T PRK11589         99 QVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPA-SQDAANIEQAFKAL  165 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEEcCC-CCCHHHHHHHHHHH
Confidence            346888999999999999999999999887654    4677888999998875 88889999988876

>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme

Probab=85.51  E-value=7.7  Score=25.08  Aligned_cols=43  Identities=14%  Similarity=0.123  Sum_probs=34.4

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEee-CCeEEEEEEEEeec
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKI  118 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtIh~qv~~  118 (137)
                      .++++.|++++.+|.++|+.+.+-.+.-. ++.--|.++.+...
T Consensus         9 ~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~   52 (80)
T cd04905           9 PNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEG   52 (80)
T ss_pred             CCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEEC
Confidence            35789999999999999999998876543 34666888888765

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

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

Probab=85.39  E-value=6.2  Score=24.55  Aligned_cols=51  Identities=20%  Similarity=0.200  Sum_probs=35.8

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      .++++.|.+|+.+|.++|+.+.+-.....+++  -.++....+      .+++.+-|++
T Consensus         9 ~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~--~~~rl~~~~------~~~~~~~L~~   59 (66)
T cd04908           9 ENKPGRLAAVTEILSEAGINIRALSIADTSEF--GILRLIVSD------PDKAKEALKE   59 (66)
T ss_pred             cCCCChHHHHHHHHHHCCCCEEEEEEEecCCC--CEEEEEECC------HHHHHHHHHH
Confidence            35799999999999999999998876555553  344444422      3466666654

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.

>PRK07334 threonine dehydratase; Provisional

Probab=85.08  E-value=6.8  Score=33.32  Aligned_cols=67  Identities=13%  Similarity=0.130  Sum_probs=47.2

Q ss_pred             CeeEEEE-EecCCCcccHHHHHHHHHHcCceEEEeEEEee-----CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           66 SSIEVVL-ISGMQRNFMLYEVISILEEEGAQVVSASFSTI-----GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        66 ~~~eV~l-~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-----~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .|+.+.+ +...+++..|.+|+.+|-++|++|.+.++..-     ++...-.+..+|.+.   -.+.++-.||++.
T Consensus       323 ~~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~---~~L~~vi~~Lr~~  395 (403)
T PRK07334        323 AGRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDA---AHLQEVIAALRAA  395 (403)
T ss_pred             CCCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCH---HHHHHHHHHHHHc
Confidence            4644444 45667899999999999999999999987643     445444555666542   3457788888763

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

Probab=84.17  E-value=7  Score=23.52  Aligned_cols=57  Identities=11%  Similarity=0.083  Sum_probs=38.6

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEee--CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTI--GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~--~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..+.++.|.++...|.++|+.+.+......  ++.....+...+.  .  -+.+.+.++|+++
T Consensus         7 ~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~--~~~~~l~~~l~~~   65 (72)
T cd04878           7 VENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEGD--D--DVIEQIVKQLNKL   65 (72)
T ss_pred             EcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEECC--H--HHHHHHHHHHhCC
Confidence            346788999999999999999998886543  3444344444432  1  3456777777654

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

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

Probab=83.94  E-value=8.4  Score=24.25  Aligned_cols=28  Identities=21%  Similarity=0.152  Sum_probs=24.7

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEee
Q 046429           77 QRNFMLYEVISILEEEGAQVVSASFSTI  104 (137)
Q Consensus        77 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~  104 (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            5899999999999999999998876544

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

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=83.91  E-value=3.2  Score=32.27  Aligned_cols=59  Identities=12%  Similarity=0.048  Sum_probs=45.9

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +-|.++++...+|-++|.+.|+++++++.+..++  +.++...|..+.  ....+|...|..+
T Consensus        13 viG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg--~Fa~i~lvs~~~--~~~~~le~~L~~l   71 (190)
T PRK11589         13 ALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGE--EFTFIMLLSGSW--NAITLIESTLPLK   71 (190)
T ss_pred             EEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCC--ceEEEEEEeCCh--hHHHHHHHHHHhh
Confidence            3577899999999999999999999999999988  445555555543  3557777777654

>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains

Probab=82.76  E-value=7.5  Score=23.85  Aligned_cols=58  Identities=16%  Similarity=0.157  Sum_probs=39.1

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEee-C-CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           75 GMQRNFMLYEVISILEEEGAQVVSASFSTI-G-DKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        75 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~-~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..++++.|.++..+|.++|+.+.+...... + +...-.+...+.+   .-+..++-++|+++
T Consensus         7 ~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~~~~---~~~l~~~i~~L~~~   66 (79)
T cd04881           7 VKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTHETS---EAALNAALAEIEAL   66 (79)
T ss_pred             eCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEccCC---HHHHHHHHHHHHcC
Confidence            346788999999999999999998876544 2 4333334444433   34456677777653

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

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

Probab=82.59  E-value=6  Score=25.05  Aligned_cols=58  Identities=16%  Similarity=0.207  Sum_probs=43.3

Q ss_pred             CcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhhhC
Q 046429           78 RNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDLVD  137 (137)
Q Consensus        78 ~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~i~  137 (137)
                      +++-|.+|+.+|..-|+++-+-+.+..++--++.|-..+.+..  -....+...|.++++
T Consensus         2 ~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~~--~~i~~l~~Ql~Klid   59 (63)
T PF13710_consen    2 QPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGDD--REIEQLVKQLEKLID   59 (63)
T ss_dssp             STTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES-C--CHHHHHHHHHHCSTT
T ss_pred             CcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeCc--hhHHHHHHHHhccCC
Confidence            5778999999999999999998888766655666666776532  345778889988875

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

Probab=80.51  E-value=2.9  Score=29.03  Aligned_cols=64  Identities=19%  Similarity=0.202  Sum_probs=50.2

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      |+-++|.++++--..+-.+|-|.|+++++-+=+...+++=  +-.-|..+.-..|.+.+..+|.+.
T Consensus         5 vITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ft--m~~lV~~~~~~~d~~~lr~~l~~~   68 (90)
T COG3830           5 VITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFT--MIMLVDISKEVVDFAALRDELAAE   68 (90)
T ss_pred             EEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhce--eeeEEcCChHhccHHHHHHHHHHH
Confidence            3345788999999999999999999999999888888654  444455543468889998888754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	137
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	2e-04

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 38.0 bits (87), Expect = 2e-04
 Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 24/53 (45%)

Query: 17 KQLRERIDKLNRMKEQAMKSIKPNSSNNIMDETNNICSNFPVVELKDLGSSIE 69
          KQ    + KL    + ++K    +S+              P + +K   +++E
Sbjct: 19 KQ---ALKKL----QASLKLYADDSA--------------PALAIK---ATME 47

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	97.13
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	97.08
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	96.91
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	96.46
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	96.36
1a0a_A	63	BHLH, protein (phosphate system positive regulator	95.49
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	95.25
1u8s_A	192	Glycine cleavage system transcriptional repressor,	95.21
2nyi_A	195	Unknown protein; protein structure initiative, PSI	94.52
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	93.65
1u8s_A	192	Glycine cleavage system transcriptional repressor,	93.31
4ati_A	118	MITF, microphthalmia-associated transcription fact	93.09
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	92.84
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	92.69
2nyi_A	195	Unknown protein; protein structure initiative, PSI	92.63
3he4_B	46	Synzip5; heterodimeric coiled-coil, de novo protei	90.79
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	89.36
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	88.65
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	87.88
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	86.6
4ath_A	83	MITF, microphthalmia-associated transcription fact	86.25
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	85.87
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	85.55
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	85.26
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	84.79
4h10_B	71	Circadian locomoter output cycles protein kaput; B	82.28

>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=97.13  E-value=0.0005  Score=45.23  Aligned_cols=33  Identities=21%  Similarity=0.257  Sum_probs=29.2

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|..|+.||++||+++++|+.+.++|..
T Consensus        46 ~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~   78 (80)
T 1hlo_A           46 ASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   78 (80)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            566788999999999999999999999888753

>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=97.08  E-value=0.00078  Score=44.51  Aligned_cols=33  Identities=21%  Similarity=0.257  Sum_probs=28.4

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|..|++||++||+++++|..++++|..
T Consensus        36 ~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~   68 (83)
T 1nkp_B           36 ASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456678999999999999999999988887754

>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=96.91  E-value=0.0013  Score=43.53  Aligned_cols=34  Identities=24%  Similarity=0.234  Sum_probs=29.6

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMKS   36 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~~   36 (137)
                      ++-.+.|.+|+.||++||.+++.|.++.+.|...
T Consensus        39 ~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   72 (82)
T 1am9_A           39 LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (82)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566789999999999999999999998888653

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

Probab=96.46  E-value=0.0045  Score=40.90  Aligned_cols=33  Identities=21%  Similarity=0.079  Sum_probs=28.6

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|..|+.||++||++.++|...+++|..
T Consensus        36 ~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A           36 HTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456788999999999999999999998887754

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

Probab=96.36  E-value=0.057  Score=34.76  Aligned_cols=60  Identities=8%  Similarity=0.089  Sum_probs=48.7

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.+.++++.|++|..+|-+.|+++.+.+....++..+-.+..++.+   ..+...|.++|+++
T Consensus        10 v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~~---~~~l~~l~~~L~~~   69 (91)
T 1zpv_A           10 VVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE---KQDFTYLRNEFEAF   69 (91)
T ss_dssp             EEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS---CCCHHHHHHHHHHH
T ss_pred             EEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeCC---CCCHHHHHHHHHHH
Confidence            5667899999999999999999999999887777666666666544   35678899998865

>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=95.49  E-value=0.0033  Score=39.77  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=19.1

Q ss_pred             CCChhhhHHHHHHHHHHHHHHH
Q 046429            2 MLSQEDRLDLACCYIKQLRERI   23 (137)
Q Consensus         2 ~~s~~d~l~eA~~YIk~Lq~kv   23 (137)
                      .+|-.+.|+.|+.||++||+++
T Consensus        40 k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A           40 APSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccHHHHHHHHHHHHHHHHHHh
Confidence            3578899999999999999865

>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=95.25  E-value=0.026  Score=37.74  Aligned_cols=31  Identities=19%  Similarity=0.141  Sum_probs=24.4

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 046429            4 SQEDRLDLACCYIKQLRERIDKLNRMKEQAM   34 (137)
Q Consensus         4 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~   34 (137)
                      |-...|..|+.||++||.+...+...+++|.
T Consensus        42 sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A           42 PKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4446789999999999999988776665543

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

Probab=95.21  E-value=0.13  Score=37.74  Aligned_cols=60  Identities=15%  Similarity=0.235  Sum_probs=48.1

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .+++.++++.+++|-.+|.+.|++++++......+..|-++......    -+...|.+.|.++
T Consensus        10 tv~~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~~~----~~~~~l~~~L~~~   69 (192)
T 1u8s_A           10 TAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP----SNITRVETTLPLL   69 (192)
T ss_dssp             EEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH----HHHHHHHHHHHHH
T ss_pred             EEEcCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEecCC----CCHHHHHHHHHHH
Confidence            34566889999999999999999999999888888888888887542    3567777777654

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

Probab=94.52  E-value=0.21  Score=37.11  Aligned_cols=66  Identities=18%  Similarity=0.141  Sum_probs=47.3

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ++.+++.++++.++.|-.+|.+.|+++++|.-....++.|=++..............+|.+.|..+
T Consensus         7 ~ltv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~~~~~~~~~~~~~l~~~L~~~   72 (195)
T 2nyi_A            7 VVSVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVSLNAKDGKLIQSALESALPGF   72 (195)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESSSSSHHHHHHHHHHSTTC
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEEecCccchhHHHHHHHHHHHH
Confidence            334566789999999999999999999999988888877777777653210001146666666543

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

Probab=93.65  E-value=0.33  Score=30.53  Aligned_cols=60  Identities=10%  Similarity=0.124  Sum_probs=42.7

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +...++++.|.+|..+|.+.|+.+.+......++.....+..++.+   .-+...+-++|+++
T Consensus        10 v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~~~~---~~~l~~l~~~L~~~   69 (88)
T 2ko1_A           10 IVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIFVKN---TDKLTTLMDKLRKV   69 (88)
T ss_dssp             EEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEEESS---HHHHHHHHHHHTTC
T ss_pred             EEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEEECC---HHHHHHHHHHHhcC
Confidence            3455789999999999999999999998877666333444444433   23456777777653

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

Probab=93.31  E-value=0.63  Score=34.01  Aligned_cols=64  Identities=13%  Similarity=0.150  Sum_probs=46.8

Q ss_pred             EEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeC--------CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           69 EVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIG--------DKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        69 eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--------~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      -++.+.+.++++.+++|..+|-+.|+++.++...+.+        +..|=.+....  +. +.+.+.|.+.|.++
T Consensus        94 ~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~~~--~~-~~~~~~l~~~l~~~  165 (192)
T 1u8s_A           94 VEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARV--DS-GCNLMQLQEEFDAL  165 (192)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEE--CT-TSCHHHHHHHHHHH
T ss_pred             EEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEEeC--CC-CCCHHHHHHHHHHH
Confidence            3444566788999999999999999999999876543        34443444443  22 66889999998765

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

Probab=93.09  E-value=0.088  Score=36.95  Aligned_cols=27  Identities=15%  Similarity=0.343  Sum_probs=22.8

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 046429            4 SQEDRLDLACCYIKQLRERIDKLNRMK   30 (137)
Q Consensus         4 s~~d~l~eA~~YIk~Lq~kve~L~~kk   30 (137)
                      +-..-|..|+.||++||++++.|.+..
T Consensus        64 ~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           64 NKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445678999999999999999998653

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

Probab=92.84  E-value=0.052  Score=33.84  Aligned_cols=22  Identities=41%  Similarity=0.434  Sum_probs=19.2

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLRERID   24 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve   24 (137)
                      +|-.++|-.|++||.+||+.++
T Consensus        37 lSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B           37 LSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Confidence            5777899999999999998764

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

Probab=92.69  E-value=0.076  Score=34.62  Aligned_cols=23  Identities=22%  Similarity=0.127  Sum_probs=19.8

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHH
Q 046429            5 QEDRLDLACCYIKQLRERIDKLN   27 (137)
Q Consensus         5 ~~d~l~eA~~YIk~Lq~kve~L~   27 (137)
                      =...|..|+.||+.||+++++++
T Consensus        43 K~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A           43 KLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Confidence            34678999999999999999874

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

Probab=92.63  E-value=0.71  Score=34.15  Aligned_cols=62  Identities=15%  Similarity=0.184  Sum_probs=45.9

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeC------CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIG------DKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~------~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ++.++|.++++.+++|-.+|-+.|+++.++...+.+      ++.|=.+......   ..+ ..|.+.|..+
T Consensus        95 iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~~~---~~~-~~l~~~l~~~  162 (195)
T 2nyi_A           95 ELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAFPF---PLY-QEVVTALSRV  162 (195)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEEEG---GGH-HHHHHHHHHH
T ss_pred             EEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEcCC---Ccc-HHHHHHHHHH
Confidence            444566789999999999999999999999987654      4444445544432   456 8888888754

>3he4_B Synzip5; heterodimeric coiled-coil, de novo protein; 2.46A {Artificial gene}

Probab=90.79  E-value=0.45  Score=27.38  Aligned_cols=30  Identities=27%  Similarity=0.354  Sum_probs=24.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            6 EDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         6 ~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +.++.|--|||++|.++--+|+.-|+-|+.
T Consensus         2 sntvkelknyiqeleernaelknlkehlkf   31 (46)
T 3he4_B            2 SNTVKELKNYIQELEERNAELKNLKEHLKF   31 (46)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHhHHHHhHHHHHHH
Confidence            457888999999999999999888877654

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

Probab=89.36  E-value=1.2  Score=35.98  Aligned_cols=63  Identities=8%  Similarity=0.151  Sum_probs=51.7

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..++|.++++..+.|-..|-+.|+++++++-+..+++.|=.+++.+...  ..+.+.|.+.|..+
T Consensus        15 lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~~~--~~~~~~l~~~l~~~   77 (415)
T 3p96_A           15 ITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCPAD--VADGPALRHDVEAA   77 (415)
T ss_dssp             EEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEECHH--HHTSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEecCC--cCCHHHHHHHHHHH
Confidence            3356778999999999999999999999999999999988888887653  23557788877654

>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=88.65  E-value=0.11  Score=33.10  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=18.0

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLRERID   24 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve   24 (137)
                      +|=.+.|-.|++||.+||+.++
T Consensus        46 lSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           46 LPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHc
Confidence            4556789999999999998653

>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=87.88  E-value=0.096  Score=32.63  Aligned_cols=21  Identities=33%  Similarity=0.368  Sum_probs=17.7

Q ss_pred             CChhhhHHHHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLRERI   23 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kv   23 (137)
                      ++-.+.|..|+.||++||++.
T Consensus        43 ~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A           43 QSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCTTTTTTTTHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHh
Confidence            466788999999999999764

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

Probab=86.60  E-value=3.1  Score=33.07  Aligned_cols=65  Identities=9%  Similarity=0.082  Sum_probs=45.5

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEe--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..++|.++++...+|-..|-+.|+++++++...  ..++.|=.+.+...-+...++.+.|.+.|..+
T Consensus        13 Ltv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~~~~~~~~~~L~~~f~~l   79 (292)
T 3lou_A           13 LTLSCPSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFFVRCVFHATDDADALRVDALRREFEPI   79 (292)
T ss_dssp             EEEEEESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEECC----CCHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceEEEEEEEccCcccCCCHHHHHHHHHHH
Confidence            345666889999999999999999999998773  44555544444443112247778898888654

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

Probab=86.25  E-value=0.89  Score=30.16  Aligned_cols=24  Identities=17%  Similarity=0.376  Sum_probs=19.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHH
Q 046429            8 RLDLACCYIKQLRERIDKLNRMKE   31 (137)
Q Consensus         8 ~l~eA~~YIk~Lq~kve~L~~kk~   31 (137)
                      -|..|+.||++||+..+.+.+.-.
T Consensus        33 IL~ksvdYI~~Lq~e~~r~~e~e~   56 (83)
T 4ath_A           33 ILKASVDYIRKLQREQQRAKDLEN   56 (83)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            477899999999998887766433

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

Probab=85.87  E-value=3.4  Score=33.07  Aligned_cols=64  Identities=13%  Similarity=0.126  Sum_probs=46.7

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEee--CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           70 VVLISGMQRNFMLYEVISILEEEGAQVVSASFSTI--GDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        70 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~--~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      |..++|.++++...+|-..|-+.|+.+++++.+.-  +++.|=.+  ++..+...++.+.|.+.|..+
T Consensus        24 iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~FfMr~--~~~~~~~~~~~~~L~~~l~~l   89 (302)
T 3o1l_A           24 RLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRH--EIRADTLPFDLDGFREAFTPI   89 (302)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEEEEE--EEEGGGSSSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEEEEE--EEecCCCCCCHHHHHHHHHHH
Confidence            33456778999999999999999999999987754  45544434  444333247788999888654

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

Probab=85.55  E-value=3.8  Score=32.44  Aligned_cols=62  Identities=11%  Similarity=-0.031  Sum_probs=45.9

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEe--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..++|.++++...+|-..|-+.|+++++.+.+.  ..++.|=.+.+.  .+. .++.+.|.+.|..+
T Consensus        11 Ltv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~--~~~-~~~~~~L~~~f~~l   74 (286)
T 3n0v_A           11 LTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFR--QPD-DFDEAGFRAGLAER   74 (286)
T ss_dssp             EEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEE--CCS-SCCHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeEEEEEEe--cCC-CCCHHHHHHHHHHH
Confidence            345667889999999999999999999998763  345554444443  333 57889999888654

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

Probab=85.26  E-value=4.1  Score=32.30  Aligned_cols=63  Identities=17%  Similarity=0.130  Sum_probs=47.0

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEE--eeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           71 VLISGMQRNFMLYEVISILEEEGAQVVSASFS--TIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        71 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s--~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ..++|.++++...+|-..|-+.|+++++.+..  ..+++.|=.+.+.+..  ..++.+.|.+.|..+
T Consensus         9 Ltv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~--~~~~~~~L~~~f~~l   73 (288)
T 3obi_A            9 LTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVVFNAAA--KVIPLASLRTGFGVI   73 (288)
T ss_dssp             EEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEESS--CCCCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEEEEcCC--CCCCHHHHHHHHHHH
Confidence            34566788999999999999999999999865  3455655555555543  246778898888654

>1y7p_A Hypothetical protein AF1403; structural genomics, protein structure initiative, PSI, alpha-beta-alpha sandwich; HET: RIP; 1.90A {Archaeoglobus fulgidus} SCOP: c.23.1.7 d.58.18.12

Probab=84.79  E-value=2.1  Score=33.24  Aligned_cols=57  Identities=14%  Similarity=0.159  Sum_probs=40.7

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEeeC----CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           74 SGMQRNFMLYEVISILEEEGAQVVSASFSTIG----DKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        74 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~----~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      ...++++.|++|+.+|-+++.++.+.+.+...    +...+ ++.++.+.    +..++-++|+++
T Consensus        10 ~a~DRpGLLsDIt~vLAe~kiNIltIn~~~~~kG~~ng~A~-I~IEV~d~----~Le~LL~kLrkI   70 (223)
T 1y7p_A           10 IAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKAL-IYFEIEGG----DFEKILERVKTF   70 (223)
T ss_dssp             EEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEE-EEEEECSS----CHHHHHHHHHTC
T ss_pred             EEcCCCCHHHHHHHHHHHcCCCceEEEEEccccCCcCCEEE-EEEEECCC----CHHHHHHHHhCC
Confidence            45678999999999999999999999987754    33333 33777652    889999999864

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

Probab=82.28  E-value=0.89  Score=29.19  Aligned_cols=22  Identities=14%  Similarity=0.199  Sum_probs=17.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHH
Q 046429            5 QEDRLDLACCYIKQLRERIDKL   26 (137)
Q Consensus         5 ~~d~l~eA~~YIk~Lq~kve~L   26 (137)
                      =.+-|..|+.||+.||+++.=|
T Consensus        43 K~sIL~~aI~yik~Lq~~~~~~   64 (71)
T 4h10_B           43 KSTVLQKSIDFLRKHKEITAWL   64 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhhhHH
Confidence            3456889999999999987544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	97.17
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	97.03
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	96.79
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	96.77
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	96.61
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.25
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	95.9
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	95.5
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	94.97
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	93.88
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	90.75
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	86.7
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	82.58

>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=97.17  E-value=0.00028  Score=42.82  Aligned_cols=33  Identities=24%  Similarity=0.165  Sum_probs=28.1

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 046429            4 SQEDRLDLACCYIKQLRERIDKLNRMKEQAMKS   36 (137)
Q Consensus         4 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~~   36 (137)
                      +-..-|.+|+.||+.||+++++|++..+.|...
T Consensus        23 ~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   55 (61)
T d1uklc_          23 HKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLA   55 (61)
T ss_dssp             CTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445678999999999999999999988877653

>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=97.03  E-value=0.00044  Score=43.68  Aligned_cols=33  Identities=21%  Similarity=0.079  Sum_probs=29.0

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|.+|++||+.|++++++|..+++.|..
T Consensus        36 ~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~   68 (79)
T d1nlwa_          36 HTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (79)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466789999999999999999999998887754

>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=96.79  E-value=0.00088  Score=43.03  Aligned_cols=33  Identities=21%  Similarity=0.153  Sum_probs=28.6

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|..|++||++|++++++|..+++.|..
T Consensus        41 ~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   73 (88)
T d1nkpa_          41 APKVVILKKATAYILSVQAEEQKLISEEDLLRK   73 (88)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466788999999999999999999988877654

>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=96.77  E-value=0.0098  Score=37.09  Aligned_cols=61  Identities=8%  Similarity=0.080  Sum_probs=50.3

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           72 LISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        72 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      -++|.++++.+++|-..|.+.|+++.+.+....++..+-.+...++.   +.|.+++.+.|..+
T Consensus         6 tv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~~~---~~~~~~l~~~l~~l   66 (83)
T d1zpva1           6 TVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE---KQDFTYLRNEFEAF   66 (83)
T ss_dssp             EEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS---CCCHHHHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEEec---CCCHHHHHHHHHHH
Confidence            35678899999999999999999999999988888766666666543   56778899988765

>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=96.61  E-value=0.0014  Score=41.39  Aligned_cols=33  Identities=24%  Similarity=0.230  Sum_probs=28.6

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|..|++||++|++++++|.++.+.|..
T Consensus        39 ~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~   71 (80)
T d1am9a_          39 LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (80)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456778999999999999999999988887754

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

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

Probab=96.25  E-value=0.019  Score=36.09  Aligned_cols=59  Identities=17%  Similarity=0.264  Sum_probs=47.8

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           73 ISGMQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        73 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      +.|.++++.+++|-.+|-+.|+++++++-...++.....+.......    +.+++...|.++
T Consensus        10 v~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~~~----~~~~l~~~L~~l   68 (86)
T d1u8sa1          10 AVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSPS----NITRVETTLPLL   68 (86)
T ss_dssp             EEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECHH----HHHHHHHHHHHH
T ss_pred             EEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcCcc----cHHHHHHHHHHH
Confidence            45778999999999999999999999999999998777776665432    456777777654

>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=95.90  E-value=0.0059  Score=38.51  Aligned_cols=33  Identities=21%  Similarity=0.257  Sum_probs=27.0

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 046429            3 LSQEDRLDLACCYIKQLRERIDKLNRMKEQAMK   35 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~L~~   35 (137)
                      +|-.+.|..|++||+.|++++..|.+..++|..
T Consensus        36 ~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   68 (83)
T d1nkpb_          36 ASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355678999999999999999999887766543

>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=95.50  E-value=0.063  Score=33.98  Aligned_cols=67  Identities=13%  Similarity=0.174  Sum_probs=49.3

Q ss_pred             eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEeeCC------eEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           67 SIEVVLISGMQRNFMLYEVISILEEEGAQVVSASFSTIGD------KIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        67 ~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~------r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .++|.+ .|.++++.+++|-+.|-+.|+++.+.+..+...      .-...++..+.-+. +.+...|.++|..+
T Consensus         6 tv~v~v-~g~DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~p~-~~~~~~l~~~l~~l   78 (93)
T d1u8sa2           6 TVEVYV-ESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVDS-GCNLMQLQEEFDAL   78 (93)
T ss_dssp             EEEEEE-EESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEECT-TSCHHHHHHHHHHH
T ss_pred             EEEEEE-EECCCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEcCc-cccHHHHHHHHHHH
Confidence            345544 577899999999999999999999998765321      22344555555554 78889999999876

>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=94.97  E-value=0.0027  Score=39.04  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=18.8

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 046429            3 LSQEDRLDLACCYIKQLRERID   24 (137)
Q Consensus         3 ~s~~d~l~eA~~YIk~Lq~kve   24 (137)
                      +|-.+.|..|++||++||+.|+
T Consensus        46 ~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          46 LPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHHHHHHhh
Confidence            4667889999999999998764

>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=93.88  E-value=0.0079  Score=36.14  Aligned_cols=20  Identities=30%  Similarity=0.620  Sum_probs=17.2

Q ss_pred             ChhhhHHHHHHHHHHHHHHH
Q 046429            4 SQEDRLDLACCYIKQLRERI   23 (137)
Q Consensus         4 s~~d~l~eA~~YIk~Lq~kv   23 (137)
                      |-.+.|..|++||++||+++
T Consensus        42 sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_          42 SKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTHHHHHHHHHHHHHHTCS
T ss_pred             cHHHHHHHHHHHHHHHHHhh
Confidence            45678999999999999875

>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=90.75  E-value=0.091  Score=32.34  Aligned_cols=58  Identities=16%  Similarity=0.146  Sum_probs=38.0

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEe-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSRACQRLHDL  135 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~~  135 (137)
                      .++++.|++|..++-++|+.+.+.+... .++..--++-..+...  +.+.+++-+||+.+
T Consensus         9 ~Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~~--~~~l~~ll~kL~~l   67 (77)
T d1y7pa2           9 ENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIE--GGDFEKILERVKTF   67 (77)
T ss_dssp             ECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEEC--SSCHHHHHHHHHTC
T ss_pred             ecCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEcC--cccHHHHHHHHHcC
Confidence            4789999999999999999999998654 4443322333344332  35789999999865

>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=86.70  E-value=2  Score=25.49  Aligned_cols=51  Identities=14%  Similarity=0.069  Sum_probs=38.1

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEeeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 046429           76 MQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSRACQRLHD  134 (137)
Q Consensus        76 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtIh~qv~~~~~~~d~~~l~~rL~~  134 (137)
                      .++++.|++++++|.++|+++........+++-  .+...+.+      +.+..+-|++
T Consensus         7 ~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~--~~vl~vdd------~~~a~~~L~~   57 (71)
T d2f06a1           7 PNVPGALAKVLGFLSAEGVFIEYMYSFANNNVA--NVVIRPSN------MDKCIEVLKE   57 (71)
T ss_dssp             ESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEE--EEEEEESC------HHHHHHHHHH
T ss_pred             cCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcE--EEEEEECC------HHHHHHHHHH
Confidence            468999999999999999999998877667765  35555543      3566665553

>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=82.58  E-value=0.11  Score=30.88  Aligned_cols=17  Identities=35%  Similarity=0.468  Sum_probs=14.3

Q ss_pred             hhhHHHHHHHHHHHHHH
Q 046429            6 EDRLDLACCYIKQLRER   22 (137)
Q Consensus         6 ~d~l~eA~~YIk~Lq~k   22 (137)
                      ...|..|++||++||++
T Consensus        46 ~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_          46 GGILSKASDYIQELRQS   62 (65)
T ss_dssp             TTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            45688999999999965