Citrus Sinensis ID: 031198

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160----
Protein Sequence
MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQPSKA
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEccEEEEEEEEcccccHHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEcccccccccHHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHcccccccccEEEEEEccEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEccccEEEEEEEEcccccccccHHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MVSRLQRRRALHRKLHILRTltnsksvkkssIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMkhnhvpkevkvekigENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFamdaiavpqnpqqaLEARDVAQVILKATEKQAVEWQPSKA
Flexible Loop (DISEMBL)
mvsrlqrrralhrklhilrtltnsksvkkssiimDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMKHNHVpkevkvekigenfiVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATekqavewqpska
Low Complexity Region (SEG)
MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQPSKA
Disordered region (IsUnstruct)
************RKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQN***ALEARDVAQVILK**************
Disordered Region (DISOPRED)
*****QRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLK**********************************KIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAI************RDVAQVI****************
Disordered Region (DISEMBL)
********RALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEK**********
Disordered Region (DISPRO)
*****QRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLD*MKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAV*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQPSKA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	164	2.2.26 [Sep-21-2011]
O49687	589	Transcription factor MYC4	no	no	0.695	0.193	0.267	0.0001
Q9LPW3	450	Transcription factor SCRE	no	no	0.865	0.315	0.254	0.0005
Q9FIP9	592	Transcription factor ATR2	no	no	0.676	0.187	0.246	0.0007

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

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/131 (26%), Positives = 67/131 (51%), Gaps = 17/131 (12%)

Query: 6   QRRRALHRKLHILRTLT-NSKSVKKSSIIMDSLLYVCKLKLKLE--------------AI 50
           QRR  L+++ + LR +  N   + K+S++ D++ Y+ +LK KL+               +
Sbjct: 423 QRREKLNQRFYSLRAVVPNVSKMDKASLLGDAISYISELKSKLQKAESDKEELQKQIDVM 482

Query: 51  KREYSNLMAIKKAYLDLMKHNHV--PKEVKVEKIGENFIVRVRCNKGENRLVSILEAFEE 108
            +E  N  +  K    L + + V    EV V+ IG + ++R++C+K  +     +EA +E
Sbjct: 483 NKEAGNAKSSVKDRKCLNQESSVLIEMEVDVKIIGWDAMIRIQCSKRNHPGAKFMEALKE 542

Query: 109 MGLIVRQATVS 119
           + L V  A++S
Sbjct: 543 LDLEVNHASLS 553

Arabidopsis thaliana (taxid: 3702)

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

 Score = 43.9 bits (102), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 43/169 (25%), Positives = 74/169 (43%), Gaps = 27/169 (15%)

Query: 6   QRRRALHRKLHILRTLTNSKS-VKKSSIIMDSLLY-------VCKLKLKLEAIKREYSNL 57
           +RR+ L+ +L++LR++    S + ++SI+ D++ Y       +  L  +LE+     S+L
Sbjct: 274 RRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDLHTELESTPPSSSSL 333

Query: 58  MAIKKAYLDL---MKHNHVPKEVKVEKIGENFIVRVR------------CNKGENRLVSI 102
             +      L   +K    P        G+   V VR            C +    L+S 
Sbjct: 334 HPLTPTPQTLSYRVKEELCPSSSLPSPKGQQPRVEVRLREGKAVNIHMFCGRRPGLLLST 393

Query: 103 LEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKA 151
           + A + +GL V+QA +SC   FA+D        +Q  E  DV    +KA
Sbjct: 394 MRALDNLGLDVQQAVISCFNGFALDVFRA----EQCQEDHDVLPEQIKA 438

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 43.1 bits (100), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/138 (24%), Positives = 67/138 (48%), Gaps = 27/138 (19%)

Query: 6   QRRRALHRKLHILRTLT-NSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAY 64
           QRR  L+++ + LR +  N   + K+S++ D++ Y+ +LK KL+  +   S+   I+K  
Sbjct: 422 QRREKLNQRFYSLRAVVPNVSKMDKASLLGDAISYINELKSKLQQAE---SDKEEIQKKL 478

Query: 65  LDLMKHNH-----------------------VPKEVKVEKIGENFIVRVRCNKGENRLVS 101
             + K  +                       +  E+ V+ IG + ++RV+C K ++    
Sbjct: 479 DGMSKEGNNGKGCGSRAKERKSSNQDSTASSIEMEIDVKIIGWDVMIRVQCGKKDHPGAR 538

Query: 102 ILEAFEEMGLIVRQATVS 119
            +EA +E+ L V  A++S
Sbjct: 539 FMEALKELDLEVNHASLS 556

Involved in tryptophan and other stress-responsive gene regulation.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	164
224079053	156	predicted protein [Populus trichocarpa]	0.945	0.993	0.596	8e-45
255562480	155	conserved hypothetical protein [Ricinus	0.932	0.987	0.602	7e-40
225443746	150	PREDICTED: uncharacterized protein LOC10	0.908	0.993	0.551	6e-37
297740533	142	unnamed protein product [Vitis vinifera]	0.853	0.985	0.557	9e-35
188509959	156	predicted protein [Gossypioides kirkii]	0.914	0.961	0.506	6e-34
356512525	169	PREDICTED: uncharacterized protein LOC10	0.981	0.952	0.475	2e-33
49333386	156	predicted protein [Gossypium hirsutum]	0.914	0.961	0.506	3e-33
188509944	156	predicted protein [Gossypium raimondii]	0.914	0.961	0.506	8e-33
356525304	169	PREDICTED: uncharacterized protein LOC10	0.951	0.923	0.484	3e-32
49333372	156	predicted protein [Gossypium hirsutum]	0.914	0.961	0.487	3e-32

>gi|224079053|ref|XP_002305731.1| predicted protein [Populus trichocarpa] gi|222848695|gb|EEE86242.1| predicted protein [Populus trichocarpa]

 Score =  184 bits (468), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 93/156 (59%), Positives = 118/156 (75%), Gaps = 1/156 (0%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           MV+RLQRR A+ R+LH+LRTLT SKSV++ S+IMD+LLY+ KLKLKLEAIKRE +NL+AI
Sbjct: 1   MVARLQRRAAMGRRLHVLRTLTCSKSVQRKSVIMDALLYIYKLKLKLEAIKRELANLVAI 60

Query: 61  KKAYLDLMKHNHVP-KEVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
           K+ YL LMK   +P KEVKVEK  +  +VRV C KG ++LVSILE FEEMGL++  A VS
Sbjct: 61  KREYLSLMKQLQLPKKEVKVEKAEQGLLVRVTCEKGGDKLVSILEVFEEMGLVILNARVS 120

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQ 155
            N +FAM+AI V    Q AL  + + Q + KA E+Q
Sbjct: 121 SNLFFAMEAIVVADQEQHALHVKSITQAVTKAIERQ 156

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562480|ref|XP_002522246.1| conserved hypothetical protein [Ricinus communis] gi|223538499|gb|EEF40104.1| conserved hypothetical protein [Ricinus communis]

 Score =  168 bits (426), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 94/156 (60%), Positives = 115/156 (73%), Gaps = 3/156 (1%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           MVS +QRR  L  KLHILRTLT SKSVK++ II D++LY+ KL LK+EAIKRE SNL AI
Sbjct: 1   MVSGVQRRMVLRNKLHILRTLTCSKSVKRNCIIADAVLYIYKLSLKVEAIKRELSNLNAI 60

Query: 61  KKAYLDLMKH-NHVPK-EVKVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATV 118
           K  YL LMK    +PK EVKVEK G+ F+VRV C KG  +LV ILEAFE+MGLIV  A V
Sbjct: 61  KSEYLRLMKQVQCLPKREVKVEKAGKGFLVRVICEKGGGKLVPILEAFEKMGLIVLNAKV 120

Query: 119 SCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEK 154
           SCN+YF ++AI V +  Q AL+  +V Q IL+A ++
Sbjct: 121 SCNFYFGLEAIVVAE-EQHALDVNNVTQEILEAIDR 155

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443746|ref|XP_002265581.1| PREDICTED: uncharacterized protein LOC100263463 [Vitis vinifera]

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 91/165 (55%), Positives = 114/165 (69%), Gaps = 16/165 (9%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M SR ++R AL RKLH LRTLT+SKSVK SSI+MD+ LY+ KLKLKLEAIKREY  L+  
Sbjct: 1   MESRFRKRMALRRKLHTLRTLTSSKSVKMSSIVMDAFLYIYKLKLKLEAIKREYLKLI-- 58

Query: 61  KKAYLDLMKHNHVPKEVKVEKI-GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
                      +  +EVKVEKI G+ F+VRV C KG++ LVSILEAFE+MGL V QA VS
Sbjct: 59  -----------NYTQEVKVEKINGKGFLVRVSCKKGQDLLVSILEAFEDMGLNVLQARVS 107

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQPSKA 164
           CN+ F M+AI   ++  QAL+ R V + +LKA EK   + +  KA
Sbjct: 108 CNHGFGMEAIVEAED--QALDVRAVTEAVLKAIEKPGGDEKHVKA 150

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740533|emb|CBI30715.3| unnamed protein product [Vitis vinifera]

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 87/156 (55%), Positives = 108/156 (69%), Gaps = 16/156 (10%)

Query: 10  ALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAIKKAYLDLMK 69
           AL RKLH LRTLT+SKSVK SSI+MD+ LY+ KLKLKLEAIKREY  L+           
Sbjct: 2   ALRRKLHTLRTLTSSKSVKMSSIVMDAFLYIYKLKLKLEAIKREYLKLI----------- 50

Query: 70  HNHVPKEVKVEKI-GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDA 128
             +  +EVKVEKI G+ F+VRV C KG++ LVSILEAFE+MGL V QA VSCN+ F M+A
Sbjct: 51  --NYTQEVKVEKINGKGFLVRVSCKKGQDLLVSILEAFEDMGLNVLQARVSCNHGFGMEA 108

Query: 129 IAVPQNPQQALEARDVAQVILKATEKQAVEWQPSKA 164
           I   ++  QAL+ R V + +LKA EK   + +  KA
Sbjct: 109 IVEAED--QALDVRAVTEAVLKAIEKPGGDEKHVKA 142

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188509959|gb|ACD56643.1| predicted protein [Gossypioides kirkii]

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 82/162 (50%), Positives = 113/162 (69%), Gaps = 12/162 (7%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M ++LQRR A  RKLH+L+TL   KSVK+S  I++ LL+  KLK+KLE I+REY NL+  
Sbjct: 1   MATKLQRRTASLRKLHLLQTLNKPKSVKRSCSIINVLLHFYKLKVKLEEIQREYQNLL-- 58

Query: 61  KKAYLDLMKHNHVPKEVKVEKI-GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
                   K+  +PKEVKVEKI GE F+V+V CNKG ++LVSILE F+E+GL V QATVS
Sbjct: 59  --------KNIRIPKEVKVEKINGEQFVVKVACNKGGDKLVSILEVFDELGLNVVQATVS 110

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKA-TEKQAVEWQ 160
           C+++F+M+AI      Q+  + +D+   +LKA  EKQ+ E +
Sbjct: 111 CSHFFSMEAIIGVGQDQKTSDIKDITDAVLKAIDEKQSGEQE 152

Source: Gossypioides kirkii

Species: Gossypioides kirkii

Genus: Gossypioides

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512525|ref|XP_003524969.1| PREDICTED: uncharacterized protein LOC100793239 [Glycine max]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 78/164 (47%), Positives = 112/164 (68%), Gaps = 3/164 (1%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M  R+Q+R +L RKL I+R LT S S K++S++  ++L + KLKL LE +KR+Y NL+A 
Sbjct: 1   MACRVQKRISLRRKLRIVRVLTCSNSAKRTSLVKSTVLRLYKLKLALETVKRQYENLLAT 60

Query: 61  KKAYLDLMKHNHVPKEVKVEKIGEN-FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
           ++ ++ L  H    K+VK+EK+G   F+VRV C KG + LVSILEAF+EM L V+QA VS
Sbjct: 61  RREFISLSNHVKENKDVKIEKVGAGTFMVRVTCEKGGDNLVSILEAFDEMCLNVQQARVS 120

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQPSK 163
           C   F+++AIAV +N  Q L+ RD+ + +LKA  KQ+ E    K
Sbjct: 121 CENGFSLEAIAVAEN--QTLDVRDITEALLKAIGKQSGEKDSQK 162

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|49333386|gb|AAT64025.1| predicted protein [Gossypium hirsutum]

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 82/162 (50%), Positives = 111/162 (68%), Gaps = 12/162 (7%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M ++LQRR A  RKLH+L+TL   KSVK+S  I++ LL+  KLK+KLE I+REY NL+  
Sbjct: 1   MATKLQRRTASLRKLHLLQTLNKPKSVKRSCSIINILLHFYKLKVKLEEIQREYQNLL-- 58

Query: 61  KKAYLDLMKHNHVPKEVKVEKI-GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
                   K+  +PKEVKVEKI GE F+VRV CNKG ++LVSILE F+E+GL V QA VS
Sbjct: 59  --------KNIRIPKEVKVEKISGEQFVVRVACNKGGDKLVSILEVFDELGLNVVQARVS 110

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKA-TEKQAVEWQ 160
           C ++F+M+AI      Q+  + +D+   +LKA  EKQ+ E +
Sbjct: 111 CRHFFSMEAIIGVGQDQKTSDMKDITDAVLKAIDEKQSGEQE 152

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188509944|gb|ACD56630.1| predicted protein [Gossypium raimondii]

 Score =  145 bits (365), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 82/162 (50%), Positives = 110/162 (67%), Gaps = 12/162 (7%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M ++LQRR A  RKLH+L+TL   KSVK+S  I++ LL+  KLK+KLE I+REY NL+  
Sbjct: 1   MATKLQRRTASLRKLHLLQTLNKPKSVKRSCSIINILLHFYKLKVKLEEIQREYQNLL-- 58

Query: 61  KKAYLDLMKHNHVPKEVKVEKI-GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
                   K+   PKEVKVEKI GE F+VRV CNKG ++LVSILE F+E+GL V QA VS
Sbjct: 59  --------KNIRTPKEVKVEKINGEQFVVRVACNKGGDKLVSILEVFDELGLNVVQARVS 110

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKA-TEKQAVEWQ 160
           C ++F+M+AI      Q+  + +D+   +LKA  EKQ+ E +
Sbjct: 111 CRHFFSMEAIIGVGQDQKTSDMKDITDAVLKAIDEKQSGEQE 152

Source: Gossypium raimondii

Species: Gossypium raimondii

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525304|ref|XP_003531265.1| PREDICTED: uncharacterized protein LOC100814945 [Glycine max]

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 77/159 (48%), Positives = 111/159 (69%), Gaps = 3/159 (1%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M  R+Q+R +L RKLHILR LT S S K++S+   ++L + KLKL LE +KR+Y NL+A 
Sbjct: 1   MACRVQKRISLRRKLHILRVLTYSNSAKRTSLAKSTVLRLYKLKLALETVKRQYENLLAT 60

Query: 61  KKAYLDLMKHNHVPKEVKVEKIGEN-FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
           ++  + L+ H    K+VK+EK+G   F+VRV C KG + LV+IL+AF+EM L V+QA VS
Sbjct: 61  RRECVRLLNHVKESKDVKIEKVGAGTFMVRVTCEKGGDNLVAILKAFDEMCLDVQQARVS 120

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE 158
           C   F ++AIAV ++  Q L+ RD+ +V+LKA  KQ+ E
Sbjct: 121 CENGFFLEAIAVAED--QTLDVRDITEVLLKAIGKQSGE 157

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|49333372|gb|AAT64012.1| predicted protein [Gossypium hirsutum]

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 79/162 (48%), Positives = 111/162 (68%), Gaps = 12/162 (7%)

Query: 1   MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
           M ++LQRR A  RKLH+L+TL   KSVK+S  I++ LL+  KLK+KLE I+REY NL+  
Sbjct: 1   MATKLQRRTASLRKLHLLQTLNKPKSVKRSCSIINVLLHFYKLKVKLEEIQREYQNLL-- 58

Query: 61  KKAYLDLMKHNHVPKEVKVEKI-GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS 119
                   K+  +P+EVKVEKI GE F+++V CNKG ++LVSILE F+E+GL V QA VS
Sbjct: 59  --------KNMRIPQEVKVEKINGEQFVLKVACNKGGDKLVSILEVFDELGLNVVQARVS 110

Query: 120 CNYYFAMDAIAVPQNPQQALEARDVAQVILKA-TEKQAVEWQ 160
           C ++F+M+AI      Q+  + +D+   +LKA  EKQ+ E +
Sbjct: 111 CRHFFSMEAIIGVGQDQKTSDMKDITDAVLKAIDEKQSGEQE 152

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

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	164
UNIPROTKB|Q8LII5	157	OJ1167_G06.116 "Putative uncha	0.859	0.898	0.36	1.8e-16
UNIPROTKB|Q5WMQ1	153	OSJNBa0053E01.1 "Putative unch	0.878	0.941	0.359	2.3e-16
TAIR|locus:2078411	156	AT3G56220 [Arabidopsis thalian	0.878	0.923	0.344	7.7e-16
UNIPROTKB|Q10LR1	163	Os03g0338400 "BHLH transcripti	0.847	0.852	0.357	2e-15
TAIR|locus:2828302	158	AT2G40435 [Arabidopsis thalian	0.871	0.905	0.344	2e-15
UNIPROTKB|Q84R79	301	OSJNBb0113I20.1 "Putative ammo	0.719	0.392	0.264	0.00015
UNIPROTKB|Q84LF9	310	RERJ1 "Transcription Factor" [	0.310	0.164	0.365	0.00027
UNIPROTKB|Q8H8E4	430	OJ1006F06.1 "Putative bHLH tra	0.914	0.348	0.243	0.00038
TAIR|locus:2039445	571	AMS "AT2G16910" [Arabidopsis t	0.640	0.183	0.252	0.00047
TAIR|locus:2046198	318	FRU "AT2G28160" [Arabidopsis t	0.359	0.185	0.333	0.00093

UNIPROTKB|Q8LII5 OJ1167_G06.116 "Putative uncharacterized protein OJ1167_G06.116" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 54/150 (36%), Positives = 87/150 (58%)

Query:     1 MVSRLQRRRA-LHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMA 59
             M+SR +++ A LH KL ILR++T+S ++  +SII D+  Y+ +LK K+  + +E      
Sbjct:     1 MMSRERKKAAALHEKLQILRSITHSHALSNTSIITDASEYIKELKQKVVRLNKE------ 54

Query:    60 IKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKG-ENRLVSILEAFEEMGLIVRQATV 118
             I  A    ++ N +P  V VE +G  F++ V  +K     LVSILEAF+E+GL V +AT 
Sbjct:    55 IACAEAAALRQNSIPT-VTVETLGHGFLINVFSDKSCPGLLVSILEAFDELGLNVLEATA 113

Query:   119 SCNYYFAMDAIAVPQNPQQALEARDVAQVI 148
             SC+  F ++A+       + +  + V Q I
Sbjct:   114 SCDDTFRLEAVGGENQVDEHVIKQTVLQAI 143

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q5WMQ1 OSJNBa0053E01.1 "Putative uncharacterized protein OSJNBa0053E01.1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 203 (76.5 bits), Expect = 2.3e-16, P = 2.3e-16
 Identities = 55/153 (35%), Positives = 90/153 (58%)

Query:     1 MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
             MVSR Q+R +LH KL ILRTLT+S +V K SII D+  Y+  LK K+ A+ +E   L   
Sbjct:     1 MVSREQKRASLHEKLQILRTLTHSHAVNKMSIISDASTYIKDLKQKIAALNKE---LGCA 57

Query:    61 KKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGENRLVS-ILEAFEEMGLIVRQATVS 119
             K   +++ +    P  V+V+ + + F++ V  +K    L+S IL+AF+E+GL V +A  S
Sbjct:    58 KN--MNICEEPS-PV-VRVQVLDKGFLINVFMDKSSPGLLSSILQAFDELGLTVIEARAS 113

Query:   120 CNYYFAMDAIAVP-QNPQQALEARDVAQVILKA 151
             C+  F ++A+    +     ++A  V   +++A
Sbjct:   114 CSNSFRLEAVGGEHEEADGGIDANAVELAVMQA 146

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2078411 AT3G56220 [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 53/154 (34%), Positives = 88/154 (57%)

Query:     1 MVSRLQRR-RALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMA 59
             MVSR  +R  +L  K H+LR++T+S +  ++SII+D+  Y+ KLK K+E I    +N   
Sbjct:     1 MVSREHKRGSSLREKFHLLRSITDSHAESETSIIVDASKYIKKLKQKVEKI----NNATT 56

Query:    60 IKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKGE-NRLVSILEAFEEMGLIVRQATV 118
              ++++ +    N +   V VE + + F+++V   K E   LV +LE FE++GL V +A V
Sbjct:    57 SEQSFRESSDPNPM---VTVETLEKGFMIKVMSRKNEAGMLVCVLETFEDLGLDVVEARV 113

Query:   119 SCNYYFAMDAIAVPQNPQ-QALEARDVAQVILKA 151
             SC   F++ AI    N     ++A  V Q + +A
Sbjct:   114 SCTDTFSLHAIGSSNNDDGDCIDAEAVKQAVAEA 147

GO:0005634 "nucleus" evidence=ISM

UNIPROTKB|Q10LR1 Os03g0338400 "BHLH transcription factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 55/154 (35%), Positives = 89/154 (57%)

Query:     1 MVSRLQRRRA--LHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM 58
             M+S  +R++A  L  KL ILR++T+S ++  +SI+MD+  Y+ +LK K+  + +E    +
Sbjct:     1 MMSSRERKKAAALQEKLQILRSITHSHALSNTSILMDASKYIKELKQKVVRLNQE----I 56

Query:    59 AIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVRCNKG-ENRLVSILEAFEEMGLIVRQAT 117
             A  +   D ++ N V     VE +   F+V V   K     LVSILEAF+E+GL V +AT
Sbjct:    57 ACAQ---DALRQNRVT----VETLRHGFLVNVFSGKSCPGLLVSILEAFDELGLSVLEAT 109

Query:   118 VSCNYYFAMDAIAVPQNPQQALEARDVAQVILKA 151
              SC   F ++AI   +N  + ++   V Q +L+A
Sbjct:   110 ASCTDTFRLEAIG-SENLMEKVDEHVVKQAVLRA 142

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2828302 AT2G40435 [Arabidopsis thaliana (taxid:3702)]

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 53/154 (34%), Positives = 85/154 (55%)

Query:     1 MVSRLQRRRALHRKLHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMAI 60
             MVSR Q+R +L  K  +LR++TNS +   +SIIMD+  Y+ KLK K+E   ++ +   + 
Sbjct:     1 MVSREQKRGSLQEKFQLLRSITNSHAENDTSIIMDASKYIQKLKQKVERFNQDPTAEQSS 60

Query:    61 KKAYLDLMKHNHVPKE--VKVEKIGENFIVRVRCNKGE-NRLVSILEAFEEMGLIVRQAT 117
              +   D       PK   V VE + + F++ V   K +   LVS+LEAFE++GL V +A 
Sbjct:    61 SEP-TD-------PKTPMVTVETLDKGFMINVFSGKNQPGMLVSVLEAFEDIGLNVLEAR 112

Query:   118 VSCNYYFAMDAIAVPQNPQQALEARDVAQVILKA 151
              SC   F++ A+ +     + ++A  V Q +  A
Sbjct:   113 ASCTDSFSLHAMGLENEDGENMDAEAVKQAVTDA 146

GO:0005634 "nucleus" evidence=ISM

UNIPROTKB|Q84R79 OSJNBb0113I20.1 "Putative ammonium transporter" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 109 (43.4 bits), Expect = 0.00015, P = 0.00015
 Identities = 33/125 (26%), Positives = 63/125 (50%)

Query:     1 MVSRLQRRRALHRK-LHILRTLTNSKSVKKSSIIMDSLLYVCKLKLKLEAIKRE----YS 55
             +V+  +RR  ++++ + +   +   K + K++I+ D+  Y+ +L+ KL+A++ +     +
Sbjct:   132 VVAERKRREKINQRFMELSAVIPKLKKMDKATILSDAASYIRELQEKLKALEEQAAARVT 191

Query:    56 NLMAIKKAYLDLMKHNHVPKEVKVEKIGENFIVRVR--CNKGENRLVSILEAFEEMGLIV 113
                    +    M H  VP E++V     N +V VR  C  GE  +V IL   EE+ L +
Sbjct:   192 EAAMATPSPARAMNHLPVPPEIEVRCSPTNNVVMVRIHCENGEGVIVRILAEVEEIHLRI 251

Query:   114 RQATV 118
               A V
Sbjct:   252 INANV 256

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q84LF9 RERJ1 "Transcription Factor" [Oryza sativa (taxid:4530)]

 Score = 80 (33.2 bits), Expect = 0.00027, Sum P(2) = 0.00027
 Identities = 19/52 (36%), Positives = 34/52 (65%)

Query:     7 RRRALHRKLHILRTLT-NSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNL 57
             RRR L+ KL+ LR++  N   + K+SII D++ Y+ +L+ + + + RE + L
Sbjct:   101 RRRKLNEKLYALRSVVPNITKMDKASIIKDAIEYIQRLQAEEQQMLREVAAL 152

GO:0005634 "nucleus" evidence=IC

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

 Score = 108 (43.1 bits), Expect = 0.00038, P = 0.00038
 Identities = 40/164 (24%), Positives = 83/164 (50%)

Query:     1 MVSRLQRRRALHRKLHILRTLTNSKS-VKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMA 59
             +++  +RR+ L+ +L +LR++    S + ++SI+ D++ YV +L  +++ ++ E   +  
Sbjct:   184 LMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDTIDYVKELTERIKTLEEEIG-VTP 242

Query:    60 IKKAYLDLMK-----HNH---VPKEVK--VEKIGE-NFIVRVRCNKGENRLVSILEAFEE 108
              +   L+ MK     +N+   V    K  VE  G  N  + + C      L+S + A E 
Sbjct:   243 EELDLLNTMKDSSSGNNNEMLVRNSTKFDVENRGSGNTRIEICCPANPGVLLSTVSALEV 302

Query:   109 MGLIVRQATVSCNYYFAMDAIAVPQN-PQQALEARDVAQVILKA 151
             +GL + Q  VSC   F M A  + ++  +Q +   ++ Q + ++
Sbjct:   303 LGLEIEQCVVSCFSDFGMQASCLQEDGKRQVVSTDEIKQTLFRS 346

GO:0005634 "nucleus" evidence=IC

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

 Score = 90 (36.7 bits), Expect = 0.00047, Sum P(2) = 0.00047
 Identities = 28/111 (25%), Positives = 50/111 (45%)

Query:    55 SNLMAIKKAYLDLMKHNHVPKE----VKVEKI-GENFIVRVRCNKGENRLVSILEAFEEM 109
             SN+ ++K+  +DL   N   +E    V V ++ G  F V+V C         ++EA + +
Sbjct:   405 SNVPSVKQD-VDLENSNDKGQEMEPQVDVAQLDGREFFVKVICEYKPGGFTRLMEALDSL 463

Query:   110 GLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQ 160
             GL V  A  +       +   V +N  + ++A  V   +L+ T   +  WQ
Sbjct:   464 GLEVTNANTTRYLSLVSNVFKVEKNDNEMVQAEHVRNSLLEITRNTSRGWQ 514

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009555 "pollen development" evidence=IMP

GO:0048658 "tapetal layer development" evidence=IMP

TAIR|locus:2046198 FRU "AT2G28160" [Arabidopsis thaliana (taxid:3702)]

 Score = 84 (34.6 bits), Expect = 0.00093, Sum P(2) = 0.00093
 Identities = 20/60 (33%), Positives = 38/60 (63%)

Query:     1 MVSRLQRRRALHRKLHILRTLT-NSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMA 59
             ++S  +RR  +  KL+ LR+L  N   + K+SI+ D++LYV +L+ + + +K + + L A
Sbjct:   133 LISERRRRGRMKDKLYALRSLVPNITKMDKASIVGDAVLYVQELQSQAKKLKSDIAGLEA 192

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:0010039 "response to iron ion" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0034756 "regulation of iron ion transport" evidence=IMP

GO:0071281 "cellular response to iron ion" evidence=IEP

GO:0071369 "cellular response to ethylene stimulus" evidence=IEP

GO:0071732 "cellular response to nitric oxide" evidence=IEP

GO:0000041 "transition metal ion transport" evidence=RCA

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00040356 hypothetical protein (156 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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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	164
smart00353	53	HLH helix loop helix domain.	99.3
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.22
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.06
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	98.59
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.52
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	98.49
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	98.46
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	98.45
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	98.26
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	98.2
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.97
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.89
KOG1318	411	consensus Helix loop helix transcription factor EB	97.76
PRK05007	884	PII uridylyl-transferase; Provisional	97.57
PRK00275	895	glnD PII uridylyl-transferase; Provisional	97.5
PRK04374	869	PII uridylyl-transferase; Provisional	97.47
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	97.45
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.36
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.33
PRK05092	931	PII uridylyl-transferase; Provisional	97.24
PRK03381	774	PII uridylyl-transferase; Provisional	97.24
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	97.2
PRK03381	774	PII uridylyl-transferase; Provisional	97.19
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	97.18
PRK03059	856	PII uridylyl-transferase; Provisional	97.16
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	97.15
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.15
KOG4304	250	consensus Transcriptional repressors of the hairy/	97.1
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	97.08
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.07
PRK05007	884	PII uridylyl-transferase; Provisional	97.06
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	97.01
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	96.98
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	96.94
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	96.9
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	96.87
PRK03059	856	PII uridylyl-transferase; Provisional	96.77
PRK00194	90	hypothetical protein; Validated	96.76
PRK00275	895	glnD PII uridylyl-transferase; Provisional	96.69
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	96.62
PRK05092	931	PII uridylyl-transferase; Provisional	96.61
KOG0561	373	consensus bHLH transcription factor [Transcription	96.58
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.53
PRK04374	869	PII uridylyl-transferase; Provisional	96.33
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	95.94
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	95.93
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	95.9
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	95.87
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	95.85
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	95.3
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	95.06
KOG4029	228	consensus Transcription factor HAND2/Transcription	95.02
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	94.81
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	94.57
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	94.48
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	94.2
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	93.73
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	93.57
cd02116	60	ACT ACT domains are commonly involved in specifica	93.49
COG0788	287	PurU Formyltetrahydrofolate hydrolase [Nucleotide	93.31
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	93.18
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	93.16
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	92.87
COG3830	90	ACT domain-containing protein [Signal transduction	92.41
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	92.01
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	91.23
PRK04435	147	hypothetical protein; Provisional	91.23
PRK08577	136	hypothetical protein; Provisional	90.77
PRK11589	190	gcvR glycine cleavage system transcriptional repre	90.25
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	90.01
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	89.21
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	88.94
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	88.92
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	88.76
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	88.15
PF05088	1528	Bac_GDH: Bacterial NAD-glutamate dehydrogenase	88.05
PLN03217	93	transcription factor ATBS1; Provisional	87.85
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	87.06
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	86.56
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	86.53
PRK00227	693	glnD PII uridylyl-transferase; Provisional	85.17
PRK11589	190	gcvR glycine cleavage system transcriptional repre	85.13
PRK07334	403	threonine dehydratase; Provisional	85.03
PRK06737	76	acetolactate synthase 1 regulatory subunit; Valida	84.65
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	84.21
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	83.48
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	82.62
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	82.55
PRK13562	84	acetolactate synthase 1 regulatory subunit; Provis	81.99
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	81.4
COG4747	142	ACT domain-containing protein [General function pr	80.79
PRK11152	76	ilvM acetolactate synthase 2 regulatory subunit; P	80.69
CHL00100	174	ilvH acetohydroxyacid synthase small subunit	80.65
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	80.65

>smart00353 HLH helix loop helix domain

Probab=99.30  E-value=3e-12  Score=81.55  Aligned_cols=47  Identities=26%  Similarity=0.424  Sum_probs=43.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhccC----CCCccccchhHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLTN----SKSVKKSSIIMDSLLYVCKLKLKLE   48 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv~----~~KmDKaSIl~dAI~YIkeLq~~v~   48 (164)
                      +.||+||.+||+.|..|+++++    ..|+||++||..||+||+.|+.+++
T Consensus         2 ~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        2 ARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999993    5789999999999999999999875

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

Probab=99.22  E-value=1.2e-11  Score=80.29  Aligned_cols=46  Identities=24%  Similarity=0.377  Sum_probs=42.5

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC---CCccccchhHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS---KSVKKSSIIMDSLLYVCKLKLKL   47 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~---~KmDKaSIl~dAI~YIkeLq~~v   47 (164)
                      +.||+||.+||+.|..|++++ ..   .|+||++||..||+||+.|+..+
T Consensus        10 ~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083          10 LRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999 44   89999999999999999999875

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

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

Probab=99.06  E-value=1.6e-10  Score=74.39  Aligned_cols=42  Identities=26%  Similarity=0.420  Sum_probs=38.9

Q ss_pred             cHHHHHHHHhHhhHHhhhcc--C----CCCccccchhHHHHHHHHHHH
Q 031198            3 SRLQRRRALHRKLHILRTLT--N----SKSVKKSSIIMDSLLYVCKLK   44 (164)
Q Consensus         3 ser~RR~kln~rl~~LRslv--~----~~KmDKaSIl~dAI~YIkeLq   44 (164)
                      .||+||.+||+.|..|+.++  .    ..|+||++||..||+||++||
T Consensus         8 ~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    8 RERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            58899999999999999999  3    378999999999999999997

; 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 ....

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

Probab=98.59  E-value=6.3e-07  Score=61.82  Aligned_cols=67  Identities=19%  Similarity=0.289  Sum_probs=55.0

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCC----HHHHHHHHHHHHH
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALE----ARDVAQVILKATE  153 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~----~~~ik~al~~ai~  153 (164)
                      +|.|.|+.+||+|.+|..+|-.+|++|.+|.|++.+.-..+++-+...++..+.    .+.|+++|..++.
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~kl~~~~~~~~l~~~L~~al~   73 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGRTLSTEGERQRVIKCLEAAIE   73 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCCccCCHHHHHHHHHHHHHHHh
Confidence            589999999999999999999999999999999998888887766443455553    3567777777765

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.

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

Probab=98.52  E-value=1.3e-06  Score=59.86  Aligned_cols=67  Identities=18%  Similarity=0.264  Sum_probs=52.8

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHHH
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKAT  152 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai  152 (164)
                      .+|+|.++.+||+|.+|..+|..+||+|..|.|++.+..+.+++-+...++..+.-+.-.+.|.+++
T Consensus         2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~kl~d~~~~~~l~~~L   68 (72)
T cd04895           2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGNKLTDDSLIAYIEKSL   68 (72)
T ss_pred             EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCCCCCCHHHHHHHHHHh
Confidence            3689999999999999999999999999999999999888888776543455564334444444444

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.

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

Probab=98.49  E-value=1.7e-06  Score=59.21  Aligned_cols=69  Identities=13%  Similarity=0.212  Sum_probs=53.5

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec-ccceEEEEEeccCCCCCCCC---HHHHHHHHHHHHHh
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC-NYYFAMDAIAVPQNPQQALE---ARDVAQVILKATEK  154 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~-~~~f~l~~~~~~~~~~~~~~---~~~ik~al~~ai~~  154 (164)
                      ++++|.|+.+||+|.++..+|..+||+|++|+|++ .++++++++.+...++...+   .+.++++|.+++++
T Consensus         1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~~~~~~~~~~~~l~~~L~~~L~~   73 (76)
T cd04927           1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDARELLHTKKRREETYDYLRAVLGD   73 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCCCCCCCHHHHHHHHHHHHHHHch
Confidence            47899999999999999999999999999999996 68889888876432222222   34466666666654

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

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

Probab=98.46  E-value=3.1e-06  Score=57.13  Aligned_cols=67  Identities=18%  Similarity=0.198  Sum_probs=50.4

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHH
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKAT  152 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai  152 (164)
                      ..|.|.|+.+||+|.++..+|..+||+|++|.|.+. ++++++++.+...++.....+.-.+.|.+.|
T Consensus         2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~~~~~~~~~~~~~~l~~~L   69 (73)
T cd04900           2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDPDGEPIGERERLARIREAL   69 (73)
T ss_pred             EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECCCCCCCChHHHHHHHHHHH
Confidence            357899999999999999999999999999999877 7899998876432333343333334444444

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.

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

Probab=98.45  E-value=2.9e-06  Score=58.56  Aligned_cols=67  Identities=15%  Similarity=0.270  Sum_probs=53.9

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEee--cccceEEEEEeccCCCCCCC-C---HHHHHHHHHHHHHh
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVS--CNYYFAMDAIAVPQNPQQAL-E---ARDVAQVILKATEK  154 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs--~~~~f~l~~~~~~~~~~~~~-~---~~~ik~al~~ai~~  154 (164)
                      +|.|.|+.+||+|.+|..+|..+||+|..|.|+  +.+.-+.+++-+ ..++..+ +   ...++++|..++..
T Consensus         2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~~g~kl~d~~~~~~L~~~L~~~l~~   74 (75)
T cd04896           2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QSDGKKIMDPKKQAALCARLREEMVC   74 (75)
T ss_pred             EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eCCCCccCCHHHHHHHHHHHHHHhcC
Confidence            589999999999999999999999999999999  988777777766 3234333 3   46778888877654

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.

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

Probab=98.26  E-value=1.4e-05  Score=54.19  Aligned_cols=64  Identities=14%  Similarity=0.169  Sum_probs=54.2

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHH
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKAT  152 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai  152 (164)
                      .|-|.|+.+||+|.++..+|..+||+|++|++.+. ++++++++.+-.  ...=+...+.++|++++
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d--~~~~~~~~~~~~~~~~~   67 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTG--WKRGETAALGHALQKEI   67 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEec--CCccchHHHHHHHHHhh
Confidence            46789999999999999999999999999999865 889999888753  33346678888988876

This CD includes a novel, yet uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=98.20  E-value=2.1e-05  Score=53.40  Aligned_cols=66  Identities=8%  Similarity=0.046  Sum_probs=51.7

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCC-CCCC-C---HHHHHHHHHHHH
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNP-QQAL-E---ARDVAQVILKAT  152 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~-~~~~-~---~~~ik~al~~ai  152 (164)
                      +|+|.++.+||+|.+|..+|..+|++|+.|++++.++.+++.+.+...+ +... +   .+.+++.|.+++
T Consensus         2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~~l   72 (74)
T cd04925           2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGAPIDDPIRLASIEDRLDNVL   72 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHHHh
Confidence            5889999999999999999999999999999999888888877754312 2222 2   356666666655

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.

>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=97.97  E-value=0.00011  Score=48.26  Aligned_cols=45  Identities=18%  Similarity=0.219  Sum_probs=39.8

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEec
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAV  131 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~  131 (164)
                      .|.|.|+.++|+|.+|+.+|.+++++|.++++.+.+++.+..+..
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i   46 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYV   46 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEE
Confidence            588999999999999999999999999999999876677766554

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

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

Probab=97.89  E-value=0.00018  Score=48.44  Aligned_cols=67  Identities=16%  Similarity=0.251  Sum_probs=50.2

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHHHH
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATE  153 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~  153 (164)
                      ..|.|.++.++|+|.+|..+|.++|++|+++.+.+.+...+..+.+...++...+. .--+.|.++|+
T Consensus         2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~~~~~~~~~-~~~~~l~~~l~   68 (72)
T cd04926           2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTDANGNPVDP-KTIEAVRQEIG   68 (72)
T ss_pred             eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEECCCCCcCCH-HHHHHHHHHhc
Confidence            46788999999999999999999999999999988877777766653323333443 34455666665

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.

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

Probab=97.76  E-value=5.2e-05  Score=67.07  Aligned_cols=46  Identities=22%  Similarity=0.337  Sum_probs=40.6

Q ss_pred             HHHHHHHHhHhhHHhhhccCC-----CCccccchhHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLTNS-----KSVKKSSIIMDSLLYVCKLKLKLEA   49 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv~~-----~KmDKaSIl~dAI~YIkeLq~~v~~   49 (164)
                      |||||+++|++...|--||+-     .+-.|.+||.-+.+||++||+..+.
T Consensus       241 ERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~  291 (411)
T KOG1318|consen  241 ERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR  291 (411)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence            788999999999999999932     3667999999999999999988773

>PRK05007 PII uridylyl-transferase; Provisional

Probab=97.57  E-value=0.00048  Score=66.39  Aligned_cols=81  Identities=15%  Similarity=0.190  Sum_probs=61.2

Q ss_pred             CcceEEEEE--cCeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCC---HHHHHHHH
Q 031198           74 PKEVKVEKI--GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALE---ARDVAQVI  148 (164)
Q Consensus        74 ~~~V~V~~~--~~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~---~~~ik~al  148 (164)
                      |+.|.+...  +.-..|+|.|..+||+|.+|..+|..+||+|.+|.|+|.+.-+.+++-+...++..++   .+.|+++|
T Consensus       795 ~~~V~~d~~~s~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~~g~~l~~~~~~~l~~~L  874 (884)
T PRK05007        795 PTEVSFLPTHTDRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATADRRALNEELQQELRQRL  874 (884)
T ss_pred             CCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcCCCCcCCHHHHHHHHHHH
Confidence            444444432  2237799999999999999999999999999999999998887777766433455555   45677777


Q ss_pred             HHHHHh
Q 031198          149 LKATEK  154 (164)
Q Consensus       149 ~~ai~~  154 (164)
                      ..++..
T Consensus       875 ~~~l~~  880 (884)
T PRK05007        875 TEALNP  880 (884)
T ss_pred             HHHHhh
Confidence            777643

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=97.50  E-value=0.0011  Score=63.91  Aligned_cols=82  Identities=15%  Similarity=0.189  Sum_probs=64.0

Q ss_pred             CCcceEEEEEc--CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCC-C---HHHHHH
Q 031198           73 VPKEVKVEKIG--ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQAL-E---ARDVAQ  146 (164)
Q Consensus        73 ~~~~V~V~~~~--~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~-~---~~~ik~  146 (164)
                      .|+.|.+....  +...|.|.+..+||+|.+|..+|..+||+|+.|.|++.++++++++.+...++..+ +   .+.|++
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~~  879 (895)
T PRK00275        800 FPTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQPLSDPQLCSRLQD  879 (895)
T ss_pred             CCCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCCCCCCHHHHHHHHH
Confidence            44555555542  33779999999999999999999999999999999999999999888754334433 3   356888


Q ss_pred             HHHHHHHh
Q 031198          147 VILKATEK  154 (164)
Q Consensus       147 al~~ai~~  154 (164)
                      +|.+++.+
T Consensus       880 ~L~~~L~~  887 (895)
T PRK00275        880 AICEQLDA  887 (895)
T ss_pred             HHHHHHhc
Confidence            88888744

>PRK04374 PII uridylyl-transferase; Provisional

Probab=97.47  E-value=0.0013  Score=63.35  Aligned_cols=80  Identities=10%  Similarity=0.099  Sum_probs=61.5

Q ss_pred             CCcceEEEEEcC-e-EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCC---HHHHHHH
Q 031198           73 VPKEVKVEKIGE-N-FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALE---ARDVAQV  147 (164)
Q Consensus        73 ~~~~V~V~~~~~-~-~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~---~~~ik~a  147 (164)
                      .|+.|.+..... + ..|.|.+..+||+|.+|..+|..+||+|+.|.|+|.++.+++++.+...++...+   ...|+++
T Consensus       782 ~~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~~~~~~~~~~l~~~  861 (869)
T PRK04374        782 FAPRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDRPLSESARQALRDA  861 (869)
T ss_pred             CCCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCCcCChHHHHHHHHH
Confidence            455666655422 3 7799999999999999999999999999999999999999988876442333332   3567777


Q ss_pred             HHHHH
Q 031198          148 ILKAT  152 (164)
Q Consensus       148 l~~ai  152 (164)
                      |..++
T Consensus       862 L~~~l  866 (869)
T PRK04374        862 LCACL  866 (869)
T ss_pred             HHHHh
Confidence            77666

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

Probab=97.45  E-value=0.0012  Score=42.20  Aligned_cols=61  Identities=13%  Similarity=0.165  Sum_probs=45.0

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccc---eEEEEEeccCCCCCCCCHHHHHHHHHHH
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYY---FAMDAIAVPQNPQQALEARDVAQVILKA  151 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~---f~l~~~~~~~~~~~~~~~~~ik~al~~a  151 (164)
                      +.|.|.|+.+||+|.++.+.|-++|++|.++.+.....   +.+-...     ....+.+.+.++|.+.
T Consensus         1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~l~~~   64 (66)
T PF01842_consen    1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIV-----VDEEDLEKLLEELEAL   64 (66)
T ss_dssp             EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEE-----EEGHGHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEE-----CCCCCHHHHHHHHHcc
Confidence            46889999999999999999999999999998887643   2222222     1234566666666654

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 ....

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

Probab=97.36  E-value=0.00034  Score=58.30  Aligned_cols=56  Identities=18%  Similarity=0.325  Sum_probs=46.8

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc--CC-CCccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT--NS-KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNL   57 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv--~~-~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~   57 (164)
                      |.||||=+|.||-|.+|.--+  |. ...-|.=||-.||.||..||.-++++.+....+
T Consensus       124 MRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  124 MRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            457767799999999998866  44 778999999999999999999999887654433

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.33  E-value=0.0015  Score=62.76  Aligned_cols=80  Identities=18%  Similarity=0.173  Sum_probs=58.1

Q ss_pred             CCcceEEEEEc-C-eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCH---HHHHHH
Q 031198           73 VPKEVKVEKIG-E-NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEA---RDVAQV  147 (164)
Q Consensus        73 ~~~~V~V~~~~-~-~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~---~~ik~a  147 (164)
                      .|+.|.+.... + -..|+|.+..+||+|.+|..+|..+|++|..|.|+|.+.-+.+++-+...++..++.   ..|+++
T Consensus       769 ~~~~V~~dn~~s~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g~~l~~~~~~~l~~~  848 (854)
T PRK01759        769 VKTEVRFLNEEKQEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQGQALDEEERKALKSR  848 (854)
T ss_pred             CCCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCCCcCChHHHHHHHHH
Confidence            34444443332 2 277999999999999999999999999999999999987777766654334555543   556666


Q ss_pred             HHHHH
Q 031198          148 ILKAT  152 (164)
Q Consensus       148 l~~ai  152 (164)
                      |..++
T Consensus       849 L~~~l  853 (854)
T PRK01759        849 LLSNL  853 (854)
T ss_pred             HHHHh
Confidence            66554

>PRK05092 PII uridylyl-transferase; Provisional

Probab=97.24  E-value=0.0032  Score=60.98  Aligned_cols=82  Identities=16%  Similarity=0.211  Sum_probs=62.8

Q ss_pred             CCcceEEEEEc--CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCC-C---HHHHHH
Q 031198           73 VPKEVKVEKIG--ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQAL-E---ARDVAQ  146 (164)
Q Consensus        73 ~~~~V~V~~~~--~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~-~---~~~ik~  146 (164)
                      .|+.|.+....  +...|.|.|..+||+|.+|..+|..+|++|.+|.|+|.+..+++.+.+...++..+ +   .+.|++
T Consensus       829 ~~~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~~~~~l~~  908 (931)
T PRK05092        829 VPPRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEARQAAIRR  908 (931)
T ss_pred             CCCEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHHHHHHHHH
Confidence            34556555542  23789999999999999999999999999999999998888888776643233333 2   467888


Q ss_pred             HHHHHHHh
Q 031198          147 VILKATEK  154 (164)
Q Consensus       147 al~~ai~~  154 (164)
                      +|..++..
T Consensus       909 ~L~~~L~~  916 (931)
T PRK05092        909 ALLAALAE  916 (931)
T ss_pred             HHHHHhcC
Confidence            88888854

>PRK03381 PII uridylyl-transferase; Provisional

Probab=97.24  E-value=0.0029  Score=60.27  Aligned_cols=77  Identities=21%  Similarity=0.163  Sum_probs=57.5

Q ss_pred             CcceEEEEEcC--eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHH
Q 031198           74 PKEVKVEKIGE--NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKA  151 (164)
Q Consensus        74 ~~~V~V~~~~~--~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~a  151 (164)
                      |+.|.+.....  -..|.|.|..+||+|.+|..+|..+|++|++|.|+|.++.+++++-+...++..++.+  .+.|.++
T Consensus       694 ~~~v~~~~~~~~~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g~~~~~~--~~~l~~~  771 (774)
T PRK03381        694 PPRVLWLDGASPDATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAGGPLADA--RAAVEQA  771 (774)
T ss_pred             CcEEEEEECCCCCeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCCCcCchH--HHHHHHH
Confidence            34444444322  3789999999999999999999999999999999999999999887754344444322  4555554


Q ss_pred             H
Q 031198          152 T  152 (164)
Q Consensus       152 i  152 (164)
                      +
T Consensus       772 L  772 (774)
T PRK03381        772 V  772 (774)
T ss_pred             h
Confidence            4

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

Probab=97.20  E-value=0.007  Score=39.06  Aligned_cols=44  Identities=23%  Similarity=0.300  Sum_probs=37.0

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEe
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIA  130 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~  130 (164)
                      .|.|.|+.++|+|.+++.+|.++|++|.++.+.+.+........
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~   45 (70)
T cd04873           2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFY   45 (70)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEE
Confidence            47899999999999999999999999999998876545444443

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

>PRK03381 PII uridylyl-transferase; Provisional

Probab=97.19  E-value=0.0025  Score=60.64  Aligned_cols=71  Identities=18%  Similarity=0.062  Sum_probs=59.9

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHh
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEK  154 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~  154 (164)
                      +.+.|.|.|+.+||++.+|..+|..+|++|++|+|.+.+++.++++.+....+.....+.+++.|.+++..
T Consensus       598 ~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~~~~~~~~~~l~~~L~~~L~~  668 (774)
T PRK03381        598 HMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPRFGSPPDAALLRQDLRRALDG  668 (774)
T ss_pred             CeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCCcchHHHHHHHHHHHHcC
Confidence            45889999999999999999999999999999999988888888877644233334568899999988876

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

Probab=97.18  E-value=0.0023  Score=43.46  Aligned_cols=70  Identities=7%  Similarity=0.107  Sum_probs=51.8

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE  158 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~  158 (164)
                      .++|.+.++.+||++..+..+|-+.|.++.+++.+.. +.|++-.....   . .-+.+.++.+|.+...+.+..
T Consensus         2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~---~-~~~~~~l~~~L~~l~~~~~l~   72 (76)
T PF13740_consen    2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSI---P-EDSLERLESALEELAEELGLD   72 (76)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEE---S-HHHHHHHHHHHHHHHHHTT-E
T ss_pred             EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEe---C-cccHHHHHHHHHHHHHHCCcE
Confidence            3789999999999999999999999999999999887 45665544321   1 226788888888887777654

>PRK03059 PII uridylyl-transferase; Provisional

Probab=97.16  E-value=0.0029  Score=60.89  Aligned_cols=77  Identities=16%  Similarity=0.150  Sum_probs=57.9

Q ss_pred             CcceEEEEEc--CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCC---HHHHHHHH
Q 031198           74 PKEVKVEKIG--ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALE---ARDVAQVI  148 (164)
Q Consensus        74 ~~~V~V~~~~--~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~---~~~ik~al  148 (164)
                      |+.|.+....  +-..|.|.|+.+||+|.+|..+|..+||+|+.|.|++.++.+++++.+.. .+ ..+   .+.|+++|
T Consensus       773 ~~~V~~~~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~-~~-~~~~~~~~~l~~~L  850 (856)
T PRK03059        773 TPRVDLRPDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDG-SG-LSDNRLQIQLETEL  850 (856)
T ss_pred             CceEEEEEcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcC-CC-CCCHHHHHHHHHHH
Confidence            3445444432  23779999999999999999999999999999999999999999888732 11 122   45667777


Q ss_pred             HHHH
Q 031198          149 LKAT  152 (164)
Q Consensus       149 ~~ai  152 (164)
                      .+++
T Consensus       851 ~~~L  854 (856)
T PRK03059        851 LDAL  854 (856)
T ss_pred             HHHh
Confidence            6665

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=97.15  E-value=0.00069  Score=54.35  Aligned_cols=55  Identities=25%  Similarity=0.343  Sum_probs=46.8

Q ss_pred             cHHHHHHHHhHhhHHhhhcc-C------C-CCccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            3 SRLQRRRALHRKLHILRTLT-N------S-KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNL   57 (164)
Q Consensus         3 ser~RR~kln~rl~~LRslv-~------~-~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~   57 (164)
                      .|++||+.+|.-+..|.-|| .      + .|..||-||.-+|+||..|.+...+-+.|...+
T Consensus        69 aEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L  131 (229)
T KOG1319|consen   69 AEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL  131 (229)
T ss_pred             HHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            58899999999999999998 1      2 277899999999999999998888777766544

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

Probab=97.15  E-value=0.00039  Score=66.06  Aligned_cols=44  Identities=14%  Similarity=0.211  Sum_probs=41.2

Q ss_pred             cHHHHHHHHhHhhHHhhhcc--CC---CCccccchhHHHHHHHHHHHHH
Q 031198            3 SRLQRRRALHRKLHILRTLT--NS---KSVKKSSIIMDSLLYVCKLKLK   46 (164)
Q Consensus         3 ser~RR~kln~rl~~LRslv--~~---~KmDKaSIl~dAI~YIkeLq~~   46 (164)
                      +|+|||+|+|.-+..|.+||  ++   -||||..||.-||.+|+.+++.
T Consensus        27 ~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   27 IEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            58999999999999999999  66   8999999999999999999885

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

Probab=97.10  E-value=0.00042  Score=57.83  Aligned_cols=46  Identities=22%  Similarity=0.296  Sum_probs=41.0

Q ss_pred             HHHHHHHHhHhhHHhhhcc----C---C--CCccccchhHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLT----N---S--KSVKKSSIIMDSLLYVCKLKLKLEA   49 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv----~---~--~KmDKaSIl~dAI~YIkeLq~~v~~   49 (164)
                      ||+||.++|+=|..|+.||    .   .  +|++||=||.=+++|+++|+..-..
T Consensus        40 EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   40 EKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            7889999999999999998    1   2  8999999999999999999987553

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

Probab=97.08  E-value=0.011  Score=39.54  Aligned_cols=70  Identities=10%  Similarity=0.133  Sum_probs=52.8

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      |.|.|+.+||++.+|...|-+.|+++.+.+..+   ...|.+.....-  +....+...++.++...-.+.+..|
T Consensus         2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~~--~~~~~~~~~l~~~l~~l~~~l~~~~   74 (74)
T cd04875           2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFEL--EGFDLSREALEAAFAPVAAEFDMDW   74 (74)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEEe--CCCCCCHHHHHHHHHHHHHHcCCcC
Confidence            789999999999999999999999999987664   244666555421  1113678999999888766655543

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.

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.07  E-value=0.0069  Score=58.31  Aligned_cols=82  Identities=17%  Similarity=0.244  Sum_probs=62.6

Q ss_pred             CcceEEEEE--cCeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec-ccceEEEEEeccCCCCCCCCH---HHHHHH
Q 031198           74 PKEVKVEKI--GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC-NYYFAMDAIAVPQNPQQALEA---RDVAQV  147 (164)
Q Consensus        74 ~~~V~V~~~--~~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~-~~~f~l~~~~~~~~~~~~~~~---~~ik~a  147 (164)
                      ++-|.+...  .+...|.|.|+.++|+|.+|..+|..+||+|++|.|.+ .+++.++++.+...++..++.   +.|+++
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~~~~~~~~~~l~~~  743 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGKLLEFDRRRQLEQA  743 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCCCCCHHHHHHHHHH
Confidence            344555443  23477999999999999999999999999999999977 688999988765433444443   357888


Q ss_pred             HHHHHHhc
Q 031198          148 ILKATEKQ  155 (164)
Q Consensus       148 l~~ai~~~  155 (164)
                      |.+++...
T Consensus       744 L~~aL~~~  751 (854)
T PRK01759        744 LTKALNTN  751 (854)
T ss_pred             HHHHHcCC
Confidence            88888654

>PRK05007 PII uridylyl-transferase; Provisional

Probab=97.06  E-value=0.0071  Score=58.44  Aligned_cols=82  Identities=13%  Similarity=0.115  Sum_probs=62.5

Q ss_pred             CcceEEEEE--cCeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCH---HHHHHH
Q 031198           74 PKEVKVEKI--GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEA---RDVAQV  147 (164)
Q Consensus        74 ~~~V~V~~~--~~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~---~~ik~a  147 (164)
                      ++-|.+...  ++...|.|.|+.++|+|.+|..+|..+||+|++|.|.+. ++++++++.+...++...+.   +.|++.
T Consensus       688 ~p~V~i~~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~~~~~~~~~~I~~~  767 (884)
T PRK05007        688 KPLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGSPLSQDRHQVIRKA  767 (884)
T ss_pred             CCeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCCCCCHHHHHHHHHH
Confidence            344555443  234789999999999999999999999999999999876 56998888764433444443   458888


Q ss_pred             HHHHHHhc
Q 031198          148 ILKATEKQ  155 (164)
Q Consensus       148 l~~ai~~~  155 (164)
                      |.+++...
T Consensus       768 L~~aL~~~  775 (884)
T PRK05007        768 LEQALTQS  775 (884)
T ss_pred             HHHHHcCC
Confidence            98888654

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=97.01  E-value=0.0044  Score=59.43  Aligned_cols=67  Identities=21%  Similarity=0.206  Sum_probs=49.5

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCC---HHHHHHHHHHHH
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALE---ARDVAQVILKAT  152 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~---~~~ik~al~~ai  152 (164)
                      ..|.|.|..+||+|.+|..+|..+|++|.+|.|++.+.-..+.+.+....+..++   .+.|+++|..++
T Consensus       780 t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~~~~~~~~~~l~~~L~~~l  849 (850)
T TIGR01693       780 TIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGLKLTDEEEQRLLEVLAASV  849 (850)
T ss_pred             EEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999999999976544444433221233333   456666666654

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.

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=96.98  E-value=0.0058  Score=58.62  Aligned_cols=73  Identities=15%  Similarity=0.098  Sum_probs=59.3

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEee-cccceEEEEEeccCCCCCCCC----HHHHHHHHHHHHHhcc
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS-CNYYFAMDAIAVPQNPQQALE----ARDVAQVILKATEKQA  156 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs-~~~~f~l~~~~~~~~~~~~~~----~~~ik~al~~ai~~~~  156 (164)
                      +...|.|.++.++|+|.+|..+|..+||+|++|.|+ +.++++++++.+...++...+    .+.|++.|.+++....
T Consensus       667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~~~~~~~~~~~i~~~L~~~L~~~~  744 (850)
T TIGR01693       667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGSPPAAERVFQELLQGLVDVLAGLA  744 (850)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCCCCCcHHHHHHHHHHHHHHHcCCC
Confidence            347799999999999999999999999999999999 568899998877543344332    4568889999987643

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.

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

Probab=96.94  E-value=0.0087  Score=40.70  Aligned_cols=69  Identities=9%  Similarity=0.076  Sum_probs=52.3

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE  158 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~  158 (164)
                      +.|.+.|+.+||+..+|.+.|.+.|.++.+++.... +.|.+-.....   + ..+...+++.+...-.+.+..
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~---~-~~~~~~l~~~l~~~~~~~~l~   71 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEG---S-WDAIAKLEAALPGLARRLDLT   71 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEe---c-cccHHHHHHHHHHHHHHcCCE
Confidence            578999999999999999999999999999887654 45655544422   1 246788888887765554543

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

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

Probab=96.90  E-value=0.0076  Score=41.74  Aligned_cols=72  Identities=11%  Similarity=0.150  Sum_probs=55.6

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      +.|.+.|+.+||++..|.+.|-..|+++.+.+..+. +.|.+......  .+...+...++..+...-.+.+.++
T Consensus         2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~--~~~~~~~~~L~~~l~~l~~~~~l~~   74 (88)
T cd04872           2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDI--SESNLDFAELQEELEELGKELGVKI   74 (88)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEe--CCCCCCHHHHHHHHHHHHHHcCCEE
Confidence            578999999999999999999999999999876554 45666654432  1224678999999988776766554

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=96.87  E-value=0.014  Score=39.18  Aligned_cols=69  Identities=9%  Similarity=0.092  Sum_probs=53.8

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-------cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-------YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-------~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      |.|.|+.++|++.+|-+.|...|+++.+.+..+.       +.|.+.....-   ....+...++..+...-.+.+..+
T Consensus         2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~---p~~~~~~~l~~~l~~l~~~~~~~~   77 (81)
T cd04869           2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLAL---PAGTDLDALREELEELCDDLNVDI   77 (81)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEec---CCCCCHHHHHHHHHHHHHHhcceE
Confidence            6799999999999999999999999999887653       34655544422   234678999999998877777654

This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.77  E-value=0.0096  Score=57.38  Aligned_cols=72  Identities=18%  Similarity=0.194  Sum_probs=56.9

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEee-cccceEEEEEeccCCCCCCC---CHHHHHHHHHHHHHhc
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS-CNYYFAMDAIAVPQNPQQAL---EARDVAQVILKATEKQ  155 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs-~~~~f~l~~~~~~~~~~~~~---~~~~ik~al~~ai~~~  155 (164)
                      +...|-|.|+.+||++.++..+|..+||+|++|+|. +.++++++++.+...++...   -.+.|++.|.+++...
T Consensus       677 ~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~~~i~~~l~~~l~~~  752 (856)
T PRK03059        677 EGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEEDVHYRDIINLVEHELAERLAEQ  752 (856)
T ss_pred             CeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCCCCChHHHHHHHHHHHHHHHcCC
Confidence            347799999999999999999999999999999995 46899999888754223311   2566788888887653

>PRK00194 hypothetical protein; Validated

Probab=96.76  E-value=0.012  Score=40.67  Aligned_cols=73  Identities=10%  Similarity=0.126  Sum_probs=53.7

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.+||++.++.+.|-+.|++|.+.+..+. +.|.+.....-  .....+...+++.|...-...+.++
T Consensus         3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~--~~~~~~~~~l~~~l~~l~~~~~~~~   76 (90)
T PRK00194          3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDI--SESKKDFAELKEELEELGKELGVKI   76 (90)
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEe--cCCCCCHHHHHHHHHHHHHHcCCEE
Confidence            4679999999999999999999999999999775543 44555433311  1223567889888888766666543

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=96.69  E-value=0.014  Score=56.54  Aligned_cols=72  Identities=10%  Similarity=0.217  Sum_probs=56.6

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEee-cccceEEEEEeccCCCCCCC--C---HHHHHHHHHHHHHhc
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS-CNYYFAMDAIAVPQNPQQAL--E---ARDVAQVILKATEKQ  155 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs-~~~~f~l~~~~~~~~~~~~~--~---~~~ik~al~~ai~~~  155 (164)
                      +...|.|.|+.+||+|.++..+|..+||+|++|+|. +.+++.++++.+-..++...  +   .+.|++.|.+++...
T Consensus       703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~~~~~~~~r~~~i~~~L~~~L~~~  780 (895)
T PRK00275        703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGEPIGDNPARIEQIREGLTEALRNP  780 (895)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCCCccchHHHHHHHHHHHHHHHcCC
Confidence            347799999999999999999999999999999985 45889999887754233332  2   345788888887543

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

Probab=96.62  E-value=0.01  Score=56.74  Aligned_cols=81  Identities=20%  Similarity=0.292  Sum_probs=57.9

Q ss_pred             CCcceEEEEE--cCeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHH
Q 031198           73 VPKEVKVEKI--GENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILK  150 (164)
Q Consensus        73 ~~~~V~V~~~--~~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~  150 (164)
                      .||+|....-  .+...+++.+..+||+|..+...|..++|++++|.|++++.=+.+++.+....+..+ -.++++.+.+
T Consensus       777 i~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~~~l-~~~~~q~l~~  855 (867)
T COG2844         777 IPPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADGQAL-NAELRQSLLQ  855 (867)
T ss_pred             cCCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEeccccccC-CHHHHHHHHH
Confidence            3455555443  234779999999999999999999999999999999999765555554432234445 3456666666


Q ss_pred             HHHh
Q 031198          151 ATEK  154 (164)
Q Consensus       151 ai~~  154 (164)
                      .+..
T Consensus       856 ~ll~  859 (867)
T COG2844         856 RLLE  859 (867)
T ss_pred             HHHH
Confidence            6554

>PRK05092 PII uridylyl-transferase; Provisional

Probab=96.61  E-value=0.025  Score=54.99  Aligned_cols=82  Identities=16%  Similarity=0.034  Sum_probs=61.9

Q ss_pred             CCcceEEEEEc--CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec-ccceEEEEEeccCCCCCCC----CHHHHH
Q 031198           73 VPKEVKVEKIG--ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC-NYYFAMDAIAVPQNPQQAL----EARDVA  145 (164)
Q Consensus        73 ~~~~V~V~~~~--~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~-~~~f~l~~~~~~~~~~~~~----~~~~ik  145 (164)
                      .|+-|.+....  +...|.|.|+.++|+|.+|..+|..+|++|++|+|.+ .++|+++++.+...++...    ..+.|.
T Consensus       718 ~~~~v~~~~~~~~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~~~~l~  797 (931)
T PRK05092        718 RPLATEVRPDPARGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRRLARLA  797 (931)
T ss_pred             CCcEEEEEecCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHHHHHHH
Confidence            34455555542  4588999999999999999999999999999999987 5889999776533223221    366788


Q ss_pred             HHHHHHHHh
Q 031198          146 QVILKATEK  154 (164)
Q Consensus       146 ~al~~ai~~  154 (164)
                      ++|.+++.+
T Consensus       798 ~~L~~~l~~  806 (931)
T PRK05092        798 KAIEDALSG  806 (931)
T ss_pred             HHHHHHHcC
Confidence            888888854

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=96.58  E-value=0.0016  Score=55.64  Aligned_cols=47  Identities=17%  Similarity=0.335  Sum_probs=39.5

Q ss_pred             HHHHHHHHhHhhHHhhhcc---CCCCccccchhHHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLT---NSKSVKKSSIIMDSLLYVCKLKLKLEAI   50 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv---~~~KmDKaSIl~dAI~YIkeLq~~v~~L   50 (164)
                      ||+|=.-+|.-|..||+|+   .--|..||.||..+.+||.+|+..--+|
T Consensus        68 ERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   68 ERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             HHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            4555578999999999999   4589999999999999999998765443

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

Probab=96.53  E-value=0.026  Score=37.93  Aligned_cols=69  Identities=6%  Similarity=0.104  Sum_probs=54.2

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCC
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE  158 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~  158 (164)
                      +|.|.++.+||++.++...|-+.|+++.+.+-++. +.|++.....-   ....+.+.++.+|.......+.+
T Consensus         1 ~vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~---p~~~~~~~l~~~l~~l~~~l~l~   70 (75)
T cd04870           1 LITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQI---PDSADSEALLKDLLFKAHELGLQ   70 (75)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEc---CCCCCHHHHHHHHHHHHHHcCce
Confidence            37899999999999999999999999999876654 45777654421   23367899999998887776654

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.

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.33  E-value=0.022  Score=55.03  Aligned_cols=72  Identities=13%  Similarity=0.122  Sum_probs=57.7

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec-ccceEEEEEeccCCCCC-CCCHHHHHHHHHHHHHhc
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC-NYYFAMDAIAVPQNPQQ-ALEARDVAQVILKATEKQ  155 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~-~~~f~l~~~~~~~~~~~-~~~~~~ik~al~~ai~~~  155 (164)
                      +...|-|.|+.++|++.+|..+|..+||+|++|+|.+ .++++++++.+....+. .-....|++.|.+++...
T Consensus       689 ~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~~l~~~l~~~  762 (869)
T PRK04374        689 DALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAAALRQVLAGD  762 (869)
T ss_pred             CeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHHHHHHHHcCC
Confidence            4477999999999999999999999999999999987 48899998876542222 223556888888888663

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=95.94  E-value=0.054  Score=46.08  Aligned_cols=74  Identities=16%  Similarity=0.251  Sum_probs=56.4

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEe---ecccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATV---SCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~v---s~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.++|+..+|-+.|-+.|+++++.+-   +..+.|.+-...... .....+...+++++...-.+.|.+|
T Consensus         9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~-~~~~~~~~~l~~~l~~l~~~l~l~~   85 (289)
T PRK13010          9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQ-SAEAASVDTFRQEFQPVAEKFDMQW   85 (289)
T ss_pred             CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcC-CCCCCCHHHHHHHHHHHHHHhCCeE
Confidence            3789999999999999999999999999999876   333555554333211 1235788999999998877777654

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

Probab=95.93  E-value=0.12  Score=34.77  Aligned_cols=36  Identities=19%  Similarity=0.307  Sum_probs=31.2

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      +.|+|.|..++|+|.+|..++.+.|.++.+.++...
T Consensus         7 ~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~   42 (80)
T PF13291_consen    7 VRLRIEAEDRPGLLADITSVISENGVNIRSINARTN   42 (80)
T ss_dssp             EEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE-
T ss_pred             EEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEe
Confidence            678999999999999999999999999999998874

>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=95.90  E-value=0.12  Score=33.37  Aligned_cols=70  Identities=11%  Similarity=0.140  Sum_probs=47.8

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc---cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCCCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN---YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQP  161 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~---~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~~~  161 (164)
                      ++|+|.+..++|.+.+++..|.+.+.++.+.+....   +...+.....      ..+...+++.+.+.=.-++.-..|
T Consensus         1 ~yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~------~~~~~~l~~~i~~L~~~~~V~~~~   73 (79)
T cd04881           1 YYLRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTH------ETSEAALNAALAEIEALDAVQGVP   73 (79)
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEc------cCCHHHHHHHHHHHHcCccccCCc
Confidence            578999999999999999999999999999876543   2233443321      245666666665543334544444

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.

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

Probab=95.87  E-value=0.023  Score=47.00  Aligned_cols=55  Identities=18%  Similarity=0.176  Sum_probs=45.2

Q ss_pred             HHHHHHHHhHhhHHhhhccCC----CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLTNS----KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv~~----~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      ||+||..|.+.|..|+=.|+.    +.-+.++||.-|..||+.|+.+..+.+..++.+.
T Consensus        67 Ek~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~  125 (232)
T KOG2483|consen   67 EKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLS  125 (232)
T ss_pred             hHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHH
Confidence            678999999999999999822    3333689999999999999999888777665543

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

Probab=95.85  E-value=0.096  Score=33.39  Aligned_cols=64  Identities=14%  Similarity=0.186  Sum_probs=42.6

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc------cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCC
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN------YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE  158 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~------~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~  158 (164)
                      +.|.++.+||.|.+|++.|.+.|++|.+.+....      +...+.... +     ..+.+++ +.+.+.|.+.|+.
T Consensus         1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v-~-----~~~~~~l-~~l~~~l~~~g~~   70 (73)
T cd04886           1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTL-E-----TRGAEHI-EEIIAALREAGYD   70 (73)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEE-E-----eCCHHHH-HHHHHHHHHcCCE
Confidence            4688999999999999999999999998775532      222333222 1     1233333 4666667776664

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.

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=95.30  E-value=0.17  Score=42.92  Aligned_cols=72  Identities=11%  Similarity=0.247  Sum_probs=57.4

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc---cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN---YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~---~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.+||+..++...|-++|+++.+.+..+.   +-|.+.+...-   ....+...+++++...-...+.++
T Consensus         7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~---p~~~~~~~L~~~L~~l~~~l~l~i   81 (286)
T PRK13011          7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHS---EEGLDEDALRAGFAPIAARFGMQW   81 (286)
T ss_pred             eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEec---CCCCCHHHHHHHHHHHHHHhCcEE
Confidence            4789999999999999999999999999999887532   46777655421   345779999999998877766544

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=95.06  E-value=0.18  Score=42.63  Aligned_cols=71  Identities=17%  Similarity=0.185  Sum_probs=53.6

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc---cceEEEEEeccCCCCCCCCHHHHHHHHHH-HHHhccCCC
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN---YYFAMDAIAVPQNPQQALEARDVAQVILK-ATEKQAVEW  159 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~---~~f~l~~~~~~~~~~~~~~~~~ik~al~~-ai~~~~~~~  159 (164)
                      .|.|.|+.++|+..+|-+.|-+.|.++++.+-+..   +.|.|-....-  .+...+..++++++.. .-...+..|
T Consensus         2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~~--~~~~~~~~~l~~~l~~~~~~~~~l~i   76 (280)
T TIGR00655         2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQL--EGFRLEESSLLAAFKSALAEKFEMTW   76 (280)
T ss_pred             EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEEe--CCCCCCHHHHHHHHHHHHHHHhCCEE
Confidence            57899999999999999999999999999886653   56776554421  1224688999999988 444445443

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.

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

Probab=95.02  E-value=0.025  Score=46.20  Aligned_cols=50  Identities=22%  Similarity=0.212  Sum_probs=43.1

Q ss_pred             HHHHHHHHhHhhHHhhhcc----C-CCCccccchhHHHHHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLT----N-SKSVKKSSIIMDSLLYVCKLKLKLEAIKRE   53 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv----~-~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e   53 (164)
                      ||+|=+.+|..|..||..+    . .+|..|..+|.-||.||+-|+.-++.-+..
T Consensus       117 ER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  117 ERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            6666689999999999988    3 689999999999999999999987765543

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=94.81  E-value=0.25  Score=41.85  Aligned_cols=73  Identities=11%  Similarity=0.157  Sum_probs=56.7

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec--c-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC--N-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~--~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.+.|+.+||++..|.+.|-++|+++.+.+.++  . +-|.+.....-  +....+.+.++++|...-...+.++
T Consensus         6 ~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~--~~~~~~~~~L~~~L~~l~~~l~l~i   81 (286)
T PRK06027          6 RYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEG--DGLIFNLETLRADFAALAEEFEMDW   81 (286)
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEe--CCCCCCHHHHHHHHHHHHHHhCCEE
Confidence            478999999999999999999999999999988776  4 45766655421  1234568899999988777666543

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

Probab=94.57  E-value=0.2  Score=48.17  Aligned_cols=81  Identities=15%  Similarity=0.124  Sum_probs=61.2

Q ss_pred             EEEEEcCeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCH---HHHHHHHHHHHH
Q 031198           78 KVEKIGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEA---RDVAQVILKATE  153 (164)
Q Consensus        78 ~V~~~~~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~---~~ik~al~~ai~  153 (164)
                      .++...++.-|-|.|+.+|+++..+..++...|++|+.|+|-++ ++|.++++.+.+-++..++.   ..+.+.+.+++.
T Consensus       677 ~~r~~~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~~~g~~~~~dr~~~~~~~l~~~l~  756 (867)
T COG2844         677 SVRPHSGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLEPDGFPVEEDRRAALRGELIEALL  756 (867)
T ss_pred             eecccCCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEecCCCCccchhHHHHHHHHHHHHHh
Confidence            44444677999999999999999999999999999999998765 89999998875433444442   234456666666


Q ss_pred             hccCC
Q 031198          154 KQAVE  158 (164)
Q Consensus       154 ~~~~~  158 (164)
                      ..-..
T Consensus       757 s~~~~  761 (867)
T COG2844         757 SGKAQ  761 (867)
T ss_pred             cCCCC
Confidence            54444

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

Probab=94.48  E-value=0.49  Score=31.45  Aligned_cols=35  Identities=11%  Similarity=0.226  Sum_probs=32.4

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .|+|.|..++|+|.+|+.+|.+.+.++.+.++...
T Consensus         2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~   36 (74)
T cd04877           2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK   36 (74)
T ss_pred             EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC
Confidence            58899999999999999999999999999998764

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

>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=94.20  E-value=0.36  Score=31.56  Aligned_cols=34  Identities=15%  Similarity=0.100  Sum_probs=31.0

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      |+|.+..+||.|.+|+.+|.+.|.+|.+.+....
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~   35 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQ   35 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEe
Confidence            6899999999999999999999999999887654

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.

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

Probab=93.73  E-value=0.89  Score=29.33  Aligned_cols=34  Identities=6%  Similarity=0.161  Sum_probs=30.1

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      .+.+.++.+||.|.++++.|.+.|+++.+.....
T Consensus         3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~   36 (69)
T cd04909           3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILE   36 (69)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEE
Confidence            5788999999999999999999999999876544

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

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

Probab=93.57  E-value=0.5  Score=30.91  Aligned_cols=43  Identities=7%  Similarity=-0.042  Sum_probs=34.1

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc--cceEEEEE
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN--YYFAMDAI  129 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~--~~f~l~~~  129 (164)
                      .+.|.++.++|.|.+|++.|.+.+.++...+.+..  +.+.+...
T Consensus         2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~   46 (76)
T cd04888           2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTIS   46 (76)
T ss_pred             EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEE
Confidence            47889999999999999999999999999876542  33444433

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.

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

Probab=93.49  E-value=0.18  Score=29.16  Aligned_cols=34  Identities=15%  Similarity=0.228  Sum_probs=30.2

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      |.+.|+..+|.+.++++.|...++++...+.+..
T Consensus         1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~   34 (60)
T cd02116           1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTS   34 (60)
T ss_pred             CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEc
Confidence            4688999999999999999999999999887543

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

>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]

Probab=93.31  E-value=0.68  Score=39.30  Aligned_cols=74  Identities=16%  Similarity=0.239  Sum_probs=56.6

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      ..+.+.++|+.++|+...|-.-|-+.|.++++++--.   .+.|-+.+....+  +...+.+.+.+++-....+-++.|
T Consensus         6 ~~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf~D~~~g~FFmR~~f~~~--~~~~~~~~l~~~f~~~a~~f~m~~   82 (287)
T COG0788           6 DTFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQFDDPETGRFFMRVEFEGE--GGPLDREALRAAFAPLAEEFGMDW   82 (287)
T ss_pred             cceEEEEecCCCCCcHHHHHHHHHHcCCceeecccccccccCeEEEEEEEecC--CCcccHHHHHHHHHHHHHhhCcee
Confidence            3478999999999999999999999999999987664   3567777766543  333777888888777555555444

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

Probab=93.18  E-value=0.71  Score=31.00  Aligned_cols=65  Identities=14%  Similarity=0.222  Sum_probs=48.9

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEec-cCCCCCCCCHHHHHHHHHHH
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAV-PQNPQQALEARDVAQVILKA  151 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~-~~~~~~~~~~~~ik~al~~a  151 (164)
                      .|.|.||.+.|+--++...+=++||.|....+++-+....-+.-+ .....-.+.-+.+|+.|..+
T Consensus         2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv~~~~~~~~rW~lLK~RL~~~   67 (69)
T cd04894           2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVVPRPPSIKVRWDLLKNRLMSA   67 (69)
T ss_pred             EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEecCCCCCcccHHHHHHHHHhc
Confidence            588999999999999999999999999999999876544333322 11123346778888887764

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

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

Probab=93.16  E-value=0.45  Score=28.96  Aligned_cols=34  Identities=15%  Similarity=0.183  Sum_probs=30.2

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      |+|.|+.++|.+.+++..|.+.++++.+..+...
T Consensus         1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~   34 (71)
T cd04876           1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTD   34 (71)
T ss_pred             CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEEC
Confidence            4788999999999999999999999999877654

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

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

Probab=92.87  E-value=1.2  Score=28.12  Aligned_cols=35  Identities=9%  Similarity=0.036  Sum_probs=31.2

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .+.+.++.++|.|.+++..|.+.+.++.+.+....
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIE   36 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEecc
Confidence            47789999999999999999999999998776654

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.

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

Probab=92.41  E-value=0.53  Score=33.57  Aligned_cols=71  Identities=10%  Similarity=0.167  Sum_probs=58.0

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE  158 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~  158 (164)
                      ++|.|.-..++|+...+-.+|-++|+++++.+=+-. +.|+|-...- - +.+..+...++..+..+..+.|..
T Consensus         4 avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV~-~-~~~~~d~~~lr~~l~~~~~~lgv~   75 (90)
T COG3830           4 AVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVD-I-SKEVVDFAALRDELAAEGKKLGVD   75 (90)
T ss_pred             EEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeEEc-C-ChHhccHHHHHHHHHHHHHhcCcE
Confidence            678899999999999999999999999999765554 6678776542 1 235688999999999999888865

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

Probab=92.01  E-value=1.2  Score=27.96  Aligned_cols=33  Identities=18%  Similarity=0.208  Sum_probs=28.4

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      +.|.=+.+||.|.++++.|.+.|.+|.+...+.
T Consensus         2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~   34 (65)
T cd04882           2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFV   34 (65)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEc
Confidence            567778999999999999999999998776543

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

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

Probab=91.23  E-value=2.7  Score=27.02  Aligned_cols=34  Identities=21%  Similarity=0.295  Sum_probs=29.8

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEee
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS  119 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs  119 (164)
                      ..+.+..+.++|.|.++++.|.+.|+++.+....
T Consensus         2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~   35 (72)
T cd04883           2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVY   35 (72)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEe
Confidence            3577889999999999999999999999987544

This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK04435 hypothetical protein; Provisional

Probab=91.23  E-value=1.5  Score=33.55  Aligned_cols=39  Identities=15%  Similarity=0.160  Sum_probs=34.9

Q ss_pred             EcCeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           82 IGENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        82 ~~~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      .|+.+.|.+.++.++|+|.+|++.|.+.|.+|...+.+.
T Consensus        66 ~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i  104 (147)
T PRK04435         66 KGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSI  104 (147)
T ss_pred             CCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEc
Confidence            366799999999999999999999999999999887654

>PRK08577 hypothetical protein; Provisional

Probab=90.77  E-value=2.5  Score=31.51  Aligned_cols=37  Identities=11%  Similarity=0.049  Sum_probs=33.2

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .+.|.|.+..++|+|.+++..|.+.+.++.+.+..+.
T Consensus        56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~   92 (136)
T PRK08577         56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEEL   92 (136)
T ss_pred             EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEe
Confidence            4889999999999999999999999999998776553

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=90.25  E-value=1.2  Score=35.65  Aligned_cols=67  Identities=4%  Similarity=-0.007  Sum_probs=51.4

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHh
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEK  154 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~  154 (164)
                      ..+.|.+.++.|||++..|-+.|-+.|.++..++.+.. +.|++-....    +...+...++.+|-..-.+
T Consensus         7 ~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lvs----~~~~~~~~le~~L~~l~~~   74 (190)
T PRK11589          7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLS----GSWNAITLIESTLPLKGAE   74 (190)
T ss_pred             cEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEEe----CChhHHHHHHHHHHhhhhh
Confidence            45789999999999999999999999999999998876 4576655442    2233667777777665444

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

Probab=90.01  E-value=3.8  Score=26.93  Aligned_cols=32  Identities=16%  Similarity=0.192  Sum_probs=27.2

Q ss_pred             EEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           89 RVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        89 ~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      -+..+.+||.|.++++.|...|+++.+.....
T Consensus         3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp   34 (75)
T cd04880           3 VFSLKNKPGALAKALKVFAERGINLTKIESRP   34 (75)
T ss_pred             EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeee
Confidence            34567899999999999999999999986554

ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech

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

Probab=89.21  E-value=4.9  Score=26.84  Aligned_cols=34  Identities=15%  Similarity=0.188  Sum_probs=28.0

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      .+.+.-+.++|.|.++++.|.+.|+++++.....
T Consensus         3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p   36 (80)
T cd04905           3 SIVFTLPNKPGALYDVLGVFAERGINLTKIESRP   36 (80)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEE
Confidence            3455667889999999999999999999875443

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

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

Probab=88.94  E-value=3.9  Score=25.37  Aligned_cols=34  Identities=9%  Similarity=0.069  Sum_probs=30.8

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      +.|.++.++|.+.+++..|.+.++++.+.++...
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~   35 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRK   35 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEecc
Confidence            5688999999999999999999999999887764

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

>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=88.92  E-value=2  Score=26.56  Aligned_cols=34  Identities=18%  Similarity=0.348  Sum_probs=30.0

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      |.+..+.+||.|.++++.|...|.+|.+..+...
T Consensus         1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~   34 (56)
T cd04889           1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAET   34 (56)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEc
Confidence            4578899999999999999999999988877654

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

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

Probab=88.76  E-value=1.5  Score=28.28  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=31.3

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeeccc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNY  122 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~  122 (164)
                      .|.|..+.+||.|.++++.|.+.|++|.+.-+....
T Consensus         3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~   38 (66)
T cd04908           3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTS   38 (66)
T ss_pred             EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecC
Confidence            467889999999999999999999999998765543

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.

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

Probab=88.15  E-value=1.1  Score=28.20  Aligned_cols=33  Identities=9%  Similarity=0.094  Sum_probs=29.8

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      +.+.++.++|.+.++...|.+.+.++.+.+...
T Consensus         2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~   34 (71)
T cd04903           2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSR   34 (71)
T ss_pred             EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEe
Confidence            678899999999999999999999999887665

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.

>PF05088 Bac_GDH: Bacterial NAD-glutamate dehydrogenase

Probab=88.05  E-value=4.4  Score=41.93  Aligned_cols=76  Identities=14%  Similarity=0.128  Sum_probs=57.2

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEE---eecc--cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQAT---VSCN--YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~---vs~~--~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.++|.....+..|.+++-.|++|||.|+...   +.+.  ..+-++.+...-..+...+...+++.+.+++.+.|...
T Consensus       489 ~~~lkiy~~~~~~~Ls~vlPilenlGl~V~~e~~~~i~~~~~~~~~i~~F~l~~~~~~~~~~~~~~~~~~~a~~~v~~g~  568 (1528)
T PF05088_consen  489 RLRLKIYHPGEPLPLSDVLPILENLGLRVIDERPYEIRRADGRRVWIHDFGLQYPDGDALDLDDIRERFEEAFEAVWNGR  568 (1528)
T ss_pred             eEEEEEEcCCCCcCHHHHHHHHHhCCCEEEEEecceeecCCCceEEEEEEEEecCCCccccHHHHHHHHHHHHHHHhcCC
Confidence            388999999999999999999999999999965   3332  23444444433223445789999999999999887654


Q ss_pred             C
Q 031198          160 Q  160 (164)
Q Consensus       160 ~  160 (164)
                      .
T Consensus       569 ~  569 (1528)
T PF05088_consen  569 A  569 (1528)
T ss_pred             C
Confidence            3

>PLN03217 transcription factor ATBS1; Provisional

Probab=87.85  E-value=1.9  Score=30.51  Aligned_cols=50  Identities=18%  Similarity=0.338  Sum_probs=40.0

Q ss_pred             HHHhHhhHHhhhcc-CC---CCccccc---hhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            9 RALHRKLHILRTLT-NS---KSVKKSS---IIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         9 ~kln~rl~~LRslv-~~---~KmDKaS---Il~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      +++|+-...|++++ .+   -.-||+|   +|.++-.||+.|...|.+|-+.+..+-
T Consensus        20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL   76 (93)
T PLN03217         20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL   76 (93)
T ss_pred             HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999988 22   2234544   899999999999999999998776654

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

Probab=87.06  E-value=0.35  Score=45.73  Aligned_cols=37  Identities=24%  Similarity=0.282  Sum_probs=32.9

Q ss_pred             HHHHHHHhHhhHHhhhcc----C-CCCccccchhHHHHHHHH
Q 031198            5 LQRRRALHRKLHILRTLT----N-SKSVKKSSIIMDSLLYVC   41 (164)
Q Consensus         5 r~RR~kln~rl~~LRslv----~-~~KmDKaSIl~dAI~YIk   41 (164)
                      |-||.|-|+-||.|.-++    . .+-.|||||+-=||.|++
T Consensus        55 RsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   55 RSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH
Confidence            568999999999999987    2 388999999999999986

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=86.56  E-value=0.62  Score=41.88  Aligned_cols=39  Identities=23%  Similarity=0.172  Sum_probs=33.9

Q ss_pred             HHHHHHHHhHhhHHhhhccC----C-CCccccchhHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLTN----S-KSVKKSSIIMDSLLYVCK   42 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv~----~-~KmDKaSIl~dAI~YIke   42 (164)
                      -|+||++-|--|+.|--+++    | +..|||||+.=+-.|||-
T Consensus         9 A~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    9 ARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             HHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            37899999999999999872    2 679999999999999974

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

Probab=86.53  E-value=5.9  Score=24.69  Aligned_cols=35  Identities=20%  Similarity=0.194  Sum_probs=30.9

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .+.+.+..++|.|.+++..|.+.+.++.+.+....
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04878           2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPT   36 (72)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeec
Confidence            46788999999999999999999999999887653

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

>PRK00227 glnD PII uridylyl-transferase; Provisional

Probab=85.17  E-value=6.2  Score=37.64  Aligned_cols=71  Identities=15%  Similarity=0.116  Sum_probs=54.5

Q ss_pred             cCeEEEEEEe-cCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHh
Q 031198           83 GENFIVRVRC-NKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEK  154 (164)
Q Consensus        83 ~~~~~I~i~c-~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~  154 (164)
                      .++..+.|.. +.++|.|.++...|--.|+.|.+|++.+.+..+.+..... ..+...++..+.|.+..++..
T Consensus       544 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~a~~~~~~~~~~~~~v~~-~~~~~~~~~~~~~~~~~~~~~  615 (693)
T PRK00227        544 EEDGFFTVIWHGDYPRELVRVLALIAAKGWNILSARMVANGPWSAEFDVRA-NGPQDFDPQEFLQAYKSGVYS  615 (693)
T ss_pred             ccCCeEEEEecCCcccHHHHHHHHHHhcCceeeEeEEecCCceEEEEEEec-CCCCCCChHHHHHHHHHhhcC
Confidence            4555666766 9999999999999999999999999998554544433322 257778999999988877643

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=85.13  E-value=7.8  Score=30.99  Aligned_cols=70  Identities=9%  Similarity=0.113  Sum_probs=54.9

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeeccc-------ceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNY-------YFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVE  158 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~-------~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~  158 (164)
                      +.|.|.-..+||++..+-+.|-+.|++|.+-+.-+..       -|.+.....   -....+...++.++.......+.+
T Consensus        96 ~~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~---lP~~~~~~~L~~~l~~l~~eL~vd  172 (190)
T PRK11589         96 VWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAH---SPASQDAANIEQAFKALCTELNAQ  172 (190)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEE---cCCCCCHHHHHHHHHHHHHHhCce
Confidence            7889999999999999999999999999986654432       466665442   245577899999999887777665

>PRK07334 threonine dehydratase; Provisional

Probab=85.03  E-value=6.7  Score=34.47  Aligned_cols=35  Identities=14%  Similarity=0.127  Sum_probs=32.8

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      +.|+|.+..++|+|.+|+..|.+.+.+|.+.+...
T Consensus       327 v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~  361 (403)
T PRK07334        327 ARLRVDIRDRPGALARVTALIGEAGANIIEVSHQR  361 (403)
T ss_pred             EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEe
Confidence            88999999999999999999999999999988764

>PRK06737 acetolactate synthase 1 regulatory subunit; Validated

Probab=84.65  E-value=11  Score=25.94  Aligned_cols=36  Identities=11%  Similarity=0.171  Sum_probs=32.3

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      ..|.+.-+++||.|.++...|...|+++.+-+++..
T Consensus         3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~t   38 (76)
T PRK06737          3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNER   38 (76)
T ss_pred             EEEEEEEecCCCHHHHHHHHHhccCcceEEEEeccc
Confidence            357888899999999999999999999999888754

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=84.21  E-value=0.51  Score=45.96  Aligned_cols=55  Identities=20%  Similarity=0.300  Sum_probs=46.9

Q ss_pred             HHHHHHHHhHhhHHhhhcc--CCCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLT--NSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv--~~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      |++=|--+|+|...||-+|  .-.|+.|.+.+.-||+||++|+..-+.+..+.+.+.
T Consensus       284 EKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  284 EKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             HHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            5566888999999999999  458999999999999999999998888777655443

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=83.48  E-value=0.77  Score=42.56  Aligned_cols=35  Identities=26%  Similarity=0.294  Sum_probs=32.1

Q ss_pred             HHHHHhHhhHHhhhcc-----CCCCccccchhHHHHHHHH
Q 031198            7 RRRALHRKLHILRTLT-----NSKSVKKSSIIMDSLLYVC   41 (164)
Q Consensus         7 RR~kln~rl~~LRslv-----~~~KmDKaSIl~dAI~YIk   41 (164)
                      -|++||.-|..|-||+     -|+|.||-|||-=++.|++
T Consensus        36 HRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   36 HRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             HHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            6899999999999998     2699999999999999975

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

Probab=82.62  E-value=5.6  Score=26.47  Aligned_cols=33  Identities=18%  Similarity=0.234  Sum_probs=27.2

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      +-+..+++||.|.++++.|...|+++.+-..-.
T Consensus         3 l~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP   35 (74)
T cd04904           3 LIFSLKEEVGALARALKLFEEFGVNLTHIESRP   35 (74)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCC
Confidence            334557899999999999999999999966443

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

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

Probab=82.55  E-value=14  Score=25.89  Aligned_cols=34  Identities=15%  Similarity=0.200  Sum_probs=28.7

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEee
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVS  119 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs  119 (164)
                      ..|-+..++++|.|.+++..|...|+++.+-..-
T Consensus        15 tslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSR   48 (90)
T cd04931          15 ISLIFSLKEEVGALAKVLRLFEEKDINLTHIESR   48 (90)
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEec
Confidence            4566667889999999999999999999996543

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

>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional

Probab=81.99  E-value=7.1  Score=27.46  Aligned_cols=35  Identities=17%  Similarity=0.259  Sum_probs=32.1

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .|.+.-+++||.|.++...|-..|+++.+-+++..
T Consensus         4 ~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~T   38 (84)
T PRK13562          4 ILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHS   38 (84)
T ss_pred             EEEEEEECCCCHHHHHHHHHhccCcCeeeEEeccc
Confidence            57888899999999999999999999999888865

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

Probab=81.40  E-value=4.1  Score=26.54  Aligned_cols=33  Identities=6%  Similarity=0.110  Sum_probs=28.5

Q ss_pred             EEEEecCCCChHHHHHHHHHcCCCeEEEEEeec
Q 031198           88 VRVRCNKGENRLVSILEAFEEMGLIVRQATVSC  120 (164)
Q Consensus        88 I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~  120 (164)
                      +.+.=+.+||.|.++++.|.+.|.+|.+.....
T Consensus         2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~   34 (72)
T cd04884           2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAF   34 (72)
T ss_pred             EEEEecCCCccHHHHHHHHHHCCCeEEEEEecc
Confidence            456778999999999999999999999876554

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.

>COG4747 ACT domain-containing protein [General function prediction only]

Probab=80.79  E-value=12  Score=28.33  Aligned_cols=40  Identities=23%  Similarity=0.325  Sum_probs=34.3

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEE
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAM  126 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l  126 (164)
                      .|.|+-+++||.|.++..+|.+.|+++---++..++.|-+
T Consensus         5 QISvFlENk~GRL~~~~~~L~eagINiRA~tiAdt~dFGI   44 (142)
T COG4747           5 QISVFLENKPGRLASVANKLKEAGINIRAFTIADTGDFGI   44 (142)
T ss_pred             EEEEEecCCcchHHHHHHHHHHcCCceEEEEeccccCcce
Confidence            4789999999999999999999999999888776655543

>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional

Probab=80.69  E-value=15  Score=25.06  Aligned_cols=36  Identities=14%  Similarity=0.200  Sum_probs=32.0

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      ..+.+.-.++||.|.+++..|...|++|.+-++...
T Consensus         4 ~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t   39 (76)
T PRK11152          4 HQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQN   39 (76)
T ss_pred             EEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeec
Confidence            357788899999999999999999999999888764

>CHL00100 ilvH acetohydroxyacid synthase small subunit

Probab=80.65  E-value=12  Score=29.58  Aligned_cols=70  Identities=11%  Similarity=0.091  Sum_probs=48.3

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc---cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN---YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~---~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      ..|.|.-+++||+|.++...|-..|+++.+-++...   +...+.....+   +... .+.|...|.+.+.-.....
T Consensus         3 ~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~~sr~TIvv~~---~~~~-ieqL~kQL~KLidVl~V~~   75 (174)
T CHL00100          3 HTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQKGISRITMVVPG---DDRT-IEQLTKQLYKLVNILKVQD   75 (174)
T ss_pred             EEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCCccEEEEEEEC---CHHH-HHHHHHHHHHHhHhhEEEe
Confidence            357888899999999999999999999999888653   22233333221   1112 6788888877765544433

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

Probab=80.65  E-value=15  Score=24.78  Aligned_cols=29  Identities=21%  Similarity=0.303  Sum_probs=24.9

Q ss_pred             EecCCCChHHHHHHHHHcCCCeEEEEEee
Q 031198           91 RCNKGENRLVSILEAFEEMGLIVRQATVS  119 (164)
Q Consensus        91 ~c~k~~g~l~~i~~ale~l~L~V~~a~vs  119 (164)
                      .-+.++|.|.+++..|+..|+++.+-..-
T Consensus         6 ~l~~~~g~L~~iL~~f~~~~inl~~IeSR   34 (74)
T cd04929           6 SLKNEVGGLAKALKLFQELGINVVHIESR   34 (74)
T ss_pred             EcCCCCcHHHHHHHHHHHCCCCEEEEEec
Confidence            34788999999999999999999996543

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	164
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

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

 Score = 38.7 bits (89), Expect = 5e-04
 Identities = 39/205 (19%), Positives = 68/205 (33%), Gaps = 58/205 (28%)

Query: 2   VSRLQRRRALHRKLHILRTLTNSKSVK------------KSSIIMDSLLYVCKLKLKLEA 49
           + RL + +     L +L  + N+K+              +   + D L       + L+ 
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 50  I-----KREYSNLMAIKKAYLDLMKHNHVPKEVK------VEKIGE---NFIVR------ 89
                   E  +L+     YLD  +   +P+EV       +  I E   + +        
Sbjct: 294 HSMTLTPDEVKSLLL---KYLD-CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH 349

Query: 90  VRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAV-PQN---PQQALE----- 140
           V C+K    + S L   E      R+       +   D ++V P +   P   L      
Sbjct: 350 VNCDKLTTIIESSLNVLEP--AEYRK------MF---DRLSVFPPSAHIPTILLSLIWFD 398

Query: 141 --ARDVAQVILKATEKQAVEWQPSK 163
               DV  V+ K  +   VE QP +
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEKQPKE 423

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	164
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.58
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.44
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.43
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.41
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.4
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.35
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.35
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.29
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.25
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.21
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.12
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	98.8
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.77
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.72
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.5
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.23
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.83
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.3
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	97.28
1u8s_A	192	Glycine cleavage system transcriptional repressor,	97.07
2nyi_A	195	Unknown protein; protein structure initiative, PSI	96.99
1u8s_A	192	Glycine cleavage system transcriptional repressor,	96.95
2nyi_A	195	Unknown protein; protein structure initiative, PSI	96.86
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	95.96
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	95.83
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	95.63
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	95.58
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	95.34
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	94.99
3nrb_A	287	Formyltetrahydrofolate deformylase; N-terminal ACT	94.95
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	93.07
2f1f_A	164	Acetolactate synthase isozyme III small subunit; f	89.66
2pc6_A	165	Probable acetolactate synthase isozyme III (small;	85.68
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	83.09
2fgc_A	193	Acetolactate synthase, small subunit; regulatory s	81.97

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

Probab=99.58  E-value=2.4e-15  Score=104.30  Aligned_cols=58  Identities=19%  Similarity=0.297  Sum_probs=53.2

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC-CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS-KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMA   59 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~-~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~~   59 (164)
                      +.||+||.+||++|..||++| +. .|+|||+||.+||+||+.||.+++.|+.+...+..
T Consensus        12 ~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   71 (82)
T 1am9_A           12 AIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999999999999 44 89999999999999999999999999998877653

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

Probab=99.44  E-value=1.9e-13  Score=94.66  Aligned_cols=57  Identities=16%  Similarity=0.289  Sum_probs=52.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-C--CCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-N--SKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~--~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      +.||+||..||+.|..||++| .  ..|+||++||.+||+||+.|+++++.|+.+...+.
T Consensus         8 ~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~   67 (83)
T 1nkp_B            8 ALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999 3  48999999999999999999999999998877664

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

Probab=99.43  E-value=2.1e-13  Score=93.93  Aligned_cols=57  Identities=16%  Similarity=0.274  Sum_probs=52.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC--CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS--KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~--~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      ++||+||..||+.|..||++| ..  .|++|++||..||+||+.|++++++|+.+...+.
T Consensus        18 ~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A           18 ALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999 33  7999999999999999999999999999887664

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

Probab=99.41  E-value=3.1e-13  Score=94.83  Aligned_cols=57  Identities=23%  Similarity=0.275  Sum_probs=51.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC---CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS---KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~---~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      ++||+||.+||+.|..||.+| .+   .|+||++||.+||+||+.|+.+.+.+..+...+.
T Consensus        12 ~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A           12 VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999 43   6999999999999999999999999888765543

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

Probab=99.40  E-value=1.8e-13  Score=92.52  Aligned_cols=50  Identities=18%  Similarity=0.256  Sum_probs=44.9

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-C-CCCccccchhHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-N-SKSVKKSSIIMDSLLYVCKLKLKLEAIK   51 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~-~~KmDKaSIl~dAI~YIkeLq~~v~~Le   51 (164)
                      +.||+||.+||++|..|+++| . ..|+||+|||..||+||+.||.++.=|+
T Consensus        14 ~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B           14 KSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            368999999999999999999 3 5799999999999999999999876554

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

Probab=99.35  E-value=2.1e-13  Score=90.29  Aligned_cols=46  Identities=17%  Similarity=0.231  Sum_probs=41.3

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CCC------CccccchhHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NSK------SVKKSSIIMDSLLYVCKLKLKL   47 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~~------KmDKaSIl~dAI~YIkeLq~~v   47 (164)
                      +.||+||.+||+.|..|+++| ...      |+|||+||.+||+||+.||++.
T Consensus        11 ~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A           11 EVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999 433      7899999999999999999764

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

Probab=99.35  E-value=9.2e-13  Score=97.07  Aligned_cols=53  Identities=25%  Similarity=0.278  Sum_probs=47.9

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC----CCccccchhHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS----KSVKKSSIIMDSLLYVCKLKLKLEAIKREY   54 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~----~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~   54 (164)
                      +.||+||.+||++|..|+++| +.    .|+|||+||.+||+||+.||++++.|+++.
T Consensus        33 ~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           33 LIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999 44    478899999999999999999999998753

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

Probab=99.29  E-value=7.6e-13  Score=89.92  Aligned_cols=43  Identities=16%  Similarity=0.223  Sum_probs=39.5

Q ss_pred             cHHHHHHHHhHhhHHhhhcc-C----CCCccccchhHHHHHHHHHHHH
Q 031198            3 SRLQRRRALHRKLHILRTLT-N----SKSVKKSSIIMDSLLYVCKLKL   45 (164)
Q Consensus         3 ser~RR~kln~rl~~LRslv-~----~~KmDKaSIl~dAI~YIkeLq~   45 (164)
                      .||+||++||+.|..|++|| .    .+|+||||||..||+||+.|+-
T Consensus        16 ~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           16 IEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            58999999999999999999 3    3899999999999999999973

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

Probab=99.25  E-value=1.3e-11  Score=85.05  Aligned_cols=57  Identities=19%  Similarity=0.143  Sum_probs=51.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC---CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS---KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~---~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      +.||+||..||+.|..||++| .+   +|+.|++||..|++||+.|+++.+.|+.+...+.
T Consensus         7 ~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~   67 (80)
T 1nlw_A            7 EMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999 33   7889999999999999999999999998876654

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1

Probab=99.21  E-value=6.6e-12  Score=82.94  Aligned_cols=46  Identities=24%  Similarity=0.270  Sum_probs=41.2

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-C-------CCCccccchhHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-N-------SKSVKKSSIIMDSLLYVCKLKLKL   47 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~-------~~KmDKaSIl~dAI~YIkeLq~~v   47 (164)
                      +.||+||.+||..|..|++++ +       -++.+||+||..||+||+.||+++
T Consensus         8 ~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            8 HAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             GGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999 2       357779999999999999999865

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

Probab=99.12  E-value=1.9e-11  Score=83.58  Aligned_cols=50  Identities=14%  Similarity=0.187  Sum_probs=43.0

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CCCCcc----ccchhHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NSKSVK----KSSIIMDSLLYVCKLKLKLEAIK   51 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~~KmD----KaSIl~dAI~YIkeLq~~v~~Le   51 (164)
                      +.||+||..+|+.|..||.+| ...+.|    |++||..||+||+.||+++++++
T Consensus        11 ~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A           11 ALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            469999999999999999999 343444    55699999999999999999876

>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=98.80  E-value=1.9e-09  Score=72.11  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=41.8

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc---CCCCccccchhHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT---NSKSVKKSSIIMDSLLYVCKLKLKLE   48 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv---~~~KmDKaSIl~dAI~YIkeLq~~v~   48 (164)
                      +.||+|+..||+.|..||.++   +-+|+.|+.||..||+||..|++.++
T Consensus        18 ~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           18 MRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            358899999999999999998   24899999999999999999998653

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

Probab=98.77  E-value=4.9e-09  Score=88.72  Aligned_cols=46  Identities=22%  Similarity=0.315  Sum_probs=41.5

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc--CCCCccccchhHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT--NSKSVKKSSIIMDSLLYVCKLKLKL   47 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv--~~~KmDKaSIl~dAI~YIkeLq~~v   47 (164)
                      ++||+||+++|+.|..|++|+  +.+|+||+|||..||.||+.|+..-
T Consensus        18 ~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A           18 KSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            468999999999999999999  4689999999999999999998653

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

Probab=98.72  E-value=9.9e-09  Score=66.97  Aligned_cols=47  Identities=19%  Similarity=0.212  Sum_probs=42.0

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-C---CCCccccchhHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-N---SKSVKKSSIIMDSLLYVCKLKLKLE   48 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~---~~KmDKaSIl~dAI~YIkeLq~~v~   48 (164)
                      +.||+|+..||+-|..||.+| .   -+|+.|..||.-||+||..|++.++
T Consensus         8 ~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            8 ARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            358999999999999999988 3   3699999999999999999998764

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

Probab=98.50  E-value=6.9e-08  Score=82.59  Aligned_cols=44  Identities=16%  Similarity=0.204  Sum_probs=40.4

Q ss_pred             cHHHHHHHHhHhhHHhhhccC-----CCCccccchhHHHHHHHHHHHHH
Q 031198            3 SRLQRRRALHRKLHILRTLTN-----SKSVKKSSIIMDSLLYVCKLKLK   46 (164)
Q Consensus         3 ser~RR~kln~rl~~LRslv~-----~~KmDKaSIl~dAI~YIkeLq~~   46 (164)
                      +||+||.++|+.|..|++|++     .+|+||+|||..||.|||.|+..
T Consensus        20 ~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           20 IEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            588999999999999999993     58999999999999999999854

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

Probab=98.23  E-value=2.3e-07  Score=61.82  Aligned_cols=42  Identities=17%  Similarity=0.263  Sum_probs=37.7

Q ss_pred             HHHHHHHHhHhhHHhhhcc-CC---CCccccchhHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLT-NS---KSVKKSSIIMDSLLYVCKLKL   45 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv-~~---~KmDKaSIl~dAI~YIkeLq~   45 (164)
                      ||+|...||+-|..||.+| .+   +|+.|.-||.-||+||..||.
T Consensus        22 ER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           22 PLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            5668899999999999998 32   799999999999999999984

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

Probab=97.83  E-value=2.3e-05  Score=53.97  Aligned_cols=47  Identities=26%  Similarity=0.282  Sum_probs=40.7

Q ss_pred             HHHHhHhhHHhhhcc-CC----CCccccchhHHHHHHHHHHHHHHHHHHHHH
Q 031198            8 RRALHRKLHILRTLT-NS----KSVKKSSIIMDSLLYVCKLKLKLEAIKREY   54 (164)
Q Consensus         8 R~kln~rl~~LRslv-~~----~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~   54 (164)
                      |..+|+++..|..+| +.    .|.+|++||.-|++||+.||+..+.+.++.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e   55 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   55 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            778999999999999 33    578999999999999999999888776543

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

Probab=97.30  E-value=0.00032  Score=49.59  Aligned_cols=46  Identities=20%  Similarity=0.327  Sum_probs=39.4

Q ss_pred             HHHHHHHHhHhhHHhhhcc-C---CCCccccchhHHHHHHHHHHHHHHHH
Q 031198            4 RLQRRRALHRKLHILRTLT-N---SKSVKKSSIIMDSLLYVCKLKLKLEA   49 (164)
Q Consensus         4 er~RR~kln~rl~~LRslv-~---~~KmDKaSIl~dAI~YIkeLq~~v~~   49 (164)
                      ||.|=..+|+-|..||..| .   -+|+.|.-+|.-||+||..|++-+++
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            3456688999999999998 2   37999999999999999999988654

>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=97.28  E-value=0.0027  Score=42.58  Aligned_cols=71  Identities=14%  Similarity=0.173  Sum_probs=55.1

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      +.|.|.|+.+||++.+|...|-+.|.+|.+.+.... +.|.+.... +.  ....+.+.+...|.+.-...+..|
T Consensus         6 ~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v-~~--~~~~~l~~l~~~L~~~~~~~~~~~   77 (91)
T 1zpv_A            6 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVV-SS--DEKQDFTYLRNEFEAFGQTLNVKI   77 (91)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE-EE--SSCCCHHHHHHHHHHHHHHHTEEE
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEE-Ee--CCCCCHHHHHHHHHHHHHHcCCEE
Confidence            779999999999999999999999999999887654 455555444 21  224578999999988766666554

>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=97.07  E-value=0.0016  Score=50.03  Aligned_cols=71  Identities=4%  Similarity=0.033  Sum_probs=54.6

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.+||++.+|...|...|++|..+++... +.|.+-.....  ..  .+.+.++.+|.....+.++.+
T Consensus         6 ~~~itv~~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~--~~--~~~~~l~~~L~~~~~~~~~~~   77 (192)
T 1u8s_A            6 HLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG--SP--SNITRVETTLPLLGQQHDLIT   77 (192)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE--CH--HHHHHHHHHHHHHHHHHTCEE
T ss_pred             EEEEEEEcCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEec--CC--CCHHHHHHHHHHHHHhcCCEE
Confidence            4789999999999999999999999999999998754 66777443321  11  356788888888776655544

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

Probab=96.99  E-value=0.0026  Score=49.27  Aligned_cols=71  Identities=13%  Similarity=0.158  Sum_probs=56.9

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-------cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-------YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAV  157 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-------~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~  157 (164)
                      .+.|.|.|+.+||++..|...|-+.|++|.+++..+.       +.|.+......   ....+ +.++.++.......+.
T Consensus        93 ~~iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~---~~~~~-~~l~~~l~~~a~~l~~  168 (195)
T 2nyi_A           93 EYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAF---PFPLY-QEVVTALSRVEEEFGV  168 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEE---EGGGH-HHHHHHHHHHHHHHTC
T ss_pred             EEEEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEc---CCCcc-HHHHHHHHHHHHHcCe
Confidence            3889999999999999999999999999999988764       46777765532   12345 8899999988777776


Q ss_pred             CC
Q 031198          158 EW  159 (164)
Q Consensus       158 ~~  159 (164)
                      +|
T Consensus       169 di  170 (195)
T 2nyi_A          169 DI  170 (195)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>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=96.95  E-value=0.0063  Score=46.60  Aligned_cols=72  Identities=8%  Similarity=-0.023  Sum_probs=57.8

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc---------cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhc
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN---------YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQ  155 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~---------~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~  155 (164)
                      .+.|.|.|+.++|++..|.+.|-+.|++|..++..+.         +.|.+......   ....+.+.++..+.......
T Consensus        93 ~~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~~~---~~~~~~~~l~~~l~~~~~~~  169 (192)
T 1u8s_A           93 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARV---DSGCNLMQLQEEFDALCTAL  169 (192)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEE---CTTSCHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEEeC---CCCCCHHHHHHHHHHHHHHh
Confidence            3789999999999999999999999999999877653         35776665422   23568899999999888777


Q ss_pred             cCCC
Q 031198          156 AVEW  159 (164)
Q Consensus       156 ~~~~  159 (164)
                      +.+|
T Consensus       170 ~~~~  173 (192)
T 1u8s_A          170 DVQG  173 (192)
T ss_dssp             TCEE
T ss_pred             CceE
Confidence            7665

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

Probab=96.86  E-value=0.0016  Score=50.49  Aligned_cols=71  Identities=13%  Similarity=0.105  Sum_probs=50.2

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCC----HHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALE----ARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~----~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.+||++..|...|..+|++|+.+++... +.|.|-......  +  .+    .+.++++|..+..+.+..|
T Consensus         5 ~~~ltv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~~~--~--~~~~~~~~~l~~~L~~~~~~~~~~~   80 (195)
T 2nyi_A            5 SFVVSVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVSLN--A--KDGKLIQSALESALPGFQISTRRAS   80 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES--S--SSSHHHHHHHHHHSTTCEEEEEECC
T ss_pred             EEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEEec--C--ccchhHHHHHHHHHHHHHHhcCCeE
Confidence            3789999999999999999999999999999998754 678774433211  1  23    4556665554443434333

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

Probab=95.96  E-value=0.062  Score=44.31  Aligned_cols=72  Identities=8%  Similarity=0.057  Sum_probs=57.5

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.++|+...|...|-+.|.++.+++-..   .+.|.+......   ....+.+.+++++...-.+.+.+|
T Consensus         8 ~~vLtv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~---~~~~~~~~L~~~f~~la~~l~m~~   82 (286)
T 3n0v_A            8 TWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQ---PDDFDEAGFRAGLAERSEAFGMAF   82 (286)
T ss_dssp             CEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEEC---CSSCCHHHHHHHHHHHHGGGTCEE
T ss_pred             cEEEEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeEEEEEEec---CCCCCHHHHHHHHHHHHHHcCCEE
Confidence            478999999999999999999999999999988662   366777665532   225789999999987766666654

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

Probab=95.83  E-value=0.057  Score=44.97  Aligned_cols=73  Identities=10%  Similarity=0.209  Sum_probs=57.5

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.+.|+.++|+...|...|-+.|.+|.+++-..   .+.|.|.......  +...+.+.+++++...-...+.+|
T Consensus        22 ~~iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~FfMr~~~~~~--~~~~~~~~L~~~l~~la~~l~m~~   97 (302)
T 3o1l_A           22 TFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHEIRAD--TLPFDLDGFREAFTPIAEEFSMDW   97 (302)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEEEEEEEEGG--GSSSCHHHHHHHHHHHHHHHTCEE
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEEEEEEEecC--CCCCCHHHHHHHHHHHHHHhCCee
Confidence            378999999999999999999999999999988664   3668777655321  224788999999987666666654

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

Probab=95.63  E-value=0.069  Score=44.09  Aligned_cols=73  Identities=11%  Similarity=0.163  Sum_probs=57.0

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.+.|+.++|+...|...|-+.|.++.+++-..   .+.|.+.....-  .+...+.+.+++++...-.+.+.+|
T Consensus         6 ~~iLtv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~--~~~~~~~~~L~~~f~~la~~~~m~~   81 (288)
T 3obi_A            6 QYVLTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVVFNA--AAKVIPLASLRTGFGVIAAKFTMGW   81 (288)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEE--SSCCCCHHHHHHHHHHHHHHTTCEE
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEEEEc--CCCCCCHHHHHHHHHHHHHHcCCEE
Confidence            478999999999999999999999999999988642   356777665422  1224788999999987766666654

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

Probab=95.58  E-value=0.087  Score=43.59  Aligned_cols=76  Identities=13%  Similarity=0.297  Sum_probs=56.4

Q ss_pred             CeEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           84 ENFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        84 ~~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      ..+.+.+.|+.++|+...|...|-+.|.+|.+++-..   .+.|.+........++...+.+.+++++...-...+.+|
T Consensus         9 ~~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~~~~~~~~~~L~~~f~~la~~~~m~~   87 (292)
T 3lou_A            9 HQFVLTLSCPSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFFVRCVFHATDDADALRVDALRREFEPIAERFRMQW   87 (292)
T ss_dssp             CEEEEEEEEESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEECC----CCHHHHHHHHHHHHHHHTCEE
T ss_pred             CcEEEEEEcCCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceEEEEEEEccCcccCCCHHHHHHHHHHHHHhcCcEE
Confidence            3578999999999999999999999999999988662   366777655422100224788999999987666666654

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

Probab=95.34  E-value=0.12  Score=33.65  Aligned_cols=38  Identities=8%  Similarity=0.028  Sum_probs=34.1

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYY  123 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~  123 (164)
                      +.|+|.++.+||+|.+|...|.+.|++|.+.++...++
T Consensus         6 ~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~   43 (88)
T 2ko1_A            6 AGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDG   43 (88)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSS
T ss_pred             EEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCC
Confidence            67899999999999999999999999999988876543

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

Probab=94.99  E-value=0.053  Score=45.82  Aligned_cols=73  Identities=7%  Similarity=0.104  Sum_probs=54.6

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.|.|+.+||+...|...|-+.|.+|++++-... +.|++-......  +...+.+.++.++...-...+..|
T Consensus        12 ~~~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~--~~~~~~~~l~~~l~~~~~~~~~~~   85 (415)
T 3p96_A           12 SVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCP--ADVADGPALRHDVEAAIRKVGLDV   85 (415)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEEC--HHHHTSHHHHHHHHHHHHHTTCEE
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEec--CCcCCHHHHHHHHHHHHHHcCeEE
Confidence            4789999999999999999999999999999876543 567776654221  112255788888877656656554

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

Probab=94.95  E-value=0.097  Score=43.18  Aligned_cols=71  Identities=15%  Similarity=0.216  Sum_probs=52.6

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeec---ccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSC---NYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~---~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.+.|+.++|+...|...|-+.|.+|.+++-..   .+.|.|.......    ..+.+.+++++...-.+.+.+|
T Consensus         7 ~~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~----~~~~~~L~~~f~~la~~~~m~~   80 (287)
T 3nrb_A            7 QYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIP----VAGVNDFNSAFGKVVEKYNAEW   80 (287)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEECC----C---CHHHHHHHHHHGGGTCEE
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCCEEeeeeeecCCCCeEEEEEEEEcC----CCCHHHHHHHHHHHHHHcCCee
Confidence            478999999999999999999999999999988642   3667777655321    1344588888876666656554

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

Probab=93.07  E-value=0.25  Score=35.98  Aligned_cols=37  Identities=14%  Similarity=0.094  Sum_probs=33.9

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYY  123 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~  123 (164)
                      .|+|.|..++|+|.+|+..|.+.++++..+++...+.
T Consensus         2 ~~~v~~~dr~g~l~~i~~~l~~~~~ni~~~~~~~~g~   38 (190)
T 2jhe_A            2 RLEVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPIGR   38 (190)
T ss_dssp             EEEEEECSCTTHHHHHHHHHHHTTCCEEEEEEETTTE
T ss_pred             EEEEEEecCCcHHHHHHHHHHHcCCCeEEEEEecCCE
Confidence            4889999999999999999999999999999987644

>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=89.66  E-value=0.85  Score=34.55  Aligned_cols=36  Identities=19%  Similarity=0.257  Sum_probs=32.9

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      ..|.|..+++||.|.+|...|...|+++.+.++...
T Consensus         4 ~~IsV~v~NrpGvLarIt~lfs~rg~NI~Sl~v~~t   39 (164)
T 2f1f_A            4 RILSVLLENESGALSRVIGLFSQRGYNIESLTVAPT   39 (164)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCCCSEEEEEEC
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHHCCCCeeeceeeec
Confidence            468899999999999999999999999999888754

>2pc6_A Probable acetolactate synthase isozyme III (small; regulatory subunit, structural genomi protein structure initiative; HET: MSE; 2.50A {Nitrosomonas europaea atcc 19718} SCOP: d.58.18.6 d.58.18.6

Probab=85.68  E-value=1.4  Score=33.48  Aligned_cols=36  Identities=14%  Similarity=0.225  Sum_probs=32.8

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      ..|.|..+++||.|.+|...|...|+++.+.++...
T Consensus         5 ~~IsV~veNrpGvL~rI~~lfs~rg~NI~Sl~v~~t   40 (165)
T 2pc6_A            5 HIISLLMENEAGALSRVAGLFSARGYNIESLSVAPT   40 (165)
T ss_dssp             EEEEEEEECSTTHHHHHHHHHHHHTCCCCEEEEEEC
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHHCCCcEEEEEEEec
Confidence            468899999999999999999999999999888754

>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=83.09  E-value=4.5  Score=32.24  Aligned_cols=58  Identities=9%  Similarity=-0.008  Sum_probs=39.6

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeeccc------ceEEEEEeccCCCCCCCCHHHHHHHHH
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNY------YFAMDAIAVPQNPQQALEARDVAQVIL  149 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~------~f~l~~~~~~~~~~~~~~~~~ik~al~  149 (164)
                      +.|.|.+..++|+|.+|+..|-+.+.++.+.+.+...      ...+. ...    +.. +.+.+-+.|.
T Consensus         5 VtL~I~a~DRpGLLsDIt~vLAe~kiNIltIn~~~~~kG~~ng~A~I~-IEV----~d~-~Le~LL~kLr   68 (223)
T 1y7p_A            5 RGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIY-FEI----EGG-DFEKILERVK   68 (223)
T ss_dssp             EEEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEE-EEE----CSS-CHHHHHHHHH
T ss_pred             EEEEEEEcCCCCHHHHHHHHHHHcCCCceEEEEEccccCCcCCEEEEE-EEE----CCC-CHHHHHHHHh
Confidence            6789999999999999999999999999999988743      35555 322    222 6666555543

>2fgc_A Acetolactate synthase, small subunit; regulatory subunit, structural genomi protein structure initiative; 2.30A {Thermotoga maritima} SCOP: d.58.18.6 d.58.18.6

Probab=81.97  E-value=3.7  Score=31.96  Aligned_cols=36  Identities=14%  Similarity=0.229  Sum_probs=32.6

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      ..|.|.-+++||.|.+|...|...|++|.+.++...
T Consensus        30 ~~LsVlVeN~pGvLaRItglfsrRG~NI~SLtV~~t   65 (193)
T 2fgc_A           30 HLVSMLVHNKPGVMRKVANLFARRGFNISSITVGES   65 (193)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEEC
T ss_pred             EEEEEEECCCChHHHHHHHHHHHCCceEEEEEeecc
Confidence            568888999999999999999999999999888754

---

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	164
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.36
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.34
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.32
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.29
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.16
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	97.66
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	97.4
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.84
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	95.84
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	95.78
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	94.98
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	91.17
d2pc6a2	77	Acetolactate synthase small subunit, IlvH {Nitroso	80.65
d2f1fa1	76	Acetolactate synthase small subunit, IlvH {Escheri	80.17

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

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

Probab=99.47  E-value=1.5e-14  Score=93.50  Aligned_cols=52  Identities=19%  Similarity=0.306  Sum_probs=47.0

Q ss_pred             HHHHhHhhHHhhhcc-CC-CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            8 RRALHRKLHILRTLT-NS-KSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLMA   59 (164)
Q Consensus         8 R~kln~rl~~LRslv-~~-~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~~   59 (164)
                      |.+||++|..||++| +. +|+|||+||.+||+||+.||+++++|++|...+..
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   54 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKL   54 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999 44 79999999999999999999999999998876643

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

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

Probab=99.44  E-value=7.9e-14  Score=94.36  Aligned_cols=57  Identities=19%  Similarity=0.292  Sum_probs=52.0

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc--CCCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT--NSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv--~~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      .+||+||.+||+.|..|+++|  ...|+||++||.+||+||+.|+++++.|+.+...+.
T Consensus        12 ~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk   70 (80)
T d1am9a_          12 AIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999  357999999999999999999999999998876654

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

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

Probab=99.37  E-value=4.9e-13  Score=90.80  Aligned_cols=57  Identities=16%  Similarity=0.288  Sum_probs=51.2

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc---CCCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT---NSKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv---~~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      .+||+||.+||+.|..||+++   +..|+||++||..||+||+.|++++..|+.+...+.
T Consensus         8 ~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   67 (83)
T d1nkpb_           8 ALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999   348999999999999999999999999998776543

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

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

Probab=99.36  E-value=6.3e-13  Score=89.46  Aligned_cols=57  Identities=21%  Similarity=0.153  Sum_probs=51.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-C---CCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-N---SKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~---~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      ..||+||.+||+.|..|+++| +   ..|++|++||..||+||+.|+.+++.+..+...+.
T Consensus         7 ~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~   67 (79)
T d1nlwa_           7 EMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999 2   46899999999999999999999999998876654

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

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

Probab=99.34  E-value=2.3e-13  Score=88.21  Aligned_cols=46  Identities=24%  Similarity=0.266  Sum_probs=42.1

Q ss_pred             ccHHHHHHHHhHhhHHhhhccC--------CCCccccchhHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLTN--------SKSVKKSSIIMDSLLYVCKLKLKL   47 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv~--------~~KmDKaSIl~dAI~YIkeLq~~v   47 (164)
                      +.||+||.+||+.|..||++|+        ..|+|||+||..||+||+.||+++
T Consensus         8 ~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           8 HAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             GGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            4799999999999999999983        479999999999999999999865

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.32  E-value=1.4e-12  Score=89.43  Aligned_cols=57  Identities=23%  Similarity=0.292  Sum_probs=50.9

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-C---CCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-N---SKSVKKSSIIMDSLLYVCKLKLKLEAIKREYSNLM   58 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~---~~KmDKaSIl~dAI~YIkeLq~~v~~Le~e~~~~~   58 (164)
                      ..||+||.+||+.|..||++| +   ..|++|++||..||+||+.|+++++.|+.+...+.
T Consensus        12 ~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   72 (88)
T d1nkpa_          12 VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999998 3   26899999999999999999999999998776554

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

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

Probab=99.29  E-value=5.1e-13  Score=87.88  Aligned_cols=46  Identities=17%  Similarity=0.307  Sum_probs=42.0

Q ss_pred             cHHHHHHHHhHhhHHhhhcc-C--CCCccccchhHHHHHHHHHHHHHHH
Q 031198            3 SRLQRRRALHRKLHILRTLT-N--SKSVKKSSIIMDSLLYVCKLKLKLE   48 (164)
Q Consensus         3 ser~RR~kln~rl~~LRslv-~--~~KmDKaSIl~dAI~YIkeLq~~v~   48 (164)
                      .||+||.+||+.|..|++++ +  ..|+||++||..||+||+.||+.|+
T Consensus        19 ~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          19 RERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            58999999999999999999 3  4789999999999999999998764

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

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

Probab=99.16  E-value=6.4e-12  Score=81.66  Aligned_cols=45  Identities=18%  Similarity=0.258  Sum_probs=40.6

Q ss_pred             ccHHHHHHHHhHhhHHhhhcc-CC------CCccccchhHHHHHHHHHHHHH
Q 031198            2 VSRLQRRRALHRKLHILRTLT-NS------KSVKKSSIIMDSLLYVCKLKLK   46 (164)
Q Consensus         2 ~ser~RR~kln~rl~~LRslv-~~------~KmDKaSIl~dAI~YIkeLq~~   46 (164)
                      ++||+||.+||+.|..|+++| ..      .|+||++||..|++||+.||++
T Consensus        11 ~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_          11 EVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            469999999999999999998 32      4999999999999999999875

>d1zpva1 d.58.18.7 (A:1-83) UPF0237 protein SP0238 {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: SP0238-like
domain: UPF0237 protein SP0238
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.66  E-value=0.00025  Score=46.34  Aligned_cols=71  Identities=14%  Similarity=0.167  Sum_probs=56.1

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      +.|.+.|+.+||++..+...|-+.|.++.+.+-... +.|.+......   +...+.+.++.+|...-.+.|.++
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~---~~~~~~~~l~~~l~~la~~l~l~i   74 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSS---DEKQDFTYLRNEFEAFGQTLNVKI   74 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE---SSCCCHHHHHHHHHHHHHHHTEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEE---ecCCCHHHHHHHHHHHHHHcCcEE
Confidence            578999999999999999999999999999876554 56777654422   345788999999988776666543

>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=97.40  E-value=0.00079  Score=44.84  Aligned_cols=71  Identities=8%  Similarity=-0.026  Sum_probs=56.3

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc---------cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhcc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN---------YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQA  156 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~---------~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~  156 (164)
                      +.|.|.|+.+||++.+|...|-+.|++|.+.+..+.         ..|.+.....-   ....+...+++.+.......+
T Consensus         7 v~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~---p~~~~~~~l~~~l~~l~~~l~   83 (93)
T d1u8sa2           7 VEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARV---DSGCNLMQLQEEFDALCTALD   83 (93)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEE---CTTSCHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEc---CccccHHHHHHHHHHHHHHce
Confidence            568899999999999999999999999998765432         24777665432   345789999999998887777


Q ss_pred             CCC
Q 031198          157 VEW  159 (164)
Q Consensus       157 ~~~  159 (164)
                      .+|
T Consensus        84 v~~   86 (93)
T d1u8sa2          84 VQG   86 (93)
T ss_dssp             CEE
T ss_pred             eEE
Confidence            664

>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=96.84  E-value=0.0025  Score=41.65  Aligned_cols=71  Identities=4%  Similarity=0.035  Sum_probs=52.9

Q ss_pred             eEEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc-cceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           85 NFIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN-YYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        85 ~~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~-~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .+.|.+.|+.+||++.++...|-+.|.+|.+++.... +.|++-.....    ...+.+.++..|.+.-.+.|..+
T Consensus         5 ~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~----~~~~~~~l~~~L~~l~~~l~l~i   76 (86)
T d1u8sa1           5 HLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG----SPSNITRVETTLPLLGQQHDLIT   76 (86)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE----CHHHHHHHHHHHHHHHHHHTCEE
T ss_pred             EEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEc----CcccHHHHHHHHHHHHHHhCCEE
Confidence            4789999999999999999999999999999987765 34544433211    11256788888877766666543

>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=95.84  E-value=0.016  Score=37.08  Aligned_cols=44  Identities=11%  Similarity=-0.114  Sum_probs=32.4

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc------cceEEEEEe
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN------YYFAMDAIA  130 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~------~~f~l~~~~  130 (164)
                      -|+|.|..++|+|.+|+..|-+.+.++.+.+....      ..|+++...
T Consensus         3 ~i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~   52 (77)
T d1y7pa2           3 GLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEI   52 (77)
T ss_dssp             EEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEE
T ss_pred             eEEEEEecCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEc
Confidence            37899999999999999999999999999886642      346666543

>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=95.78  E-value=0.042  Score=34.63  Aligned_cols=62  Identities=13%  Similarity=0.128  Sum_probs=46.3

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCC
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEW  159 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~  159 (164)
                      .|.|..+++||.|.++...|...|+++...+++....|.+--..+.       +++...    +.+.+.||..
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Riiv~-------~~e~a~----~~L~~~g~~v   66 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGILRGIVS-------DPDKAY----KALKDNHFAV   66 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEEES-------CHHHHH----HHHHHTTCCE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEEEEC-------ChHHHH----HHHHHCCCEE
Confidence            3789999999999999999999999999999888776655444331       334443    3456666654

>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=94.98  E-value=0.1  Score=32.59  Aligned_cols=64  Identities=14%  Similarity=0.197  Sum_probs=46.1

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecccceEEEEEeccCCCCCCCCHHHHHHHHHHHHHhccCCCCC
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCNYYFAMDAIAVPQNPQQALEARDVAQVILKATEKQAVEWQP  161 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~~~f~l~~~~~~~~~~~~~~~~~ik~al~~ai~~~~~~~~~  161 (164)
                      .|.|..+++||.|.++++.|.+.|++|....+....++.+-...+.       +++    ...+++.+.||+.+.
T Consensus         1 ViaV~v~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~vd-------d~~----~a~~~L~~~G~~vl~   64 (71)
T d2f06a1           1 VVGISCPNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRPS-------NMD----KCIEVLKEKKVDLLA   64 (71)
T ss_dssp             EEEEEEESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEES-------CHH----HHHHHHHHTTCEEEC
T ss_pred             CEEEEecCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEEC-------CHH----HHHHHHHHCCCEEEc
Confidence            3678889999999999999999999999988776666655444332       344    334555666766543

>d2fgca2 d.58.18.6 (A:27-104) Acetolactate synthase small subunit, IlvH {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Thermotoga maritima [TaxId: 2336]

Probab=91.17  E-value=0.54  Score=29.91  Aligned_cols=36  Identities=14%  Similarity=0.229  Sum_probs=33.0

Q ss_pred             EEEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           86 FIVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        86 ~~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      ..|.+..+++||.|.++...|...|+++.+-+++..
T Consensus         4 ~tisvlv~n~pGvL~Ri~~lF~rRg~NI~SL~v~~t   39 (78)
T d2fgca2           4 HLVSMLVHNKPGVMRKVANLFARRGFNISSITVGES   39 (78)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEEC
T ss_pred             EEEEEEEeCCCcHHHHHHHHHhhCCcceEEEEEeec
Confidence            568899999999999999999999999999888765

>d2pc6a2 d.58.18.6 (A:1-77) Acetolactate synthase small subunit, IlvH {Nitrosomonas europaea [TaxId: 915]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Nitrosomonas europaea [TaxId: 915]

Probab=80.65  E-value=1.6  Score=27.50  Aligned_cols=35  Identities=14%  Similarity=0.232  Sum_probs=31.6

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .|.+.-+++||.|.++...|...|+++.+-+++..
T Consensus         4 tisv~veN~pGvL~Ris~lF~rRg~NI~Sltv~~t   38 (77)
T d2pc6a2           4 IISLLMENEAGALSRVAGLFSARGYNIESLSVAPT   38 (77)
T ss_dssp             EEEEEEECSTTHHHHHHHHHHHHTCCCCEEEEEEC
T ss_pred             EEEEEEECCccHHHHHHHHHhccCcceEEEEEecc
Confidence            57788899999999999999999999999888764

>d2f1fa1 d.58.18.6 (A:2-77) Acetolactate synthase small subunit, IlvH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Escherichia coli [TaxId: 562]

Probab=80.17  E-value=2.7  Score=26.27  Aligned_cols=35  Identities=20%  Similarity=0.295  Sum_probs=31.0

Q ss_pred             EEEEEecCCCChHHHHHHHHHcCCCeEEEEEeecc
Q 031198           87 IVRVRCNKGENRLVSILEAFEEMGLIVRQATVSCN  121 (164)
Q Consensus        87 ~I~i~c~k~~g~l~~i~~ale~l~L~V~~a~vs~~  121 (164)
                      .|.+.-+++||.|.++...|...|+++.+-+++..
T Consensus         3 tlsv~v~N~~GVL~RisglF~rRg~NI~Sl~v~~t   37 (76)
T d2f1fa1           3 ILSVLLENESGALSRVIGLFSQRGYNIESLTVAPT   37 (76)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHTTTCCCSEEEEEEC
T ss_pred             EEEEEEECCCcHHHHHHHHHHhcCcceEEEEEccc
Confidence            46777899999999999999999999999888755