Citrus Sinensis ID: 032643

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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
MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEEEEEccccEEEEEEEcccccccHHHHHHHHHHHccEEEEEEEEEEccEEEEEEEEEEEcccccccHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccEEEEEEcccEEEEEEEEccccccEHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEccccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MLSQEDQLDLACCYIKQLRERIDKLNRMkgqamksikpnssnnildetnnicsnlpvvelrdlgsSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD
Flexible Loop (DISEMBL)
MLSQEDQLDLACCYIKQLRERIDKLNrmkgqamksikpnssnnilDETNNICSNLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAkisrlgvetsiacqrlhdlvd
Low Complexity Region (SEG)
MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD
Disordered region (IsUnstruct)
*******LDLACCYIKQLRERID********************ILDETNNICSNLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLH****
Disordered Region (DISOPRED)
**S**DQLDLACCYIKQL*****************************************LRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLV*
Disordered Region (DISEMBL)
MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD
Disordered Region (DISPRO)
*LSQEDQLDLACCYIKQLRERIDKLNRMKGQA*K*******************NLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLSQEDQLDLACCYxxxxxxxxxxxxxxxxxxxxxIKPNSSNNILDETNNICSNLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD
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	136
255540707	173	DNA binding protein, putative [Ricinus c	0.911	0.716	0.669	6e-43
224135791	178	predicted protein [Populus trichocarpa]	0.970	0.741	0.592	2e-40
224121682	179	predicted protein [Populus trichocarpa]	0.970	0.737	0.595	4e-39
356508667	190	PREDICTED: uncharacterized protein LOC10	0.955	0.684	0.607	2e-38
356516682	193	PREDICTED: uncharacterized protein LOC10	0.970	0.683	0.585	1e-37
356513596	191	PREDICTED: uncharacterized protein LOC10	0.977	0.696	0.592	1e-37
225457062	178	PREDICTED: uncharacterized protein LOC10	0.970	0.741	0.6	7e-37
358248500	161	uncharacterized protein LOC100787505 [Gl	0.779	0.658	0.601	3e-25
242056735	232	hypothetical protein SORBIDRAFT_03g00856	0.985	0.577	0.436	1e-22
226531322	229	putative HLH DNA-binding domain superfam	0.985	0.585	0.445	9e-22

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

 Score =  178 bits (452), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 83/124 (66%), Positives = 105/124 (84%)

Query: 2   LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVELR 61
           LSQ+DQLD A  YIK L+ERI+KL +MK QAM+S+  NS+NN   +   + S LP++ELR
Sbjct: 48  LSQQDQLDHAAAYIKHLKERIEKLKKMKEQAMRSLATNSTNNNALDATTMGSRLPMIELR 107

Query: 62  DLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLG 121
           DLGSSIEV+LISG+++NFMLYEVI+I+EEEGA+VVSASFST+GDK+FH + AQ KISR+G
Sbjct: 108 DLGSSIEVILISGLKKNFMLYEVITIVEEEGAEVVSASFSTVGDKVFHIIHAQVKISRVG 167

Query: 122 VETS 125
           VETS
Sbjct: 168 VETS 171

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 =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 80/135 (59%), Positives = 108/135 (80%), Gaps = 3/135 (2%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVEL 60
           MLSQ+DQL+LA CYIKQ+RER++KL R+K QA+ +I+ + S      +  I   LPV+EL
Sbjct: 46  MLSQQDQLELAACYIKQMRERVEKLKRVKEQAITTIQTSRSGMT---SMMIGLRLPVIEL 102

Query: 61  RDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 120
           RD GSSIEVVL+SG+ +NFM YEVI++L +EGA+VVSAS+ST+GDK+FHT+ AQ +ISR+
Sbjct: 103 RDFGSSIEVVLVSGLNKNFMFYEVITVLSDEGAEVVSASYSTVGDKVFHTIHAQVRISRV 162

Query: 121 GVETSIACQRLHDLV 135
           GVETS   +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 =  165 bits (418), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 81/136 (59%), Positives = 108/136 (79%), Gaps = 4/136 (2%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKG-QAMKSIKPNSSNNILDETNNICSNLPVVE 59
           MLSQ+DQL+LA CYIKQLRER++ L R+K  QA+ + + +SS      +  I   LPVVE
Sbjct: 46  MLSQQDQLELAACYIKQLRERVEGLKRVKEEQAITTTRTSSSAKT---SMMIGLRLPVVE 102

Query: 60  LRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISR 119
           LRD GS+IEVVLISG+ +NFM YEVI++L +EGA+V+SAS+ST+GDK+FHT+ AQ +ISR
Sbjct: 103 LRDFGSTIEVVLISGLNKNFMFYEVINVLSDEGAEVISASYSTVGDKVFHTIHAQVRISR 162

Query: 120 LGVETSIACQRLHDLV 135
           +GVETS  C+RL +L+
Sbjct: 163 VGVETSRVCERLQELI 178

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 82/135 (60%), Positives = 102/135 (75%), Gaps = 5/135 (3%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVEL 60
           ML Q DQLDLA  YIK + ERI+KL R K Q M +   N    + +  NN+ S LP+VEL
Sbjct: 51  MLGQRDQLDLAARYIKHMNERIEKLKRQKEQVMSN---NDDRKMFN--NNVESKLPIVEL 105

Query: 61  RDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 120
           RDLGSSIEV+L+SG+ + FMLYEVIS+LEEEGA+VV+ASFST+GDKIF+ V AQ KISR+
Sbjct: 106 RDLGSSIEVMLVSGLNKAFMLYEVISVLEEEGAEVVTASFSTVGDKIFYVVHAQVKISRV 165

Query: 121 GVETSIACQRLHDLV 135
           GVET+ A  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 =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 79/135 (58%), Positives = 104/135 (77%), Gaps = 3/135 (2%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVEL 60
           ML  +DQLDLA  YI+Q+ ER++KL R K QAM S + N    + +  NN+ S LP++EL
Sbjct: 52  MLGLQDQLDLAARYIRQMTERVEKLKRQKEQAM-SNQSNDGRKMFN--NNVESKLPILEL 108

Query: 61  RDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 120
           RDLGS IEV+L++G+ + FMLYEVIS+LEEEGA+VV+ASFST+GDKIF+ V AQAKISR+
Sbjct: 109 RDLGSGIEVILVTGLNKTFMLYEVISVLEEEGAEVVTASFSTVGDKIFYVVHAQAKISRV 168

Query: 121 GVETSIACQRLHDLV 135
           GVET+    RL + +
Sbjct: 169 GVETTRVYNRLQEFI 183

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 80/135 (59%), Positives = 106/135 (78%), Gaps = 2/135 (1%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVEL 60
           MLSQ+DQLDLA  YIK+L+ERI+KL   K + M  +  ++ NN  +   NI S LP++E+
Sbjct: 49  MLSQQDQLDLATTYIKRLKERIEKLKGEKEKIMNMMMSSNQNN--NSIFNIGSQLPLLEI 106

Query: 61  RDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 120
           +DLGS IEV+LISG+ +NFMLYEVIS+LEEEGA+VV+A+FST+ DKIF+TV AQ KISR+
Sbjct: 107 KDLGSGIEVMLISGLNKNFMLYEVISVLEEEGAEVVTANFSTVADKIFYTVHAQVKISRV 166

Query: 121 GVETSIACQRLHDLV 135
           GVE +   QRL +L+
Sbjct: 167 GVEPTRVYQRLQELI 181

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 =  158 bits (399), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 81/135 (60%), Positives = 106/135 (78%), Gaps = 3/135 (2%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVEL 60
           MLSQ+DQL+ A  YIKQL+ERI++L   KG+   + +   +NN L +   I   LPV++L
Sbjct: 46  MLSQQDQLEQAANYIKQLKERIEEL---KGRKELATRVAGTNNNLIDAVMIGLRLPVIDL 102

Query: 61  RDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRL 120
           RDLGSS+EV+LISG+ +NFMLYEVIS+LEEEGA+VVSAS ST+GDK+FH++ AQ KISR+
Sbjct: 103 RDLGSSLEVMLISGLNKNFMLYEVISVLEEEGAEVVSASVSTVGDKVFHSLHAQVKISRV 162

Query: 121 GVETSIACQRLHDLV 135
           GVETS   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 =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 65/108 (60%), Positives = 82/108 (75%), Gaps = 2/108 (1%)

Query: 1   MLSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVEL 60
           MLSQ+DQL LA  YIK LRERI+KL   K +AM  +    SN   +   N  S LP++E+
Sbjct: 49  MLSQQDQLHLAATYIKHLRERIEKLKGEKEKAMNMMM--MSNQSNNRIFNTGSELPLLEI 106

Query: 61  RDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIF 108
           +DLGS 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 =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 62/142 (43%), Positives = 89/142 (62%), Gaps = 8/142 (5%)

Query: 2   LSQEDQLDLACCYIKQLRERIDKLNRMK-GQAMKSIKPNSSNNILDETNNICS------- 53
           ++Q DQLD A  YIKQLRERI+ L + K G    +   N    +    +   +       
Sbjct: 84  VTQLDQLDSAAAYIKQLRERIEALKQRKAGGPGPAAGCNGGGAVTASASASSASGGGAGV 143

Query: 54  NLPVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRA 113
            +PV+E+R    +++VVLIS   R F L+EVI++LE+EGA+VVSASFS IGD+IF+TV +
Sbjct: 144 RMPVIEVRYQDGTLDVVLISDAGRPFKLHEVITVLEQEGAEVVSASFSVIGDRIFYTVHS 203

Query: 114 QAKISRLGVETSIACQRLHDLV 135
           QA    +G++ +   QRLHDL+
Sbjct: 204 QALSPWVGLDAARVSQRLHDLL 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 =  108 bits (269), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 61/137 (44%), Positives = 86/137 (62%), Gaps = 3/137 (2%)

Query: 2   LSQEDQLDLACCYIKQLRERIDKLNRMKG---QAMKSIKPNSSNNILDETNNICSNLPVV 58
           ++Q DQLD A  YIKQL+ERI+ L + K        +    ++             +PV+
Sbjct: 86  VTQLDQLDSAAAYIKQLKERIEALKQRKAGCCNGGGAATEAATAAAGSTGGGGGVRMPVI 145

Query: 59  ELRDLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKIS 118
           E+R    +++VVLIS   R F L+EVI++LE+EGA+VVSASFS IGDKIF+TV +QA   
Sbjct: 146 EVRCQDGTLDVVLISEAARPFKLHEVITVLEQEGAEVVSASFSVIGDKIFYTVHSQALSP 205

Query: 119 RLGVETSIACQRLHDLV 135
           R+GV+ +   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	136
TAIR|locus:4515102513	174	AT1G10586 [Arabidopsis thalian	0.882	0.689	0.356	1.6e-15
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.985	0.705	0.295	3.4e-13
TAIR|locus:505006117	181	AT1G10585 [Arabidopsis thalian	0.882	0.662	0.325	1.9e-12
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.897	0.491	0.251	6.1e-07
TAIR|locus:2080615	258	bHLH39 "basic helix-loop-helix	0.867	0.457	0.268	0.00059
TAIR|locus:2080600	253	bHLH38 "basic helix-loop-helix	0.948	0.509	0.227	0.00091

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

 Score = 195 (73.7 bits), Expect = 1.6e-15, P = 1.6e-15
 Identities = 46/129 (35%), Positives = 77/129 (59%)

Query:     8 LDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVELRDLGSSI 67
             +D A  Y+ QL+E+++ LN MK + +     N S           S LP + +R L S I
Sbjct:    53 IDQAVSYMIQLKEKVNYLNEMKRRMLGGEVKNRSEG--------SSLLPKLSIRSLDSII 104

Query:    68 EVVLISGVQ-RNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSI 126
             E+ L+  +  +  ML++++S+ EEEGAQV+SA+   + D+ F+T+ AQA I R+G++ S 
Sbjct:   105 EMNLVMDLNMKGVMLHKLVSVFEEEGAQVMSANLQNLNDRTFYTIIAQAIICRIGIDPSR 164

Query:   127 ACQRLHDLV 135
               +RL D++
Sbjct:   165 IEERLRDII 173

GO:0005634 "nucleus" evidence=ISM

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

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 42/142 (29%), Positives = 78/142 (54%)

Query:     2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSI---KPNS--SNNILDETN-NICSNL 55
             L+  DQLD A  YIK+L+  ++K    K   + +    K NS  S+++    + ++   L
Sbjct:    47 LTLPDQLDEAANYIKKLQVNVEKKRERKRNLVATTTLEKLNSVGSSSVSSSVDVSVPRKL 106

Query:    56 PVVELRDLGSSIEVVLISGVQRNFMLYEVISILEEE-GAQVVSASFSTIGDKIFHTVRAQ 114
             P +E+++ GS   + L++ ++  FM  E+I +L EE GA++  A +S + D +FHT+  +
Sbjct:   107 PKIEIQETGSIFHIFLVTSLEHKFMFCEIIRVLTEELGAEITHAGYSIVDDAVFHTLHCK 166

Query:   115 AKISRLGVETSIACQRLHDLVD 136
              +    G  + I  +RL  +V+
Sbjct:   167 VEEHDYGARSQIP-ERLEKIVN 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

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

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 42/129 (32%), Positives = 75/129 (58%)

Query:     8 LDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVELRDLGSSI 67
             +D A  Y+ QL+E ++ L   K    +++      N+ + +      LP + +R   S+I
Sbjct:    53 IDQATSYMIQLKENVNYLKEKK----RTLLQGELGNLYEGS----FLLPKLSIRSRDSTI 104

Query:    68 EVVLISGVQ-RNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSI 126
             E+ LI  +  +  ML+E++SI EEEGAQV+SA+   + D+  +T+ AQA ISR+G++ S 
Sbjct:   105 EMNLIMDLNMKRVMLHELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQAIISRIGIDPSR 164

Query:   127 ACQRLHDLV 135
               +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

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

 Score = 118 (46.6 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 32/127 (25%), Positives = 62/127 (48%)

Query:    14 YIKQLRERIDKLNRMKGQAMKSIKPNSSNNILDETNNICSNLPVVE---LRDLGSSIEVV 70
             YI +L+++++ L R K +   +   N    +L          P+V    + D+   ++V 
Sbjct:   116 YIPELQKQVENLERKKKELTTTSTTNCKPGVLGSQLMSEGMAPIVSATCINDMEIMVQVS 175

Query:    71 LISGVQRNFM-LYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSIAC 128
             L+S V  + + L + I +LE EG   +S+S S+  G++ F+++  Q     +  E    C
Sbjct:   176 LLSNVAGSVLPLSKCIKVLENEGLHFISSSTSSGFGNRTFYSIHLQRSEGTINEECPAFC 235

Query:   129 QRLHDLV 135
             +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 = 97 (39.2 bits), Expect = 0.00059, P = 0.00059
 Identities = 33/123 (26%), Positives = 61/123 (49%)

Query:    14 YIKQLRERIDKLNRMKGQAMKSI--KPNSSNNILDETNNICSNLPVVELRDLGSSIEVVL 71
             YI +L+E++ KL + K + +  I  + N+   +      + + +  V    LG +  +V 
Sbjct:   124 YIPELQEQVKKLIKKKEELLVQISGQRNTECYVKQPPKAVANYISTVSATRLGDNEVMVQ 183

Query:    72 ISGVQ-RNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQA-KISRLGVETSIAC 128
             IS  +  NF +  V+S LEE+   +V  S S + G+++F+T+  Q  KI    +      
Sbjct:   184 ISSSKIHNFSISNVLSGLEEDRFVLVDMSSSRSQGERLFYTLHLQVEKIENYKLNCEELS 243

Query:   129 QRL 131
             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 = 96 (38.9 bits), Expect = 0.00091, P = 0.00091
 Identities = 31/136 (22%), Positives = 67/136 (49%)

Query:     2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSIKPNSSNNILD--ETNNICSNLPVVE 59
             LS  + +  +  YI +L++++ +L + K + +  +       + D  +   + S L  V 
Sbjct:   107 LSIPETVSKSLKYIPELQQQVKRLIQKKEEILVRVSGQRDFELYDKQQPKAVASYLSTVS 166

Query:    60 LRDLGSSIEVVLISGVQ-RNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKI 117
                LG +  +V +S  +  NF +  V+  +EE+G  +V  S S + G+++F+T+  Q  +
Sbjct:   167 ATRLGDNEVMVQVSSSKIHNFSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQ--V 224

Query:   118 SRLGVETSIACQRLHD 133
               +  +  I C+ L +
Sbjct:   225 ENMD-DYKINCEELSE 239


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   0.133   0.363    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      136       136   0.00091  102 3  11 22  0.41    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:  522 (56 KB)
  Total size of DFA:  109 KB (2075 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:  15.58u 0.09s 15.67t   Elapsed:  00:00:01
  Total cpu time:  15.58u 0.09s 15.67t   Elapsed:  00:00:01
  Start:  Thu May  9 19:24:02 2013   End:  Thu May  9 19:24:03 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	136
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.76
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.57
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.52
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.44
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.44
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.29
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.17
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.14
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	97.08
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	96.96
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.89
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.82
PRK00194	90	hypothetical protein; Validated	96.51
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	96.39
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	96.37
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.3
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	96.2
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	96.18
PRK03059	856	PII uridylyl-transferase; Provisional	96.15
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	96.12
PRK00275	895	glnD PII uridylyl-transferase; Provisional	96.0
PRK03381	774	PII uridylyl-transferase; Provisional	95.88
PRK04374	869	PII uridylyl-transferase; Provisional	95.8
PRK05092	931	PII uridylyl-transferase; Provisional	95.76
PRK05007	884	PII uridylyl-transferase; Provisional	95.58
smart00353	53	HLH helix loop helix domain.	94.88
PRK03381	774	PII uridylyl-transferase; Provisional	94.88
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.57
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	94.56
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.19
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	94.19
PRK05007	884	PII uridylyl-transferase; Provisional	94.1
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.09
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.09
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	93.55
PRK04374	869	PII uridylyl-transferase; Provisional	93.44
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	93.43
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	93.26
PRK05092	931	PII uridylyl-transferase; Provisional	93.22
PRK00275	895	glnD PII uridylyl-transferase; Provisional	92.43
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	92.31
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	92.19
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	92.04
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	91.89
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	91.67
PRK03059	856	PII uridylyl-transferase; Provisional	91.57
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	91.56
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	91.55
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	91.42
cd02116	60	ACT ACT domains are commonly involved in specifica	91.42
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	91.37
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	91.35
PRK08577	136	hypothetical protein; Provisional	91.12
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	90.95
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	90.71
PLN03217	93	transcription factor ATBS1; Provisional	90.23
PRK04435	147	hypothetical protein; Provisional	90.18
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	90.06
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	88.36
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	88.22
PRK11589	190	gcvR glycine cleavage system transcriptional repre	87.75
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	87.29
PRK07334	403	threonine dehydratase; Provisional	86.94
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	86.3
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	85.66
PRK11589	190	gcvR glycine cleavage system transcriptional repre	84.79
PF13710	63	ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.	84.5
COG3830	90	ACT domain-containing protein [Signal transduction	83.3
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	82.4
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	81.92

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

Probab=97.76  E-value=0.00038  Score=46.27  Aligned_cols=65  Identities=11%  Similarity=0.182  Sum_probs=51.2

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      |+-+++.++++.|++|.++|.+.|++|.+|..++.|+++.-+++-.-.++. .++-+...++|++.
T Consensus         3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~-kl~d~~~~~~l~~~   67 (72)
T cd04895           3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGN-KLTDDSLIAYIEKS   67 (72)
T ss_pred             EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCC-CCCCHHHHHHHHHH
Confidence            334577789999999999999999999999999999999999998765433 45444555555543

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=97.57  E-value=0.0011  Score=44.44  Aligned_cols=66  Identities=23%  Similarity=0.275  Sum_probs=52.2

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccch----HHHHHHHhhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET----SIACQRLHDLV  135 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~----~~l~erL~~~i  135 (136)
                      |+-+.+.++|+.|++|..+|-+.|++|.+|..++.|+++.=+++-.-.++. .+..    .++.++|.+.+
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            344577889999999999999999999999999999999999998776553 4433    45555555543

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=97.52  E-value=0.0019  Score=41.93  Aligned_cols=64  Identities=14%  Similarity=0.158  Sum_probs=46.3

Q ss_pred             EEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEe-CCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           68 EVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        68 eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      +|.+ .+.+++++|+++-.+|...|++|++|...+. +++++=+++-.-.+.. .++.+.-.++|++
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-YTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDPDGE-PIGERERLARIRE   67 (73)
T ss_pred             EEEE-EecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECCCCC-CCChHHHHHHHHH
Confidence            4544 4558999999999999999999999998665 7899999887643322 3444444444443

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=97.44  E-value=0.0024  Score=40.41  Aligned_cols=62  Identities=18%  Similarity=0.265  Sum_probs=47.7

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccch---HHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET---SIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~---~~l~erL~~~  134 (136)
                      +.+.++++.|.++..+|.+.|++++++.....+++.+-+++.+-..+. ..+.   .+++++|.+.
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   2355565544

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=97.44  E-value=0.0026  Score=41.66  Aligned_cols=62  Identities=19%  Similarity=0.275  Sum_probs=47.2

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeec-cCcccc----hHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKI-SRLGVE----TSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~-~~~~~d----~~~l~erL~~~  134 (136)
                      +.+.+++++|++|-.+|.+.|++|++|..++.|++++-+++..-.+ .. .++    ..++.+.|.+.
T Consensus         5 v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~-~~~~~~~~~~i~~~L~~~   71 (74)
T cd04925           5 LTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGA-PIDDPIRLASIEDRLDNV   71 (74)
T ss_pred             EEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCC-CCCCHHHHHHHHHHHHHH
Confidence            4566899999999999999999999999988899999999876432 21 232    34555555544

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=97.29  E-value=0.0042  Score=41.03  Aligned_cols=45  Identities=16%  Similarity=0.132  Sum_probs=39.9

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEE-eCCeEEEEEEEEee
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAK  116 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtI~~qv~  116 (136)
                      +.+.++++.|+++..+|.+.|++|.+|..++ .|++++-+++-+-.
T Consensus         5 i~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~   50 (76)
T cd04927           5 LFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDA   50 (76)
T ss_pred             EEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCC
Confidence            4556899999999999999999999999874 99999999998643

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.

>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=97.17  E-value=0.0071  Score=39.29  Aligned_cols=65  Identities=20%  Similarity=0.233  Sum_probs=47.4

Q ss_pred             eEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           67 IEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        67 ~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .+|.+. ..+++++|+++..+|.+.|++|++|.....+++.+-+++.+-.+.. .++. ...+++++.
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 3478999999999999999999999988778888888887643332 2443 455566554

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

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

Probab=97.14  E-value=0.0059  Score=40.86  Aligned_cols=63  Identities=19%  Similarity=0.329  Sum_probs=49.8

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEE--EeCCeEEEEEEEEeeccCccc-c---hHHHHHHHhhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFS--TIGDKIFHTVRAQAKISRLGV-E---TSIACQRLHDLV  135 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s--~~~~r~fhtI~~qv~~~~~~~-d---~~~l~erL~~~i  135 (136)
                      -+.+.++++.|++|.++|.+.|++|.+|..+  +.|+|+.=+++-.-.+ . .+ |   ...|.++|.+.+
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   456677776654

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.

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

Probab=97.08  E-value=0.0075  Score=39.74  Aligned_cols=61  Identities=16%  Similarity=0.234  Sum_probs=52.9

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           70 VLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        70 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.++|.++++..++|-++|.+.|+++++++....+++.|..+...+..    .+.+.|.++|.++
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            346788899999999999999999999999999999999999999752    4678888888765

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=96.96  E-value=0.015  Score=38.14  Aligned_cols=65  Identities=18%  Similarity=0.169  Sum_probs=53.8

Q ss_pred             EEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EEeCCeEEEEEEEEeeccCcccchHHHHHHHhhhhC
Q 032643           68 EVVLISGVQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD  136 (136)
Q Consensus        68 eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~i~  136 (136)
                      +|.+.+ .+++.+|+++-.+|...|++|++|.. +..++.++-+++.+-.   -+=|...+.++|.+.++
T Consensus         3 eI~V~~-~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~---~~~~~~~~~~~~~~~~~   68 (68)
T cd04928           3 EITFAA-GDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGW---KRGETAALGHALQKEID   68 (68)
T ss_pred             EEEEEE-CCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecC---CccchHHHHHHHHHhhC
Confidence            565544 48899999999999999999999996 5678899998887743   36788999999988764

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=96.89  E-value=0.01  Score=38.99  Aligned_cols=59  Identities=15%  Similarity=0.206  Sum_probs=49.0

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.|.++++.++++..+|.+.|+++++++.++.++++-..++.++..    -+.++|...|.++
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            5677899999999999999999999999999999999888888862    3668888888765

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

Probab=96.82  E-value=0.013  Score=38.20  Aligned_cols=61  Identities=11%  Similarity=0.198  Sum_probs=51.1

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -+.|.++++...++-++|.+.|+++.+.+.++.++.  +++...+..+. +.+.++|.+.|..+
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            356888999999999999999999999998888865  56667777665 57789999988875

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.

>PRK00194 hypothetical protein; Validated

Probab=96.51  E-value=0.016  Score=38.79  Aligned_cols=64  Identities=11%  Similarity=0.130  Sum_probs=50.7

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ++.+.+.++++.+++|.++|-+.|+++++.+....++..+-.+-+....  ...+.+.|.+.|.++
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            4456778899999999999999999999999887777666666666643  246678888888765

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

Probab=96.39  E-value=0.019  Score=38.42  Aligned_cols=63  Identities=13%  Similarity=0.125  Sum_probs=51.1

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           70 VLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        70 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.+.|.++++.+++|-+.|-+.|+++++.+..+.+++.+-.+.+....  .+.+.++|.+.|.++
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            445777899999999999999999999999888788777777666542  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.

>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=0.046  Score=35.47  Aligned_cols=63  Identities=17%  Similarity=0.236  Sum_probs=48.0

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEeC----CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTIG----DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~----~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -+.+.++++.+++|-+.|.+.|+++.+.+....+    +--.+.+.+++..+. ..+..++.+.|..+
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    223334444454443 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

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

Probab=96.30  E-value=0.084  Score=32.74  Aligned_cols=46  Identities=17%  Similarity=0.284  Sum_probs=37.0

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeec
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKI  117 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~  117 (136)
                      +.+.++++.|+++..+|.+.|+.+.++.....+++..-.++..-..
T Consensus         5 i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~   50 (70)
T cd04873           5 VYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSD   50 (70)
T ss_pred             EEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCC
Confidence            3555789999999999999999999999877777666666665543

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=96.20  E-value=0.059  Score=34.72  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=46.9

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEE-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           70 VLISGVQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        70 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.+.|.++++.+++|-++|-+.|+++++.+..+ .++..|+. .+++..+....+...+.+.|.++
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            345677899999999999999999999999875 34444443 55555443125678888888765

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.

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

Probab=96.18  E-value=0.049  Score=35.50  Aligned_cols=66  Identities=21%  Similarity=0.225  Sum_probs=50.7

Q ss_pred             eeEEEE-EecCCCcccHHHHHHHHHHcCceEEEeEEEE--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           66 SIEVVL-ISGVQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        66 ~~eV~l-~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .+.+.+ +...+.++.|.+|..++.++|+.+.+.+...  .++...-+|..+|.+.   -++..+-++|+++
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 4556789999999999999999999999976  4788889999999764   4667888888764

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.15  E-value=0.054  Score=50.51  Aligned_cols=82  Identities=21%  Similarity=0.209  Sum_probs=58.4

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHh
Q 032643           54 NLPVVELRDLG-SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLH  132 (136)
Q Consensus        54 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~  132 (136)
                      ..|.|.+.... .+.-++.+.+.++++.|++|-.+|.+.|++|.+|..++.|++++=+++-+-.+....-...++.++|.
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            34567776543 35555556677899999999999999999999999998899999999874221111112356666666


Q ss_pred             hhh
Q 032643          133 DLV  135 (136)
Q Consensus       133 ~~i  135 (136)
                      +.+
T Consensus       852 ~~L  854 (856)
T PRK03059        852 DAL  854 (856)
T ss_pred             HHh
Confidence            554

>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=96.12  E-value=0.071  Score=32.68  Aligned_cols=59  Identities=20%  Similarity=0.083  Sum_probs=43.8

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhhh
Q 032643           74 GVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLV  135 (136)
Q Consensus        74 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~i  135 (136)
                      ..++++.|+++.++|.++|++|.++.....++...+.+-+...+   .-+...+.++|+++.
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            34789999999999999999999999988776322222222322   356788899988764

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 ....

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=96.00  E-value=0.088  Score=49.38  Aligned_cols=81  Identities=14%  Similarity=0.114  Sum_probs=62.0

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccch----HHHH
Q 032643           54 NLPVVELRDLG-SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVET----SIAC  128 (136)
Q Consensus        54 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~----~~l~  128 (136)
                      ..|.|.+.... .+.-++.+++.++++.|++|-.+|.+.|++|++|..++.|++++=+++-.-.++. .++.    .++.
T Consensus       800 ~~~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~-~l~~~~~~~~l~  878 (895)
T PRK00275        800 FPTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQ-PLSDPQLCSRLQ  878 (895)
T ss_pred             CCCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCC-CCCCHHHHHHHH
Confidence            45788887654 3555566778899999999999999999999999998889999999998765433 2322    4466


Q ss_pred             HHHhhhh
Q 032643          129 QRLHDLV  135 (136)
Q Consensus       129 erL~~~i  135 (136)
                      ++|.+.+
T Consensus       879 ~~L~~~L  885 (895)
T PRK00275        879 DAICEQL  885 (895)
T ss_pred             HHHHHHH
Confidence            6666544

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.88  E-value=0.12  Score=47.83  Aligned_cols=80  Identities=16%  Similarity=0.127  Sum_probs=61.5

Q ss_pred             CCCeEEEEEc-CCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHh
Q 032643           54 NLPVVELRDL-GSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLH  132 (136)
Q Consensus        54 ~~p~V~V~~~-~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~  132 (136)
                      ..|.|.++.. .++.+|.+ .+.++++.|++|..+|...|++|++|...+.++.++=++...-.... ..+.+++.+.|.
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 46777655 56689999999999999999999999988788898888888754332 355678888887


Q ss_pred             hhh
Q 032643          133 DLV  135 (136)
Q Consensus       133 ~~i  135 (136)
                      +++
T Consensus       664 ~~L  666 (774)
T PRK03381        664 RAL  666 (774)
T ss_pred             HHH
Confidence            654

>PRK04374 PII uridylyl-transferase; Provisional

Probab=95.80  E-value=0.12  Score=48.48  Aligned_cols=81  Identities=16%  Similarity=0.187  Sum_probs=61.4

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 032643           54 NLPVVELRDLG-SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSIACQ  129 (136)
Q Consensus        54 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d---~~~l~e  129 (136)
                      ..|.|.+.... .+.-++-+...++++.|++|-.+|.+.|++|.+|..++.|+++.-+++-+-.++. .++   ...|.+
T Consensus       782 ~~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~-~~~~~~~~~l~~  860 (869)
T PRK04374        782 FAPRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDR-PLSESARQALRD  860 (869)
T ss_pred             CCCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCC-cCChHHHHHHHH
Confidence            45678887644 4666666778889999999999999999999999999999999999998754433 232   245555


Q ss_pred             HHhhhh
Q 032643          130 RLHDLV  135 (136)
Q Consensus       130 rL~~~i  135 (136)
                      +|.+.+
T Consensus       861 ~L~~~l  866 (869)
T PRK04374        861 ALCACL  866 (869)
T ss_pred             HHHHHh
Confidence            555443

>PRK05092 PII uridylyl-transferase; Provisional

Probab=95.76  E-value=0.12  Score=48.49  Aligned_cols=82  Identities=17%  Similarity=0.265  Sum_probs=63.1

Q ss_pred             CCCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCccc-c---hHHH
Q 032643           53 SNLPVVELRDLGS-SIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGV-E---TSIA  127 (136)
Q Consensus        53 ~~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~-d---~~~l  127 (136)
                      ...|.|.+....+ +.-++.+.+.++++.|++|..+|.+.|++|.+|..++.|+++.=+++..-.++. .+ +   ..+|
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 444555778889999999999999999999999999999999999998764433 22 2   3457


Q ss_pred             HHHHhhhh
Q 032643          128 CQRLHDLV  135 (136)
Q Consensus       128 ~erL~~~i  135 (136)
                      +++|.+++
T Consensus       907 ~~~L~~~L  914 (931)
T PRK05092        907 RRALLAAL  914 (931)
T ss_pred             HHHHHHHh
Confidence            77777665

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.58  E-value=0.099  Score=48.96  Aligned_cols=80  Identities=16%  Similarity=0.143  Sum_probs=59.4

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 032643           54 NLPVVELRDLG-SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSIACQ  129 (136)
Q Consensus        54 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d---~~~l~e  129 (136)
                      ..|.|.+..-. +..-++-+.+.+.++.|++|.++|.+.|++|.+|..++.|+|+.=+++-+=..+. -++   ...|.+
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            34677776543 4455555788899999999999999999999999999999999999888654332 355   234455


Q ss_pred             HHhhh
Q 032643          130 RLHDL  134 (136)
Q Consensus       130 rL~~~  134 (136)
                      +|.+.
T Consensus       873 ~L~~~  877 (884)
T PRK05007        873 RLTEA  877 (884)
T ss_pred             HHHHH
Confidence            55443

>smart00353 HLH helix loop helix domain

Probab=94.88  E-value=0.025  Score=34.18  Aligned_cols=22  Identities=45%  Similarity=0.650  Sum_probs=19.0

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLRERID   23 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve   23 (136)
                      ++-.+.|.+|++||++|+++++
T Consensus        31 ~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353       31 LSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Confidence            3567889999999999999886

>PRK03381 PII uridylyl-transferase; Provisional

Probab=94.88  E-value=0.31  Score=45.07  Aligned_cols=78  Identities=18%  Similarity=0.189  Sum_probs=58.3

Q ss_pred             CCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHh
Q 032643           54 NLPVVELRDLGS-SIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLH  132 (136)
Q Consensus        54 ~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~  132 (136)
                      ..|.|.+....+ +.-++-+.+.++++.|++|-.+|.+.|++|.+|..++.|++++=+++-+-.+.. .+.-.  .+.|+
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            345677765443 455666778889999999999999999999999999999999999988754433 33222  55555


Q ss_pred             hh
Q 032643          133 DL  134 (136)
Q Consensus       133 ~~  134 (136)
                      +.
T Consensus       770 ~~  771 (774)
T PRK03381        770 QA  771 (774)
T ss_pred             HH
Confidence            43

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.57  E-value=0.5  Score=43.94  Aligned_cols=81  Identities=17%  Similarity=0.072  Sum_probs=57.2

Q ss_pred             CCCeEEEEE-cCCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEE-EeCCeEEEEEEEEeeccCcccchH----HH
Q 032643           54 NLPVVELRD-LGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKISRLGVETS----IA  127 (136)
Q Consensus        54 ~~p~V~V~~-~~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtI~~qv~~~~~~~d~~----~l  127 (136)
                      ..|.|.+.. ...+.-.+.|.+.++++.|++|..+|...|++|++|..+ +.|++++=+++.+-.++. .++.+    ++
T Consensus       654 ~~~~v~~~~~~~~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~-~~~~~~~~~~i  732 (850)
T TIGR01693       654 GGPLALIDGTRPSGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGS-PPAAERVFQEL  732 (850)
T ss_pred             CCCEEEEeccCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCC-CCCcHHHHHHH
Confidence            356776643 333333345556688999999999999999999999976 789999999888876543 34433    35


Q ss_pred             HHHHhhhh
Q 032643          128 CQRLHDLV  135 (136)
Q Consensus       128 ~erL~~~i  135 (136)
                      .+.|.+.+
T Consensus       733 ~~~L~~~L  740 (850)
T TIGR01693       733 LQGLVDVL  740 (850)
T ss_pred             HHHHHHHH
Confidence            55555543

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=94.56  E-value=0.49  Score=29.91  Aligned_cols=59  Identities=15%  Similarity=0.136  Sum_probs=44.1

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEEe-CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           73 SGVQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        73 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ...++++.|.+|..++.++|+++.+.+.... ++.....+..++.+.   -.+.++-.+|+++
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            3456889999999999999999999888654 455555666666543   4557788887764

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=94.19  E-value=0.38  Score=44.99  Aligned_cols=80  Identities=15%  Similarity=0.136  Sum_probs=59.6

Q ss_pred             CCCeEEEEEcC-CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 032643           54 NLPVVELRDLG-SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSIACQ  129 (136)
Q Consensus        54 ~~p~V~V~~~~-~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d---~~~l~e  129 (136)
                      ..|.|.+..-. ...-|+-+...+.++.|++|.++|.+.|++|.+|..++.|+|+.=+++-.-..+. -++   ...|.+
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            34677775433 4556666788899999999999999999999999999999999988888654332 343   245555


Q ss_pred             HHhhh
Q 032643          130 RLHDL  134 (136)
Q Consensus       130 rL~~~  134 (136)
                      +|.+.
T Consensus       848 ~L~~~  852 (854)
T PRK01759        848 RLLSN  852 (854)
T ss_pred             HHHHH
Confidence            55443

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

Probab=94.19  E-value=0.25  Score=46.07  Aligned_cols=79  Identities=16%  Similarity=0.206  Sum_probs=60.9

Q ss_pred             CCCCeEEEEEcCCe-eEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHH
Q 032643           53 SNLPVVELRDLGSS-IEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRL  131 (136)
Q Consensus        53 ~~~p~V~V~~~~~~-~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL  131 (136)
                      ...|.|++.+..+. .-++-+.+++.++.|+++-.+|.+.|+++.+|..+++|.|+--++..+.-... .+ ...+++.|
T Consensus       776 ~i~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~~-~l-~~~~~q~l  853 (867)
T COG2844         776 PIPPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADGQ-AL-NAELRQSL  853 (867)
T ss_pred             ccCCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEeccccc-cC-CHHHHHHH
Confidence            34688999876543 55555688899999999999999999999999999999998888877775543 44 34455554


Q ss_pred             hh
Q 032643          132 HD  133 (136)
Q Consensus       132 ~~  133 (136)
                      .+
T Consensus       854 ~~  855 (867)
T COG2844         854 LQ  855 (867)
T ss_pred             HH
Confidence            43

>PRK05007 PII uridylyl-transferase; Provisional

Probab=94.10  E-value=0.76  Score=43.15  Aligned_cols=80  Identities=15%  Similarity=0.183  Sum_probs=56.0

Q ss_pred             CCCeEEEEEcC--CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEE-EeCCeEEEEEEEEeeccCcccch---HHH
Q 032643           54 NLPVVELRDLG--SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKISRLGVET---SIA  127 (136)
Q Consensus        54 ~~p~V~V~~~~--~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtI~~qv~~~~~~~d~---~~l  127 (136)
                      ..|.|.+....  ++.+|. |++.++++.|++|..+|...|++|++|... ..+|+++=+++..-.++. .++.   .++
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 DKPLVLLSKQATRGGTEIF-IWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGS-PLSQDRHQVI  764 (884)
T ss_pred             CCCeEEEEecCCCCeEEEE-EEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCC-CCCHHHHHHH
Confidence            45777787643  455554 456688999999999999999999999965 556699777776654433 2333   335


Q ss_pred             HHHHhhhh
Q 032643          128 CQRLHDLV  135 (136)
Q Consensus       128 ~erL~~~i  135 (136)
                      .+.|.+.+
T Consensus       765 ~~~L~~aL  772 (884)
T PRK05007        765 RKALEQAL  772 (884)
T ss_pred             HHHHHHHH
Confidence            66665543

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.09  E-value=0.48  Score=44.08  Aligned_cols=80  Identities=20%  Similarity=0.182  Sum_probs=61.0

Q ss_pred             CCCeEEEEEcCC-eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccc---hHHHHH
Q 032643           54 NLPVVELRDLGS-SIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVE---TSIACQ  129 (136)
Q Consensus        54 ~~p~V~V~~~~~-~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d---~~~l~e  129 (136)
                      ..|.|.+....+ ..-++-+.+.++|+.|++|.++|.+.|++|.+|..++.+++..-+++.+-.... -++   ...|.+
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 232   345555


Q ss_pred             HHhhh
Q 032643          130 RLHDL  134 (136)
Q Consensus       130 rL~~~  134 (136)
                      +|.+.
T Consensus       844 ~L~~~  848 (850)
T TIGR01693       844 VLAAS  848 (850)
T ss_pred             HHHHH
Confidence            55544

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=94.09  E-value=0.75  Score=43.03  Aligned_cols=80  Identities=11%  Similarity=0.115  Sum_probs=57.1

Q ss_pred             CCCeEEEEEcC--CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EEeCCeEEEEEEEEeeccCcccchH---HH
Q 032643           54 NLPVVELRDLG--SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGVETS---IA  127 (136)
Q Consensus        54 ~~p~V~V~~~~--~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtI~~qv~~~~~~~d~~---~l  127 (136)
                      ..|.|.++...  ++.+| .|.+.++++.|++|..+|...|++|++|.. +..+++++=+++..-.++. .++.+   ++
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 GDLLVKISNRFSRGGTEI-FIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGK-LLEFDRRRQL  740 (854)
T ss_pred             CCCEEEEEecCCCCeEEE-EEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCC-CCCHHHHHHH
Confidence            35777776543  44555 445668899999999999999999999996 4599999999988755433 34432   34


Q ss_pred             HHHHhhhh
Q 032643          128 CQRLHDLV  135 (136)
Q Consensus       128 ~erL~~~i  135 (136)
                      .+.|.+.+
T Consensus       741 ~~~L~~aL  748 (854)
T PRK01759        741 EQALTKAL  748 (854)
T ss_pred             HHHHHHHH
Confidence            55555443

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

Probab=93.55  E-value=0.63  Score=29.41  Aligned_cols=60  Identities=12%  Similarity=0.089  Sum_probs=41.4

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEEe-CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           73 SGVQRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        73 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ...++++.|.+|+.+|.++|+++...+.+.. ++  ..++++.+.-....-...++-++|+++
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            3446789999999999999999999887543 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.

>PRK04374 PII uridylyl-transferase; Provisional

Probab=93.44  E-value=0.96  Score=42.52  Aligned_cols=81  Identities=16%  Similarity=0.239  Sum_probs=57.0

Q ss_pred             CCCeEEEE---EcCCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EEeCCeEEEEEEEEeeccCcccchHHHHH
Q 032643           54 NLPVVELR---DLGSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGVETSIACQ  129 (136)
Q Consensus        54 ~~p~V~V~---~~~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtI~~qv~~~~~~~d~~~l~e  129 (136)
                      ..|.|.+.   +..++.+|.+.+ .+++++|+++-.+|...|++|++|.. +..+|.++=+++..-.+....-...++.+
T Consensus       675 ~~~~v~~~~~~~~~~~~~v~v~~-~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~  753 (869)
T PRK04374        675 GQTLVKARRAVPDNDALEVFVYS-PDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAA  753 (869)
T ss_pred             CCCeEEEeeeccCCCeEEEEEEe-CCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHH
Confidence            34655553   345778886654 47899999999999999999999996 46899999999887543321122344555


Q ss_pred             HHhhhh
Q 032643          130 RLHDLV  135 (136)
Q Consensus       130 rL~~~i  135 (136)
                      .|.+.+
T Consensus       754 ~l~~~l  759 (869)
T PRK04374        754 ALRQVL  759 (869)
T ss_pred             HHHHHH
Confidence            555543

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

Probab=93.43  E-value=0.87  Score=27.79  Aligned_cols=56  Identities=13%  Similarity=0.169  Sum_probs=39.3

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEEe-----CCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFSTI-----GDKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-----~~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      .++++.|.+++.+|.++|+++.+..+...     ++.....+..++.+   .-+...+-++|++
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            46899999999999999999998887654     24444445555532   2445677777765

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.

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

Probab=93.26  E-value=1.3  Score=28.36  Aligned_cols=59  Identities=8%  Similarity=-0.032  Sum_probs=40.9

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEEeCC-eEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFSTIGD-KIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~-r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      .++++.|++||.+|.+.|+.+.+--|.-..+ .--|.+..++.......+...+-++|++
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            3579999999999999999999997765443 5557777777643112334455555554

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

>PRK05092 PII uridylyl-transferase; Provisional

Probab=93.22  E-value=1.3  Score=41.69  Aligned_cols=80  Identities=18%  Similarity=0.178  Sum_probs=56.1

Q ss_pred             CCCeEEEEEcC--CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEE-EeCCeEEEEEEEEeeccCcccc---hHHH
Q 032643           54 NLPVVELRDLG--SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFS-TIGDKIFHTVRAQAKISRLGVE---TSIA  127 (136)
Q Consensus        54 ~~p~V~V~~~~--~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s-~~~~r~fhtI~~qv~~~~~~~d---~~~l  127 (136)
                      ..|.|.++...  ++.+|.+++ .++++.|+++..+|...|++|++|... ..|++++=++..+-......-+   ..+|
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 5788888878766433321112   3455


Q ss_pred             HHHHhhh
Q 032643          128 CQRLHDL  134 (136)
Q Consensus       128 ~erL~~~  134 (136)
                      .+.|.++
T Consensus       797 ~~~L~~~  803 (931)
T PRK05092        797 AKAIEDA  803 (931)
T ss_pred             HHHHHHH
Confidence            5555544

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=92.43  E-value=1.8  Score=40.79  Aligned_cols=80  Identities=6%  Similarity=0.074  Sum_probs=57.0

Q ss_pred             CCCeEEEEEcC-----CeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EEeCCeEEEEEEEEeeccCccc-ch--
Q 032643           54 NLPVVELRDLG-----SSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKISRLGV-ET--  124 (136)
Q Consensus        54 ~~p~V~V~~~~-----~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtI~~qv~~~~~~~-d~--  124 (136)
                      ..|.|.+++..     ++.+|.+ .+.++++.|+++..+|...|++|++|.. |..+|.++=+++.+-.++.... +.  
T Consensus       687 ~~~~v~~~~~~~~~~~~~t~V~V-~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~~~~~~~~r  765 (895)
T PRK00275        687 GGPLVLIKETTQREFEGGTQIFI-YAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGEPIGDNPAR  765 (895)
T ss_pred             CCCeEEEEecCccCCCCeEEEEE-EeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCCCccchHHH
Confidence            34666676543     5677755 4558899999999999999999999995 6788899999888765544212 22  


Q ss_pred             -HHHHHHHhhh
Q 032643          125 -SIACQRLHDL  134 (136)
Q Consensus       125 -~~l~erL~~~  134 (136)
                       .++.+.|.+.
T Consensus       766 ~~~i~~~L~~~  776 (895)
T PRK00275        766 IEQIREGLTEA  776 (895)
T ss_pred             HHHHHHHHHHH
Confidence             2355555544

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

Probab=92.31  E-value=0.12  Score=31.67  Aligned_cols=22  Identities=41%  Similarity=0.532  Sum_probs=18.2

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLRERID   23 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve   23 (136)
                      ++-...|..|++||+.|+++++
T Consensus        39 ~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083          39 LSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhC
Confidence            3556789999999999998763

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=92.19  E-value=0.14  Score=31.33  Aligned_cols=18  Identities=50%  Similarity=0.564  Sum_probs=15.5

Q ss_pred             CChhhhHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLR   19 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq   19 (136)
                      +|-.+.|..|+.||++||
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            356778999999999997

; 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 ....

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

Probab=92.04  E-value=0.2  Score=31.14  Aligned_cols=58  Identities=14%  Similarity=0.146  Sum_probs=40.8

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ++...+++++|.++..+|.++|+.+.+.+....++..+-.+...+.      +...+-++|+++
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            3455678999999999999999999776544334554444444442      667888888763

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-

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

Probab=91.89  E-value=1  Score=27.37  Aligned_cols=50  Identities=22%  Similarity=0.181  Sum_probs=34.4

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEEeC--CeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           76 QRNFMLYEVISILEEEGAQVVSASFSTIG--DKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        76 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      ++++.|.+++.+|.++|+.+.+...+...  +.....++.+  .      ..++.+.|++
T Consensus         8 d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve--~------~~~~~~~L~~   59 (65)
T cd04882           8 DKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE--D------IEKAIEVLQE   59 (65)
T ss_pred             CCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC--C------HHHHHHHHHH
Confidence            58999999999999999999877654332  4444444433  2      4566666654

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.

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=91.67  E-value=1.6  Score=35.81  Aligned_cols=62  Identities=18%  Similarity=0.116  Sum_probs=47.4

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEE--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -+.|.++++...+|-++|-+.|+++.+.+.++  .++.  .++..++.-..-..+.++|.+.|.++
T Consensus        10 tv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~--F~m~i~v~~~~~~~~~~~L~~~L~~l   73 (286)
T PRK06027         10 TLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGR--FFMRVEFEGDGLIFNLETLRADFAAL   73 (286)
T ss_pred             EEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCe--EEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence            34677899999999999999999999999998  7773  44455554311235578898888765

>PRK03059 PII uridylyl-transferase; Provisional

Probab=91.57  E-value=2.5  Score=39.62  Aligned_cols=64  Identities=14%  Similarity=0.253  Sum_probs=51.0

Q ss_pred             CCCeEEEEEc--CCeeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEE-EEeCCeEEEEEEEEeecc
Q 032643           54 NLPVVELRDL--GSSIEVVLISGVQRNFMLYEVISILEEEGAQVVSASF-STIGDKIFHTVRAQAKIS  118 (136)
Q Consensus        54 ~~p~V~V~~~--~~~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~-s~~~~r~fhtI~~qv~~~  118 (136)
                      ..|.|.++..  .++.+|.+.| .++++.|+++-.+|...|++|++|.. +..+|.++=+++.+-...
T Consensus       664 ~~~~v~~~~~~~~~~~~v~i~~-~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~  730 (856)
T PRK03059        664 DTPIVRARLSPAGEGLQVMVYT-PDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEE  730 (856)
T ss_pred             CCCeEEEEecCCCCeEEEEEEe-cCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCC
Confidence            3465557653  4677886654 48899999999999999999999997 678999999999876443

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

Probab=91.56  E-value=1.8  Score=26.13  Aligned_cols=55  Identities=13%  Similarity=0.092  Sum_probs=39.7

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEEeC--CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           74 GVQRNFMLYEVISILEEEGAQVVSASFSTIG--DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        74 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..+.+++|.++..+|.++|+.+.+..+...+  +...  +...+.+ .   ....+-++|+++
T Consensus         6 ~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~--~~~~v~~-~---~~~~l~~~l~~~   62 (71)
T cd04879           6 HKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAY--MVLDVDS-P---VPEEVLEELKAL   62 (71)
T ss_pred             ecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEE--EEEEcCC-C---CCHHHHHHHHcC
Confidence            3457899999999999999999999876544  4444  4444433 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

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=91.55  E-value=1.5  Score=36.01  Aligned_cols=61  Identities=13%  Similarity=0.128  Sum_probs=49.6

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEE-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.|.++++...+|-+.|-+.|+++.+.+..+ .++..|+ +.+++..+. +.+.+.|++.|.++
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 4555555 577886544 67889999998875

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=91.42  E-value=1.8  Score=35.46  Aligned_cols=63  Identities=16%  Similarity=0.308  Sum_probs=47.7

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeC--CeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIG--DKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      |+.+.|.++++..+.|=+.|-+.|+++++.+.+.-.  ++.|  +..++..+...++.+.+.+.|.+
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            345677889999999999999999999999988754  5444  44455433334677888888877

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.

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

Probab=91.42  E-value=1.4  Score=24.17  Aligned_cols=54  Identities=24%  Similarity=0.220  Sum_probs=34.9

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHH
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRL  131 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL  131 (136)
                      .+++..|.+++.+|.+.|+.+.....+..++.-...+...+...  . +..++.++|
T Consensus         6 ~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~l   59 (60)
T cd02116           6 PDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGD--G-DLEKLLEAL   59 (60)
T ss_pred             cCCCchHHHHHHHHHHCCCcEEEEEeEEcCCCCeEEEEEEEech--H-HHHHHHHHh
Confidence            35678999999999999999999987655422122233333321  1 556666655

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

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

Probab=91.37  E-value=0.99  Score=28.10  Aligned_cols=57  Identities=16%  Similarity=0.251  Sum_probs=41.7

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEE--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +...+.++.+.++.++|.++|+++.+...+.  -+++.+..++.+...      ...+-++|++.
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            3455689999999999999999998887654  457777777665421      34666777653

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=91.35  E-value=1.8  Score=25.19  Aligned_cols=58  Identities=12%  Similarity=0.156  Sum_probs=40.3

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEEeC-CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           74 GVQRNFMLYEVISILEEEGAQVVSASFSTIG-DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        74 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~-~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..++++.+.++.+.|.++|+++.+......+ +.....+...+..   ..+..++.++|..+
T Consensus         5 ~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~   63 (71)
T cd04876           5 AIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRD---LEHLARIMRKLRQI   63 (71)
T ss_pred             EeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECC---HHHHHHHHHHHhCC
Confidence            3457889999999999999999998876554 4333334443332   34667777777653

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

>PRK08577 hypothetical protein; Provisional

Probab=91.12  E-value=2.1  Score=30.93  Aligned_cols=60  Identities=13%  Similarity=0.219  Sum_probs=43.0

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEEeC-CeEEE-EEEEEeeccCcccchHHHHHHHhhh
Q 032643           73 SGVQRNFMLYEVISILEEEGAQVVSASFSTIG-DKIFH-TVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        73 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~-~r~fh-tI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ...+.++.|.++..+|.++|+++.+.++.... +..++ .+...+.+.  ..+.+.+.++|+++
T Consensus        62 ~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~~--~~~l~~l~~~L~~l  123 (136)
T PRK08577         62 VVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSKS--DIDLEELEEELKKL  123 (136)
T ss_pred             EEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCCc--hhhHHHHHHHHHcC
Confidence            34567899999999999999999998876544 44333 334455432  25678899988764

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

Probab=90.95  E-value=1.4  Score=28.32  Aligned_cols=56  Identities=11%  Similarity=0.103  Sum_probs=40.0

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           73 SGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        73 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .+.++++.|.+|..++.++|+.+.+..+..- +.++  +..++.+   --+++.+-.||+++
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   23567888888764

ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence

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

Probab=90.71  E-value=2.5  Score=25.60  Aligned_cols=55  Identities=11%  Similarity=0.151  Sum_probs=39.1

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEEe--CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           74 GVQRNFMLYEVISILEEEGAQVVSASFSTI--GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        74 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~--~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..+.++.|.+++..|.++|+.+.+......  ++..+..  ..+.+.    +...+-++|+++
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  3343333  455432    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=90.23  E-value=0.68  Score=31.96  Aligned_cols=33  Identities=24%  Similarity=0.466  Sum_probs=28.3

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 032643            3 SQEDQLDLACCYIKQLRERIDKLNRMKGQAMKS   35 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~~   35 (136)
                      |-.--+-|+.+||+.|+..|+.|.++=-+|+..
T Consensus        46 saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         46 SAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            445568899999999999999999998888765

>PRK04435 hypothetical protein; Provisional

Probab=90.18  E-value=2.5  Score=31.29  Aligned_cols=75  Identities=13%  Similarity=0.180  Sum_probs=51.9

Q ss_pred             EEEEEcCCeeEEEEE-ecCCCcccHHHHHHHHHHcCceEEEeEEEE-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           58 VELRDLGSSIEVVLI-SGVQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        58 V~V~~~~~~~eV~l~-s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +..+....|=.+.+. ...+.++.|++|+.+|.++|++|..-+.+. .++...-+|-.++.+.  ..+...+-++|+++
T Consensus        59 f~~~~~~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~--~~~L~~Li~~L~~i  135 (147)
T PRK04435         59 FPFDEMVKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSM--EGDIDELLEKLRNL  135 (147)
T ss_pred             ECccccCCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCCh--HHHHHHHHHHHHcC
Confidence            333443344444442 233578999999999999999999988764 4566666677776542  35778888888764

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

Probab=90.06  E-value=2.9  Score=25.40  Aligned_cols=57  Identities=7%  Similarity=0.052  Sum_probs=38.2

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           73 SGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        73 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      ...+.++.|++++..|.++|+.+.+......++..+ .+...+...   -....+-++|++
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            445678999999999999999999887654432222 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.

>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=88.36  E-value=5.1  Score=25.92  Aligned_cols=42  Identities=14%  Similarity=0.145  Sum_probs=34.1

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEEe-CCeEEEEEEEEeec
Q 032643           76 QRNFMLYEVISILEEEGAQVVSASFSTI-GDKIFHTVRAQAKI  117 (136)
Q Consensus        76 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~~r~fhtI~~qv~~  117 (136)
                      ++++.|++++.+|.+.|+.+.+-.+.-. ++.--|.++.+...
T Consensus        10 d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~   52 (80)
T cd04905          10 NKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEG   52 (80)
T ss_pred             CCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEEC
Confidence            5789999999999999999998876544 34666888888764

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

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=88.22  E-value=3.1  Score=34.22  Aligned_cols=65  Identities=15%  Similarity=0.180  Sum_probs=48.8

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEE--EeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFS--TIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s--~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      |+.+.|.++++....|=..|-|.|+++++.+..  ...+..|=.+........ .++.+.|.+.|.++
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            444567789999999999999999999999985  455666655444432222 67889999888765

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=87.75  E-value=3.5  Score=31.95  Aligned_cols=63  Identities=6%  Similarity=0.056  Sum_probs=53.8

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEe----CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTI----GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~----~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -+.|.++|+..++|-++|-+.|+++.+-++-+.    .+.-.|.+++++.-+. +.+...|++.|.++
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            346888999999999999999999999888755    4677888999998775 77889999988876

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

Probab=87.29  E-value=4.4  Score=25.20  Aligned_cols=50  Identities=20%  Similarity=0.228  Sum_probs=35.5

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           76 QRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        76 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      ++++.|.+|+.+|.++|+++.+-.....+++  -.++....      |.+++.+-|++
T Consensus        10 d~pG~La~v~~~l~~~~inI~~i~~~~~~~~--~~~rl~~~------~~~~~~~~L~~   59 (66)
T cd04908          10 NKPGRLAAVTEILSEAGINIRALSIADTSEF--GILRLIVS------DPDKAKEALKE   59 (66)
T ss_pred             CCCChHHHHHHHHHHCCCCEEEEEEEecCCC--CEEEEEEC------CHHHHHHHHHH
Confidence            5799999999999999999998876655554  33444332      23466666654

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=86.94  E-value=4.4  Score=34.42  Aligned_cols=67  Identities=13%  Similarity=0.114  Sum_probs=47.8

Q ss_pred             CeeEEEE-EecCCCcccHHHHHHHHHHcCceEEEeEEEEe-----CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           65 SSIEVVL-ISGVQRNFMLYEVISILEEEGAQVVSASFSTI-----GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        65 ~~~eV~l-~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-----~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .|+.+.+ +...++++.|.+|+.+|-++|++|.+.++..-     ++...-.+..+|.+.   -.+.++-.||++.
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 45667899999999999999999999998643     455445555666542   3557888888763

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

Probab=86.30  E-value=6  Score=24.91  Aligned_cols=28  Identities=21%  Similarity=0.152  Sum_probs=24.8

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEEe
Q 032643           76 QRNFMLYEVISILEEEGAQVVSASFSTI  103 (136)
Q Consensus        76 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~  103 (136)
                      ++|+.|.+++..|.++|+.+++-.....
T Consensus         8 d~pG~L~~l~~~i~~~g~nI~~i~~~~~   35 (72)
T cd04884           8 DKPGTLKPVVDTLREFNARIISILTAFE   35 (72)
T ss_pred             CCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence            5899999999999999999999876654

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

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

Probab=85.66  E-value=5.8  Score=23.85  Aligned_cols=57  Identities=11%  Similarity=0.064  Sum_probs=39.3

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEEe--CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           74 GVQRNFMLYEVISILEEEGAQVVSASFSTI--GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        74 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~--~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..+.++.|.++...|.++|+.+.+......  ++.....+...+.  .  -+.+.+-++|+++
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            346788999999999999999998887653  3444444444432  1  3457777777654

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

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=84.79  E-value=3  Score=32.32  Aligned_cols=59  Identities=12%  Similarity=0.080  Sum_probs=45.8

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +-|.++++...+|-++|.+.|+++++++.+..++  +.++...|..+.  ....+|...|..+
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            4577899999999999999999999999999998  444444554443  3557777777654

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

Probab=84.50  E-value=4.7  Score=25.53  Aligned_cols=59  Identities=15%  Similarity=0.188  Sum_probs=44.1

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhhhC
Q 032643           76 QRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD  136 (136)
Q Consensus        76 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~i~  136 (136)
                      ++++-|.+|+.+|.--|+++-+=+.+..++--++.|-..+.+..  -....+...|.++++
T Consensus         1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~~--~~i~~l~~Ql~Klid   59 (63)
T PF13710_consen    1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGDD--REIEQLVKQLEKLID   59 (63)
T ss_dssp             SSTTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES-C--CHHHHHHHHHHCSTT
T ss_pred             CCcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeCc--hhHHHHHHHHhccCC
Confidence            35788999999999999999988888766655666666776532  355789999988875

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

Probab=83.30  E-value=2  Score=29.82  Aligned_cols=64  Identities=19%  Similarity=0.203  Sum_probs=50.6

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      |+-++|.++++--..|-.+|-|.|+++++-+=+...+++=-.+.  |..+.-..|.+.+.++|.+.
T Consensus         5 vITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~l--V~~~~~~~d~~~lr~~l~~~   68 (90)
T COG3830           5 VITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIML--VDISKEVVDFAALRDELAAE   68 (90)
T ss_pred             EEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeE--EcCChHhccHHHHHHHHHHH
Confidence            44467888999999999999999999999998888886644444  44443468889999888754

>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=82.40  E-value=9  Score=23.44  Aligned_cols=58  Identities=16%  Similarity=0.154  Sum_probs=39.8

Q ss_pred             cCCCcccHHHHHHHHHHcCceEEEeEEEEe-C-CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           74 GVQRNFMLYEVISILEEEGAQVVSASFSTI-G-DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        74 ~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~-~-~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..++++.|.++..+|.++|+.+.+...... + +...-.+...+.+   .-+..++-++|+++
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 4443344444432   34556777777753

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.

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

Probab=81.92  E-value=6.5  Score=23.39  Aligned_cols=41  Identities=20%  Similarity=0.126  Sum_probs=31.1

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEEeC-CeEEEEEEEEe
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFSTIG-DKIFHTVRAQA  115 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~-~r~fhtI~~qv  115 (136)
                      .++++.|.++.+.|-++|+++.+......+ ++.+..|....
T Consensus         6 ~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~~   47 (56)
T cd04889           6 ENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFSD   47 (56)
T ss_pred             CCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEECC
Confidence            357899999999999999999887765444 66665555443

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

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	136
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	97.2
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	97.11
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	96.96
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	96.56
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	96.54
1a0a_A	63	BHLH, protein (phosphate system positive regulator	95.6
1u8s_A	192	Glycine cleavage system transcriptional repressor,	95.42
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	95.33
2nyi_A	195	Unknown protein; protein structure initiative, PSI	94.79
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	94.02
1u8s_A	192	Glycine cleavage system transcriptional repressor,	93.56
4ati_A	118	MITF, microphthalmia-associated transcription fact	93.4
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	93.19
2nyi_A	195	Unknown protein; protein structure initiative, PSI	93.12
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	92.91
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	90.6
3he4_B	46	Synzip5; heterodimeric coiled-coil, de novo protei	89.82
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	89.21
4ath_A	83	MITF, microphthalmia-associated transcription fact	88.42
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	88.13
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	87.18
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	86.85
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	86.58
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	86.2
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	85.77
4h10_B	71	Circadian locomoter output cycles protein kaput; B	82.53
2f1f_A	164	Acetolactate synthase isozyme III small subunit; f	80.72
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	80.38

>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=97.20  E-value=0.00041  Score=45.59  Aligned_cols=33  Identities=21%  Similarity=0.236  Sum_probs=29.0

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      +|-.+.|..|+.||++||+++++|+.+.++|..
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            455678999999999999999999999888754

>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=97.11  E-value=0.00065  Score=44.81  Aligned_cols=33  Identities=21%  Similarity=0.236  Sum_probs=28.1

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      +|-.+.|..|++||++||+++++|..++++|..
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            355678999999999999999999988887754

>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=96.96  E-value=0.0011  Score=43.89  Aligned_cols=35  Identities=23%  Similarity=0.246  Sum_probs=29.9

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 032643            2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMKSI   36 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~~~   36 (136)
                      ++-.+.|.+|+.||++||++++.|.++.+.|....
T Consensus        39 ~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   73 (82)
T 1am9_A           39 LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAV   73 (82)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999988887643

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

Probab=96.56  E-value=0.0034  Score=41.43  Aligned_cols=32  Identities=22%  Similarity=0.080  Sum_probs=28.0

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            3 SQEDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      |-.+.|..|+.||++||++.++|..+++.|..
T Consensus        37 sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A           37 TTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55688999999999999999999998887754

>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=96.54  E-value=0.039  Score=35.49  Aligned_cols=60  Identities=8%  Similarity=0.093  Sum_probs=49.2

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.+.++++.|.+|..+|-+.|+++.+.+....++..+-.+..++.+   ..+...+.++|+++
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            5677899999999999999999999999888777766666666643   35778999998865

>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=95.60  E-value=0.0025  Score=40.26  Aligned_cols=21  Identities=29%  Similarity=0.558  Sum_probs=18.4

Q ss_pred             CChhhhHHHHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLRERI   22 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kv   22 (136)
                      +|-.+.|+.|+.||++||+++
T Consensus        41 ~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A           41 PSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             SCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccHHHHHHHHHHHHHHHHHHh
Confidence            467889999999999999865

>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=95.42  E-value=0.1  Score=38.28  Aligned_cols=60  Identities=13%  Similarity=0.199  Sum_probs=48.6

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .+++.++++.+++|-.+|.+.|+++++++.....++.|-++......    .+...|.+.|.++
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            34566889999999999999999999999888888888888887642    3567777777654

>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=95.33  E-value=0.024  Score=37.88  Aligned_cols=30  Identities=20%  Similarity=0.118  Sum_probs=23.8

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032643            4 QEDQLDLACCYIKQLRERIDKLNRMKGQAM   33 (136)
Q Consensus         4 ~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~   33 (136)
                      --..|..|+.||++|+++..+|...++.|.
T Consensus        43 K~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A           43 KVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345789999999999999988777665543

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

Probab=94.79  E-value=0.17  Score=37.60  Aligned_cols=66  Identities=18%  Similarity=0.142  Sum_probs=48.1

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ++.+++.++++.++.|-.+|.+.|+++++|.-....++.|=++..............+|.+.|..+
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            344567789999999999999999999999988888887777777654210001156677666543

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

Probab=94.02  E-value=0.25  Score=31.00  Aligned_cols=60  Identities=10%  Similarity=0.122  Sum_probs=43.2

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +...++++.|.+|..+|.+.|+++.+......++.....+..++.+   .-+...+-++|+++
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            3455789999999999999999999999877666333444444432   24556777777654

>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=93.56  E-value=0.55  Score=34.29  Aligned_cols=64  Identities=13%  Similarity=0.133  Sum_probs=47.4

Q ss_pred             EEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeC--------CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           68 EVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIG--------DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        68 eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~--------~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -++.+.+.++++.+++|..+|-+.|+++.++...+.+        ++.|=.+.....  . +.+.+.|.+.|.++
T Consensus        94 ~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~~~~--~-~~~~~~l~~~l~~~  165 (192)
T 1u8s_A           94 VEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVD--S-GCNLMQLQEEFDAL  165 (192)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEEC--T-TSCHHHHHHHHHHH
T ss_pred             EEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEEeCC--C-CCCHHHHHHHHHHH
Confidence            3444566779999999999999999999999876543        344444554432  2 66889999998865

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

Probab=93.40  E-value=0.075  Score=37.25  Aligned_cols=26  Identities=15%  Similarity=0.351  Sum_probs=22.3

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHH
Q 032643            4 QEDQLDLACCYIKQLRERIDKLNRMK   29 (136)
Q Consensus         4 ~~d~l~eA~~YIk~Lq~kve~L~~kk   29 (136)
                      -..-|..|+.||++||+++++|.+..
T Consensus        65 Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           65 KGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44678899999999999999998753

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

Probab=93.19  E-value=0.044  Score=34.12  Aligned_cols=22  Identities=41%  Similarity=0.437  Sum_probs=19.1

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLRERID   23 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve   23 (136)
                      +|-.++|-.|++||.+||+.++
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            5677899999999999998764

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

Probab=93.12  E-value=0.55  Score=34.73  Aligned_cols=62  Identities=15%  Similarity=0.148  Sum_probs=46.9

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeC------CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIG------DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~------~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ++.++|.++++.+++|-.+|-+.|+++.++...+.+      ++.|=.+.....  . ..+ ..|.+.|.++
T Consensus        95 iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~~--~-~~~-~~l~~~l~~~  162 (195)
T 2nyi_A           95 ELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAFP--F-PLY-QEVVTALSRV  162 (195)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEEE--G-GGH-HHHHHHHHHH
T ss_pred             EEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEcC--C-Ccc-HHHHHHHHHH
Confidence            444567789999999999999999999999987665      455555555543  2 456 8888888754

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

Probab=92.91  E-value=0.07  Score=34.73  Aligned_cols=22  Identities=23%  Similarity=0.117  Sum_probs=19.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHH
Q 032643            5 EDQLDLACCYIKQLRERIDKLN   26 (136)
Q Consensus         5 ~d~l~eA~~YIk~Lq~kve~L~   26 (136)
                      ...|..|+.||+.||+++++++
T Consensus        44 ~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A           44 LLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999874

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

Probab=90.60  E-value=0.86  Score=36.87  Aligned_cols=64  Identities=9%  Similarity=0.167  Sum_probs=52.6

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      |+.++|.++++..+.|-..|-+.|+++++++.+..++++|=.+++.+...  .++.+.|.+.|..+
T Consensus        14 ~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~~~--~~~~~~l~~~l~~~   77 (415)
T 3p96_A           14 LITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCPAD--VADGPALRHDVEAA   77 (415)
T ss_dssp             EEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEECHH--HHTSHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEecCC--cCCHHHHHHHHHHH
Confidence            33456778999999999999999999999999999999999898888653  24557888877654

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

Probab=89.82  E-value=0.58  Score=26.87  Aligned_cols=30  Identities=23%  Similarity=0.307  Sum_probs=24.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            5 EDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         5 ~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      +.++.|--|||++|.+|--+|+.-|+-|+.
T Consensus         2 sntvkelknyiqeleernaelknlkehlkf   31 (46)
T 3he4_B            2 SNTVKELKNYIQELEERNAELKNLKEHLKF   31 (46)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHhHHHHhHHHHHHH
Confidence            457888899999999999999887776654

>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=89.21  E-value=0.1  Score=33.31  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=17.8

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLRERID   23 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve   23 (136)
                      +|=.+.|-.|++||.+||+.++
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

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

Probab=88.42  E-value=0.53  Score=31.20  Aligned_cols=24  Identities=17%  Similarity=0.376  Sum_probs=19.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHH
Q 032643            7 QLDLACCYIKQLRERIDKLNRMKG   30 (136)
Q Consensus         7 ~l~eA~~YIk~Lq~kve~L~~kk~   30 (136)
                      -|..|+.||++||+...++.+.-.
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            477899999999998888876444

>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=88.13  E-value=0.089  Score=32.71  Aligned_cols=20  Identities=35%  Similarity=0.421  Sum_probs=16.8

Q ss_pred             ChhhhHHHHHHHHHHHHHHH
Q 032643            3 SQEDQLDLACCYIKQLRERI   22 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kv   22 (136)
                      +-.+.|..|+.||++||++.
T Consensus        44 ~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A           44 SKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CTTTTTTTTHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHHHHHHHHh
Confidence            55678899999999999764

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

Probab=87.18  E-value=2.7  Score=33.41  Aligned_cols=65  Identities=9%  Similarity=0.084  Sum_probs=46.2

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEE--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           70 VLISGVQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        70 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..++|.++++...+|-..|-+.|+++++++...  ..++.|=.+.+...-+...++.+.|.+.|.++
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            345667889999999999999999999999773  45566555554443112247788899888654

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

Probab=86.85  E-value=2.8  Score=33.48  Aligned_cols=64  Identities=14%  Similarity=0.115  Sum_probs=47.3

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEe--CCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFSTI--GDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~--~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      |..++|.++++...+|-..|-+.|+++++++....  +++.|=.+.+..  +...++.+.|.+.|..+
T Consensus        24 iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~FfMr~~~~~--~~~~~~~~~L~~~l~~l   89 (302)
T 3o1l_A           24 RLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHEIRA--DTLPFDLDGFREAFTPI   89 (302)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEEEEEEEEG--GGSSSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEEEEEEEec--CCCCCCHHHHHHHHHHH
Confidence            34456778999999999999999999999998754  455554444443  33247788999888654

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

Probab=86.58  E-value=3  Score=32.96  Aligned_cols=62  Identities=11%  Similarity=-0.038  Sum_probs=46.7

Q ss_pred             EEEecCCCcccHHHHHHHHHHcCceEEEeEEEE--eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           70 VLISGVQRNFMLYEVISILEEEGAQVVSASFST--IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        70 ~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~--~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ..+++.++++...+|-..|-+.|+++++.+...  ..++.|=.+.+..  +. .++.+.|.+.|.++
T Consensus        11 Ltv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~--~~-~~~~~~L~~~f~~l   74 (286)
T 3n0v_A           11 LTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQ--PD-DFDEAGFRAGLAER   74 (286)
T ss_dssp             EEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEEC--CS-SCCHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeEEEEEEec--CC-CCCHHHHHHHHHHH
Confidence            345677889999999999999999999999773  4455554444443  33 57889999888754

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

Probab=86.20  E-value=3.5  Score=32.66  Aligned_cols=64  Identities=19%  Similarity=0.141  Sum_probs=48.1

Q ss_pred             EEEEecCCCcccHHHHHHHHHHcCceEEEeEEE--EeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           69 VVLISGVQRNFMLYEVISILEEEGAQVVSASFS--TIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        69 V~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s--~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      |..++|.++++...+|-..|-+.|+++++.+..  ..+++.|=.+.+.+..  ..++.+.|.+.|..+
T Consensus         8 iLtv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~--~~~~~~~L~~~f~~l   73 (288)
T 3obi_A            8 VLTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVVFNAAA--KVIPLASLRTGFGVI   73 (288)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEESS--CCCCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEEEEcCC--CCCCHHHHHHHHHHH
Confidence            334567789999999999999999999999975  3456666556665543  247788999888654

>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=85.77  E-value=1.8  Score=33.55  Aligned_cols=57  Identities=16%  Similarity=0.167  Sum_probs=40.9

Q ss_pred             ecCCCcccHHHHHHHHHHcCceEEEeEEEEeC----CeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           73 SGVQRNFMLYEVISILEEEGAQVVSASFSTIG----DKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        73 s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~----~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      ...++++.|++|+.+|-+++.++.+.+.+...    +...+ ++.++.+   . ++.++-++|+++
T Consensus        10 ~a~DRpGLLsDIt~vLAe~kiNIltIn~~~~~kG~~ng~A~-I~IEV~d---~-~Le~LL~kLrkI   70 (223)
T 1y7p_A           10 IAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKAL-IYFEIEG---G-DFEKILERVKTF   70 (223)
T ss_dssp             EEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEE-EEEEECS---S-CHHHHHHHHHTC
T ss_pred             EEcCCCCHHHHHHHHHHHcCCCceEEEEEccccCCcCCEEE-EEEEECC---C-CHHHHHHHHhCC
Confidence            45578999999999999999999999988754    43333 3377764   2 889999999875

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

Probab=82.53  E-value=0.86  Score=29.20  Aligned_cols=21  Identities=14%  Similarity=0.192  Sum_probs=17.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHH
Q 032643            5 EDQLDLACCYIKQLRERIDKL   25 (136)
Q Consensus         5 ~d~l~eA~~YIk~Lq~kve~L   25 (136)
                      .+-|..|+.||++||++..=|
T Consensus        44 ~sIL~~aI~yik~Lq~~~~~~   64 (71)
T 4h10_B           44 STVLQKSIDFLRKHKEITAWL   64 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhhhHH
Confidence            456889999999999987544

>2f1f_A Acetolactate synthase isozyme III small subunit; ferredoxin fold, ACT domain, transferase; HET: P33 1PE; 1.75A {Escherichia coli} SCOP: d.58.18.6 d.58.18.6

Probab=80.72  E-value=2.5  Score=30.95  Aligned_cols=60  Identities=20%  Similarity=0.218  Sum_probs=42.3

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhhhC
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDLVD  136 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~i~  136 (136)
                      .++++.|++|..+|.+.|+++.+.+.....+.-+..|...+...  --..+.+..+|+++++
T Consensus        11 ~NrpGvLarIt~lfs~rg~NI~Sl~v~~t~d~~~sriti~V~~d--~~~leqI~kqL~Kl~d   70 (164)
T 2f1f_A           11 ENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGD--EKVLEQIEKQLHKLVD   70 (164)
T ss_dssp             ECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEEEESC--HHHHHHHHHHHHHSTT
T ss_pred             eCCCcHHHHHHHHHHHCCCCeeeceeeecCCCCEEEEEEEEecc--HHHHHHHHHHHcCCCC
Confidence            47899999999999999999999888654432234444444322  2345788888887754

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

Probab=80.38  E-value=4.5  Score=27.90  Aligned_cols=57  Identities=11%  Similarity=0.051  Sum_probs=39.5

Q ss_pred             EecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           72 ISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        72 ~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      +.+.+++++|.+|+++|-+.|+++.+...... +.    +...+.... .-+...+.++|+++
T Consensus         5 v~~~dr~g~l~~i~~~l~~~~~ni~~~~~~~~-g~----i~~~~~~~~-~~~~~~L~~~l~~i   61 (190)
T 2jhe_A            5 VFCEDRLGLTRELLDLLVLRGIDLRGIEIDPI-GR----IYLNFAELE-FESFSSLMAEIRRI   61 (190)
T ss_dssp             EEECSCTTHHHHHHHHHHHTTCCEEEEEEETT-TE----EEEEECCCC-HHHHHHHHHHHHHS
T ss_pred             EEEecCCcHHHHHHHHHHHcCCCeEEEEEecC-CE----EEEEEEeCC-HHHHHHHHHHHHcC
Confidence            35668899999999999999999999998654 33    334443211 23356666666654

---

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	136
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	97.21
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	97.05
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	96.8
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	96.78
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	96.66
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.42
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	95.96
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	95.55
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	95.01
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	93.97
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	91.94
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	88.71
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	82.72
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	81.89

>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=97.21  E-value=0.00023  Score=43.10  Aligned_cols=33  Identities=24%  Similarity=0.155  Sum_probs=27.9

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 032643            3 SQEDQLDLACCYIKQLRERIDKLNRMKGQAMKS   35 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~~   35 (136)
                      +-..-|.+|+.||+.||+++++|+++.+.|...
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            344678999999999999999999988877654

>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=97.05  E-value=0.0004  Score=43.78  Aligned_cols=33  Identities=21%  Similarity=0.059  Sum_probs=28.7

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      +|-.+.|.+|++||+.|++++++|..+++.|..
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            356788999999999999999999998887754

>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=96.80  E-value=0.00081  Score=43.13  Aligned_cols=33  Identities=21%  Similarity=0.131  Sum_probs=28.3

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            2 LSQEDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      +|-.+.|..|++||++|++++++|..+++.|..
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            456778999999999999999999988877654

>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=96.78  E-value=0.0098  Score=37.04  Aligned_cols=61  Identities=8%  Similarity=0.085  Sum_probs=51.0

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -++|.++++.+++|-.+|-+.|+++.+.+....++..+-.+...++.   ..|.+++.+.|..+
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            45677899999999999999999999999988888777766666643   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=96.66  E-value=0.0012  Score=41.66  Aligned_cols=33  Identities=21%  Similarity=0.190  Sum_probs=28.4

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 032643            3 SQEDQLDLACCYIKQLRERIDKLNRMKGQAMKS   35 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~~   35 (136)
                      |-.+.|..|++||++|++++++|.++.+.|...
T Consensus        40 ~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~   72 (80)
T d1am9a_          40 NKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999988877553

>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=96.42  E-value=0.013  Score=36.82  Aligned_cols=60  Identities=13%  Similarity=0.199  Sum_probs=48.8

Q ss_pred             EEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           71 LISGVQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        71 l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      -+.|.++|+.+++|-.+|-+.|+++++++....++.....+......    -+.+++...|.++
T Consensus         9 tv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~~----~~~~~l~~~L~~l   68 (86)
T d1u8sa1           9 TAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP----SNITRVETTLPLL   68 (86)
T ss_dssp             EEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH----HHHHHHHHHHHHH
T ss_pred             EEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcCc----ccHHHHHHHHHHH
Confidence            34677899999999999999999999999999999887777766643    2457777777654

>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=95.96  E-value=0.005  Score=38.80  Aligned_cols=32  Identities=22%  Similarity=0.256  Sum_probs=26.3

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032643            3 SQEDQLDLACCYIKQLRERIDKLNRMKGQAMK   34 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kve~L~~kk~~l~~   34 (136)
                      |-.+.|..|++||++|++++..|.++.++|..
T Consensus        37 sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   68 (83)
T d1nkpb_          37 SRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677899999999999999999887766543

>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=95.55  E-value=0.06  Score=34.04  Aligned_cols=67  Identities=13%  Similarity=0.157  Sum_probs=49.2

Q ss_pred             eeEEEEEecCCCcccHHHHHHHHHHcCceEEEeEEEEeCC------eEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           66 SIEVVLISGVQRNFMLYEVISILEEEGAQVVSASFSTIGD------KIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        66 ~~eV~l~s~~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~------r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .++|.+ .|.++++.+++|-+.|-+.|+++.+.+..+...      .-...++..+.-+. +.+...|.++|.++
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 677899999999999999999999998765321      22344555555454 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=95.01  E-value=0.0026  Score=39.03  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=18.4

Q ss_pred             CChhhhHHHHHHHHHHHHHHHH
Q 032643            2 LSQEDQLDLACCYIKQLRERID   23 (136)
Q Consensus         2 ~s~~d~l~eA~~YIk~Lq~kve   23 (136)
                      +|-.+.|..|++||++||+.|+
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            3556789999999999998764

>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=93.97  E-value=0.0075  Score=36.19  Aligned_cols=20  Identities=30%  Similarity=0.624  Sum_probs=16.9

Q ss_pred             ChhhhHHHHHHHHHHHHHHH
Q 032643            3 SQEDQLDLACCYIKQLRERI   22 (136)
Q Consensus         3 s~~d~l~eA~~YIk~Lq~kv   22 (136)
                      |-.+.|..|++||++||+++
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            44568999999999999875

>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=91.94  E-value=0.061  Score=33.15  Aligned_cols=58  Identities=16%  Similarity=0.119  Sum_probs=38.4

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEE-eCCeEEEEEEEEeeccCcccchHHHHHHHhhh
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFST-IGDKIFHTVRAQAKISRLGVETSIACQRLHDL  134 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~-~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~~  134 (136)
                      .++++.|++|..++-++|+.+.+.+... .++..--++-..+...  +.+.+++-+||+.+
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            4789999999999999999999998664 4443333334444332  35789999999875

>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=88.71  E-value=1.4  Score=26.11  Aligned_cols=51  Identities=14%  Similarity=0.042  Sum_probs=38.0

Q ss_pred             CCCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           75 VQRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        75 ~~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      .++++.|++++++|.++|+++........+++-.  +...+.      |+++..+-|++
T Consensus         7 ~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~--~vl~vd------d~~~a~~~L~~   57 (71)
T d2f06a1           7 PNVPGALAKVLGFLSAEGVFIEYMYSFANNNVAN--VVIRPS------NMDKCIEVLKE   57 (71)
T ss_dssp             ESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEE--EEEEES------CHHHHHHHHHH
T ss_pred             cCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEE--EEEEEC------CHHHHHHHHHH
Confidence            3689999999999999999999988777777653  555554      44556665553

>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=82.72  E-value=0.11  Score=30.89  Aligned_cols=17  Identities=35%  Similarity=0.477  Sum_probs=14.1

Q ss_pred             hhhHHHHHHHHHHHHHH
Q 032643            5 EDQLDLACCYIKQLRER   21 (136)
Q Consensus         5 ~d~l~eA~~YIk~Lq~k   21 (136)
                      ...|..|++||++||++
T Consensus        46 ~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_          46 GGILSKASDYIQELRQS   62 (65)
T ss_dssp             TTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            34688999999999975

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

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

Probab=81.89  E-value=3.5  Score=24.41  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=37.9

Q ss_pred             CCcccHHHHHHHHHHcCceEEEeEEEEeCCeEEEEEEEEeeccCcccchHHHHHHHhh
Q 032643           76 QRNFMLYEVISILEEEGAQVVSASFSTIGDKIFHTVRAQAKISRLGVETSIACQRLHD  133 (136)
Q Consensus        76 ~~~~~Ls~vl~vLeEeGl~Vvsa~~s~~~~r~fhtI~~qv~~~~~~~d~~~l~erL~~  133 (136)
                      |+++.|.++..+|.+.|+++.+-+.+-.++.-+.-|  -+.      |+.+..+.|++
T Consensus        12 NkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Ri--iv~------~~e~a~~~L~~   61 (70)
T d2f06a2          12 NKSGRLTEVTEVLAKENINLSALCIAENADFGILRG--IVS------DPDKAYKALKD   61 (70)
T ss_dssp             SSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEE--EES------CHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEE--EEC------ChHHHHHHHHH
Confidence            589999999999999999999988876666555444  232      55666666664