Citrus Sinensis ID: 030331

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
Protein Sequence
MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEEccEEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccHHHHHcccccccccccccccccHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEEEcccEEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEccc
Coil and Loop (DISEMBL)
mgylgqsleakgsmkrkqcssssptkieRKTIEKNRRDQMKNLYSTLKsllpnqpskeelslpdqvDEAINYIKMLETKLKECKKRKEslqgrershacisdgtearlmtssspkapeieiheMGSNLEVILtsgvddqfIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
Flexible Loop (DISEMBL)
mgylgqsleakgsmkrkqcssssptkierktieknRRDQMKNLYSTLKsllpnqpskeelslpdqVDEAINYIKMLETKLKECKkrkeslqgrershacisdgtearlmtsssPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
Low Complexity Region (SEG)
MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
Disordered region (IsUnstruct)
********************************************************************AINYIKML***********************************************MGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCY*
Disordered Region (DISOPRED)
**********************************NRRDQMKNLYSTLKSLLPN********LPDQVDEAINYIKMLE******************************************EIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCY*
Disordered Region (DISEMBL)
MGYLGQSL*******************ERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKEC**************ACISDGTE********PKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
Disordered Region (DISPRO)
**************************IERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESL************************KAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQxxxxxxxxxxxxxxxxxxxxxxxxxxxxERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVCYN
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	179	2.2.26 [Sep-21-2011]
Q9FLI1	174	Transcription factor bHLH	no	no	0.843	0.867	0.309	8e-12
Q9STJ6	221	Transcription factor bHLH	no	no	0.804	0.651	0.276	5e-09
Q9STJ7	163	Transcription factor bHLH	no	no	0.770	0.846	0.296	3e-08
Q9M1K1	253	Transcription factor ORG2	no	no	0.810	0.573	0.246	1e-05
Q9LQ08	259	Transcription factor bHLH	no	no	0.368	0.254	0.333	5e-05
Q9LN95	257	Transcription factor bHLH	no	no	0.368	0.256	0.363	5e-05
Q9FYE6	240	Transcription factor bHLH	no	no	0.379	0.283	0.352	0.0003
Q9ZPY8	566	Transcription factor ABA-	no	no	0.681	0.215	0.258	0.0005

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

 Score = 70.1 bits (170), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 47/152 (30%), Positives = 81/152 (53%), Gaps = 1/152 (0%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K+  +  E+ RR +M +LY++L+SLLP    K + S  DQV+EA+NYIK L+ K+KE   
Sbjct: 3   KMMHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKELSV 62

Query: 86  RKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTS-GVDDQFIFYE 144
           R++ L    R     S   + +           + + +    +E++L+S     Q  F  
Sbjct: 63  RRDDLMVLSRGSLLGSSNGDFKEDVEMISGKNHVVVRQCLVGVEIMLSSRCCGGQPRFSS 122

Query: 145 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           V+++L + G  +LN+  S+V + + + I AEV
Sbjct: 123 VLQVLSEYGLCLLNSISSIVDDRLVYTIQAEV 154

Arabidopsis thaliana (taxid: 3702)

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

 Score = 60.8 bits (146), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 79/152 (51%), Gaps = 8/152 (5%)

Query: 30  KTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKES 89
           + IE+ RR +M  L++TL++ LP +  K + ++ D V+ A+N+IK  E ++KE   R++ 
Sbjct: 48  RDIERQRRQEMATLFATLRTHLPLKYIKGKRAVSDHVNGAVNFIKDTEARIKELSARRDE 107

Query: 90  LQGRERSHACISD---GTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVD--DQFIFYE 144
           L  RE      S+   G     +  S P    ++ H  G  LEV+++S     +     +
Sbjct: 108 L-SRETGQGYKSNPDPGKTGSDVGKSEPATVMVQPHVSG--LEVVVSSNSSGPEALPLSK 164

Query: 145 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           V+  + + G E++++  + V + + H I  EV
Sbjct: 165 VLETIQEKGLEVMSSFTTRVNDRLMHTIQVEV 196

Arabidopsis thaliana (taxid: 3702)

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

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 79/155 (50%), Gaps = 17/155 (10%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K+  K IEK RR +M +LY++L+SLLP +  + + S  DQV  A+NYI  L+  +K+   
Sbjct: 3   KLVHKEIEKRRRQEMASLYASLRSLLPLEFIQGKRSTSDQVKGAVNYIDYLQRNIKDINS 62

Query: 86  RKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGS----NLEVILTSGVDDQFI 141
           +++ L         +  G   R  +S+  +  EI  H +       +E++L+     Q  
Sbjct: 63  KRDDL--------VLLSGRSFR--SSNEQEWNEISNHVVIRPCLVGIEIVLSIL---QTP 109

Query: 142 FYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           F  V+++L + G  +L    S V + + H + AEV
Sbjct: 110 FSSVLQVLREHGLYVLGYICSSVNDRLIHTLQAEV 144

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M1K1|ORG2_ARATH Transcription factor ORG2 OS=Arabidopsis thaliana GN=ORG2 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 39/158 (24%), Positives = 77/158 (48%), Gaps = 13/158 (8%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K+     E++RR ++  L+S+L+S LP     ++LS+P+ V +++ YI  L+ ++K   +
Sbjct: 73  KLNHNASERDRRKKINTLFSSLRSCLPASDQSKKLSIPETVSKSLKYIPELQQQVKRLIQ 132

Query: 86  RKESLQGRERSHACISDGTEARLMTSSSPKA-----PEIEIHEMGSN-LEVILTSGVDDQ 139
           +KE +  R      +S   +  L     PKA       +    +G N + V ++S     
Sbjct: 133 KKEEILVR------VSGQRDFELYDKQQPKAVASYLSTVSATRLGDNEVMVQVSSSKIHN 186

Query: 140 FIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEV 176
           F    V+  + +DG  +++   S   G  +F+ +H +V
Sbjct: 187 FSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQV 224

Arabidopsis thaliana (taxid: 3702)

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

 Score = 47.4 bits (111), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 44/66 (66%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K++ + IE+ RR ++ +L+  L++LLP Q  + + S  D + +A+NYIK L+ K+KE  +
Sbjct: 75  KMKHRDIERQRRQEVSSLFKRLRTLLPFQYIQGKRSTSDHIVQAVNYIKDLQIKIKELNE 134

Query: 86  RKESLQ 91
           ++  ++
Sbjct: 135 KRNRVK 140

Arabidopsis thaliana (taxid: 3702)

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

 Score = 47.4 bits (111), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 43/66 (65%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           + + K +E+ RR +  +L+  L+ LLP+Q  K + S  D V EA+NYIK L+ K+KE  +
Sbjct: 76  RAKHKELERQRRQENTSLFKILRYLLPSQYIKGKRSSADHVLEAVNYIKDLQKKIKEVSE 135

Query: 86  RKESLQ 91
           +++ ++
Sbjct: 136 KRDRIK 141

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FYE6|BH101_ARATH Transcription factor bHLH101 OS=Arabidopsis thaliana GN=BHLH101 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K+     E++RR ++  LYS+L++LLP    K +LS+P  V   + YI   + +L+   +
Sbjct: 67  KLNHNASERDRRRKLNALYSSLRALLPLSDQKRKLSIPMTVARVVKYIPEQKQELQRLSR 126

Query: 86  RKESLQGR 93
           RKE L  R
Sbjct: 127 RKEELLKR 134

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZPY8|AIB_ARATH Transcription factor ABA-INDUCIBLE bHLH-TYPE OS=Arabidopsis thaliana GN=AIB PE=2 SV=2

 Score = 43.9 bits (102), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 71/143 (49%), Gaps = 21/143 (14%)

Query: 33  EKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG 92
           E+ RR+++   +  L+S++PN    ++ SL   + +AI+YIK L+ K+K        +  
Sbjct: 400 ERQRREKLNQRFYALRSVVPNISKMDKASL---LGDAISYIKELQEKVK--------IME 448

Query: 93  RERSHACISDGTEARLMTSSS---PKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRIL 149
            ER       GT+  L  S++    ++PE++I  M   + V + S +D       +I+ +
Sbjct: 449 DERV------GTDKSLSESNTITVEESPEVDIQAMNEEVVVRVISPLDSHPA-SRIIQAM 501

Query: 150 HQDGAEILNAKFSVVGNTIFHVI 172
                 ++ AK S+  +T+FH  
Sbjct: 502 RNSNVSLMEAKLSLAEDTMFHTF 524

Transcription activator. Regulates positively abscisic acid (ABA) response. Confers drought tolerance and sensitivity to ABA.

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	179
356544962	211	PREDICTED: transcription factor bHLH36-l	0.865	0.734	0.557	7e-45
356543837	222	PREDICTED: transcription factor bHLH36-l	0.826	0.666	0.572	2e-41
147822237	174	hypothetical protein VITISV_010916 [Viti	0.843	0.867	0.535	2e-41
359496902	152	PREDICTED: transcription factor bHLH36-l	0.837	0.986	0.532	6e-41
356515176	224	PREDICTED: transcription factor bHLH36-l	0.865	0.691	0.535	4e-40
224125352	183	predicted protein [Populus trichocarpa]	0.826	0.808	0.537	3e-39
302143302	215	unnamed protein product [Vitis vinifera]	0.832	0.693	0.552	4e-39
225446384	206	PREDICTED: transcription factor bHLH118-	0.832	0.723	0.552	4e-39
255536797	210	DNA binding protein, putative [Ricinus c	0.810	0.690	0.536	2e-38
224121740	218	predicted protein [Populus trichocarpa]	0.893	0.733	0.542	6e-38

>gi|356544962|ref|XP_003540915.1| PREDICTED: transcription factor bHLH36-like [Glycine max]

 Score =  185 bits (469), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 87/156 (55%), Positives = 121/156 (77%), Gaps = 1/156 (0%)

Query: 22  SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK 81
           SS TK+ER+ +EKNRR+QMKNLY+ L SLLP+   KE L LPDQVDEAINYIK LE K+K
Sbjct: 10  SSSTKVERRLVEKNRRNQMKNLYNKLNSLLPSYNPKEALPLPDQVDEAINYIKSLEAKVK 69

Query: 82  ECKKRKESLQG-RERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQF 140
             +++KE+LQG R+RS  C S+ +     TS  PK+P++EIHE+GS+L+V+LT G+D QF
Sbjct: 70  MAQEKKENLQGIRKRSRGCFSNNSANFAATSGFPKSPQLEIHEVGSSLQVVLTCGLDHQF 129

Query: 141 IFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           IFYE+I+ILH++  E+ +   S+ G+++ HV+HAE+
Sbjct: 130 IFYEIIQILHEENIEVRSVNSSLAGDSVLHVVHAEI 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543837|ref|XP_003540366.1| PREDICTED: transcription factor bHLH36-like [Glycine max]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 87/152 (57%), Positives = 114/152 (75%), Gaps = 4/152 (2%)

Query: 25  TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECK 84
           TK+ERK +EKNRR QMKNLYS L SLLP +  KE +SLPDQ+DEAINYIK LETK+K  +
Sbjct: 13  TKVERKIVEKNRRSQMKNLYSELNSLLPTRNPKEAMSLPDQIDEAINYIKSLETKVKLEQ 72

Query: 85  KRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYE 144
           ++KE L+ R+R+    S  +EA+     S K+P I+IHE G+ LEVILT GVD QF+F E
Sbjct: 73  EKKERLKERKRTRGGCSSSSEAQ----GSLKSPNIQIHETGNLLEVILTCGVDSQFMFCE 128

Query: 145 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           +IRILH++  E++NA  S+VG+ + HV+H EV
Sbjct: 129 IIRILHEENVEVINANSSMVGDLVIHVVHGEV 160

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147822237|emb|CAN61967.1| hypothetical protein VITISV_010916 [Vitis vinifera]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 84/157 (53%), Positives = 118/157 (75%), Gaps = 6/157 (3%)

Query: 20  SSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETK 79
           S+ S ++ +RKTIE+NRR+ MK+LYS L SL+P+Q S+E ++LPDQ+DEA NYIK L+ K
Sbjct: 3   SNPSSSRTDRKTIERNRRNHMKSLYSKLNSLVPHQTSREAITLPDQLDEAANYIKRLQEK 62

Query: 80  LKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQ 139
           L++ K+RK++L G ER +   + G    L      K P+I+IHE GS LEV+L +G+D Q
Sbjct: 63  LEKMKERKDNLMGFERPNTSPNSGAMVGL------KPPQIDIHEKGSALEVVLITGLDFQ 116

Query: 140 FIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           F+F E IR+LH++GAEI+NA FSVV +T+FH IHA+V
Sbjct: 117 FMFNETIRVLHEEGAEIVNASFSVVDDTVFHTIHAQV 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496902|ref|XP_003635365.1| PREDICTED: transcription factor bHLH36-like, partial [Vitis vinifera] gi|296086982|emb|CBI33238.3| unnamed protein product [Vitis vinifera]

 Score =  172 bits (435), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 83/156 (53%), Positives = 117/156 (75%), Gaps = 6/156 (3%)

Query: 20  SSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETK 79
           S+ S ++ +RKTIE+NRR+ MK+LYS L SL+P+Q S+E ++LPDQ+DEA NYIK L+ K
Sbjct: 3   SNPSSSRTDRKTIERNRRNHMKSLYSKLNSLVPHQTSREAITLPDQLDEAANYIKRLQEK 62

Query: 80  LKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQ 139
           L++ K+RK++L G ER +   + G    L      K P+I+IHE GS LEV+L +G+D Q
Sbjct: 63  LEKMKERKDNLMGFERPNTSPNSGAMVGL------KPPQIDIHEKGSALEVVLITGLDFQ 116

Query: 140 FIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE 175
           F+F E IR+LH++GAEI+NA FSVV +T+FH IHA+
Sbjct: 117 FMFNETIRVLHEEGAEIVNASFSVVDDTVFHTIHAQ 152

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356515176|ref|XP_003526277.1| PREDICTED: transcription factor bHLH36-like [Glycine max]

 Score =  169 bits (428), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 84/157 (53%), Positives = 119/157 (75%), Gaps = 2/157 (1%)

Query: 22  SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK 81
           SS TK+ER+ +EKNRR+QMK L + L SLLP+   KE L LPDQVDEAINYIK LE K+K
Sbjct: 10  SSSTKVERRLVEKNRRNQMKILCNKLNSLLPSYNPKEALPLPDQVDEAINYIKSLEAKVK 69

Query: 82  ECKKRKESLQG-RERSHACISDGTEARLMTSSS-PKAPEIEIHEMGSNLEVILTSGVDDQ 139
             +++KE LQG R+RS  C S+ +     TS+  PK+P++EIHE+GS+L+V+LT G+D Q
Sbjct: 70  MAQEKKECLQGIRKRSRDCFSNNSTNFAATSAGFPKSPQLEIHEVGSSLQVVLTCGLDHQ 129

Query: 140 FIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           FIF E+IR+LH++  ++ +A  S+ G+++ HV+HAE+
Sbjct: 130 FIFSEIIRMLHEENIDVRSANSSLAGDSMLHVVHAEI 166

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125352|ref|XP_002329784.1| predicted protein [Populus trichocarpa] gi|222870846|gb|EEF07977.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 85/158 (53%), Positives = 120/158 (75%), Gaps = 10/158 (6%)

Query: 23  SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEE-LSLPDQVDEAINYIKMLETKLK 81
           S ++ +RKTIE+NRR+QMK LYS L SL+P+Q S+E  LSLPDQ+DEA +YIK L+T L+
Sbjct: 6   SSSRTDRKTIERNRRNQMKALYSQLNSLVPHQSSREPVLSLPDQLDEAASYIKRLQTNLE 65

Query: 82  ECKKRKESLQGRER-SHACIS--DGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDD 138
             K++K++L G ER ++A +S  +GT   L      ++P+IEI E GS LEV+L +G+D 
Sbjct: 66  RMKEKKDNLMGTERKNYASMSSCNGTTTGL------RSPQIEIRETGSTLEVVLITGLDG 119

Query: 139 QFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           QF+F E IR+LH++GAEI+NA FSVV +T+FH IH++V
Sbjct: 120 QFMFNETIRVLHEEGAEIINASFSVVEDTVFHTIHSKV 157

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143302|emb|CBI21863.3| unnamed protein product [Vitis vinifera]

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 84/152 (55%), Positives = 115/152 (75%), Gaps = 3/152 (1%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K ERK +EKNRR+ MKNLYS L SLLP+Q SKE  S+PDQVDEA++YIK L+  L++ K+
Sbjct: 21  KAERKIVEKNRRNLMKNLYSKLNSLLPDQSSKEAQSIPDQVDEAVSYIKSLQGNLEKLKE 80

Query: 86  RKESL-QGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYE 144
           +KESL   R+R H C +  T     ++ S ++P +EI EMGSNL+V L +G++DQ IFY+
Sbjct: 81  KKESLMSSRKRPHTCST--TSVGETSTPSLRSPVMEIREMGSNLQVTLVTGLEDQSIFYD 138

Query: 145 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           +I ILH++ AE+L+A FSVVGN+ FHV+ A+V
Sbjct: 139 IIGILHEESAEVLSASFSVVGNSAFHVLIAQV 170

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446384|ref|XP_002274262.1| PREDICTED: transcription factor bHLH118-like [Vitis vinifera]

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 84/152 (55%), Positives = 115/152 (75%), Gaps = 3/152 (1%)

Query: 26  KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
           K ERK +EKNRR+ MKNLYS L SLLP+Q SKE  S+PDQVDEA++YIK L+  L++ K+
Sbjct: 12  KAERKIVEKNRRNLMKNLYSKLNSLLPDQSSKEAQSIPDQVDEAVSYIKSLQGNLEKLKE 71

Query: 86  RKESL-QGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYE 144
           +KESL   R+R H C +  T     ++ S ++P +EI EMGSNL+V L +G++DQ IFY+
Sbjct: 72  KKESLMSSRKRPHTCST--TSVGETSTPSLRSPVMEIREMGSNLQVTLVTGLEDQSIFYD 129

Query: 145 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           +I ILH++ AE+L+A FSVVGN+ FHV+ A+V
Sbjct: 130 IIGILHEESAEVLSASFSVVGNSAFHVLIAQV 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255536797|ref|XP_002509465.1| DNA binding protein, putative [Ricinus communis] gi|223549364|gb|EEF50852.1| DNA binding protein, putative [Ricinus communis]

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 80/149 (53%), Positives = 114/149 (76%), Gaps = 4/149 (2%)

Query: 28  ERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRK 87
           +RKTIE+NRR+QMK LYS L SL+P+  S+E +SLPDQ+DEA NYIK L+ KL++ K+RK
Sbjct: 39  DRKTIERNRRNQMKALYSQLNSLVPHHSSRESVSLPDQLDEAANYIKKLQIKLEKMKERK 98

Query: 88  ESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIR 147
           +SL G ER +A     T A +      ++P+IE++ +GS LEV+L +G+D QF+F E IR
Sbjct: 99  DSLMGIERPNASAGCSTRAGMRL----RSPQIEVNGIGSALEVVLVTGLDCQFLFNETIR 154

Query: 148 ILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           IL ++GAEI+NA FSV+ +T+FH+IH++V
Sbjct: 155 ILQEEGAEIVNATFSVLDDTVFHIIHSKV 183

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224121740|ref|XP_002330641.1| predicted protein [Populus trichocarpa] gi|222872245|gb|EEF09376.1| predicted protein [Populus trichocarpa]

 Score =  162 bits (409), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 90/166 (54%), Positives = 124/166 (74%), Gaps = 6/166 (3%)

Query: 12  GSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAIN 71
           G++  +  S+ S TK ERK IEKNRR+QMK LYS L SLLPNQ  KE   LPDQ+DEAI+
Sbjct: 7   GTVIMESSSNISSTKTERKIIEKNRRNQMKTLYSKLNSLLPNQNFKEPQPLPDQIDEAIS 66

Query: 72  YIKMLETKLKECKKRKESL-QGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEV 130
           +IK LE KLK+ K++KE L   R+RS+ C  D      M  +SPK P+++I E+GS LE+
Sbjct: 67  HIKSLEEKLKKAKEKKEGLTSSRKRSYTCTYDP-----MPIASPKPPQLKIQELGSALEI 121

Query: 131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
           +LTSG D+QF+FYE+IRILH++G E+++A F V+G++IF V+HA++
Sbjct: 122 VLTSGPDNQFLFYEIIRILHEEGVEVVSANFQVLGDSIFQVLHAQM 167

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	179
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.910	0.857	0.401	5.6e-29
TAIR|locus:2165311	174	AT5G51780 "AT5G51780" [Arabido	0.843	0.867	0.309	4.9e-14
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.860	0.620	0.265	5e-12
TAIR|locus:2138019	163	AT4G25400 "AT4G25400" [Arabido	0.770	0.846	0.296	2e-10
TAIR|locus:2080600	253	bHLH38 "basic helix-loop-helix	0.810	0.573	0.246	4.5e-09
TAIR|locus:4515102513	174	AT1G10586 [Arabidopsis thalian	0.798	0.821	0.243	7.6e-09
TAIR|locus:504956298	259	AT1G62975 "AT1G62975" [Arabido	0.491	0.339	0.315	6.9e-07
TAIR|locus:2146663	240	BHLH101 "AT5G04150" [Arabidops	0.832	0.620	0.233	7.9e-07
TAIR|locus:2080615	258	bHLH39 "basic helix-loop-helix	0.810	0.562	0.253	9.9e-07
TAIR|locus:505006117	181	AT1G10585 [Arabidopsis thalian	0.787	0.779	0.243	1.2e-06

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

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 67/167 (40%), Positives = 107/167 (64%)

Query:    14 MKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYI 73
             M+    ++     ++RKT+EKNRR QMK+LYS L SLLP+  S E L+LPDQ+DEA NYI
Sbjct:     1 MEPSHSNTGQSRSVDRKTVEKNRRMQMKSLYSELISLLPHHSSTEPLTLPDQLDEAANYI 60

Query:    74 KMLETKLKECKKRKESLQGR---ERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEV 130
             K L+  +++ ++RK +L      E+ ++  S    + +  S   K P+IEI E GS   +
Sbjct:    61 KKLQVNVEKKRERKRNLVATTTLEKLNSVGSSSVSSSVDVSVPRKLPKIEIQETGSIFHI 120

Query:   131 ILTSGVDDQFIFYEVIRILHQD-GAEILNAKFSVVGNTIFHVIHAEV 176
              L + ++ +F+F E+IR+L ++ GAEI +A +S+V + +FH +H +V
Sbjct:   121 FLVTSLEHKFMFCEIIRVLTEELGAEITHAGYSIVDDAVFHTLHCKV 167

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0050832 "defense response to fungus" evidence=IEP

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

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 47/152 (30%), Positives = 81/152 (53%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
             K+  +  E+ RR +M +LY++L+SLLP    K + S  DQV+EA+NYIK L+ K+KE   
Sbjct:     3 KMMHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKELSV 62

Query:    86 RKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGV-DDQFIFYE 144
             R++ L    R     S   + +           + + +    +E++L+S     Q  F  
Sbjct:    63 RRDDLMVLSRGSLLGSSNGDFKEDVEMISGKNHVVVRQCLVGVEIMLSSRCCGGQPRFSS 122

Query:   145 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
             V+++L + G  +LN+  S+V + + + I AEV
Sbjct:   123 VLQVLSEYGLCLLNSISSIVDDRLVYTIQAEV 154

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

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

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 42/158 (26%), Positives = 82/158 (51%)

Query:    21 SSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL 80
             S S  K+     E++RR Q+  LYS+L++LLP+    ++LS+P  V   + YI  L+ ++
Sbjct:    65 SGSHRKLSHNAYERDRRKQLNELYSSLRALLPDADHTKKLSIPTTVSRVLKYIPELQKQV 124

Query:    81 KECKKRKESLQGRERSHACISDGTEARLMTSS-SPKAPEIEIHEMGSNLEVILTSGVDDQ 139
             +  +++K+ L     ++ C      ++LM+   +P      I++M   ++V L S V   
Sbjct:   125 ENLERKKKELTTTSTTN-CKPGVLGSQLMSEGMAPIVSATCINDMEIMVQVSLLSNVAGS 183

Query:   140 FI-FYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAE 175
              +   + I++L  +G   +++  S   GN  F+ IH +
Sbjct:   184 VLPLSKCIKVLENEGLHFISSSTSSGFGNRTFYSIHLQ 221

GO:0005634 "nucleus" evidence=IC

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

 Score = 147 (56.8 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 46/155 (29%), Positives = 79/155 (50%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
             K+  K IEK RR +M +LY++L+SLLP +  + + S  DQV  A+NYI  L+  +K+   
Sbjct:     3 KLVHKEIEKRRRQEMASLYASLRSLLPLEFIQGKRSTSDQVKGAVNYIDYLQRNIKDINS 62

Query:    86 RKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGS----NLEVILTSGVDDQFI 141
             +++ L         +  G   R  +S+  +  EI  H +       +E++L+     Q  
Sbjct:    63 KRDDL--------VLLSGRSFR--SSNEQEWNEISNHVVIRPCLVGIEIVLSIL---QTP 109

Query:   142 FYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV 176
             F  V+++L + G  +L    S V + + H + AEV
Sbjct:   110 FSSVLQVLREHGLYVLGYICSSVNDRLIHTLQAEV 144

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

 Score = 137 (53.3 bits), Expect = 4.5e-09, P = 4.5e-09
 Identities = 39/158 (24%), Positives = 77/158 (48%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
             K+     E++RR ++  L+S+L+S LP     ++LS+P+ V +++ YI  L+ ++K   +
Sbjct:    73 KLNHNASERDRRKKINTLFSSLRSCLPASDQSKKLSIPETVSKSLKYIPELQQQVKRLIQ 132

Query:    86 RKESLQGRERSHACISDGTEARLMTSSSPKA-----PEIEIHEMGSN-LEVILTSGVDDQ 139
             +KE +  R      +S   +  L     PKA       +    +G N + V ++S     
Sbjct:   133 KKEEILVR------VSGQRDFELYDKQQPKAVASYLSTVSATRLGDNEVMVQVSSSKIHN 186

Query:   140 FIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEV 176
             F    V+  + +DG  +++   S   G  +F+ +H +V
Sbjct:   187 FSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQV 224

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

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0055072 "iron ion homeostasis" evidence=IGI

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

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 39/160 (24%), Positives = 87/160 (54%)

Query:    21 SSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL 80
             S+S  + +R   EK RR +MK+L+S L S +   P++  L +P  +D+A++Y+  L+ K+
Sbjct:    11 SASSLREQRNLREKERRMRMKHLFSILSSHV--SPTRR-LPVPQLIDQAVSYMIQLKEKV 67

Query:    81 KECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQF 140
                 + K  + G E  +   S+G+   L+       P++ I  + S +E+ L   ++ + 
Sbjct:    68 NYLNEMKRRMLGGEVKNR--SEGSS--LL-------PKLSIRSLDSIIEMNLVMDLNMKG 116

Query:   141 IF-YEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE--VC 177
             +  ++++ +  ++GA++++A    + +  F+ I A+  +C
Sbjct:   117 VMLHKLVSVFEEEGAQVMSANLQNLNDRTFYTIIAQAIIC 156

GO:0005634 "nucleus" evidence=ISM

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

 Score = 126 (49.4 bits), Expect = 6.9e-07, P = 6.9e-07
 Identities = 29/92 (31%), Positives = 56/92 (60%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKEC-K 84
             K++ + IE+ RR ++ +L+  L++LLP Q  + + S  D + +A+NYIK L+ K+KE  +
Sbjct:    75 KMKHRDIERQRRQEVSSLFKRLRTLLPFQYIQGKRSTSDHIVQAVNYIKDLQIKIKELNE 134

Query:    85 KR---KESLQGRERSHACISDGTEARLMTSSS 113
             KR   K+ +     +H+ I + T +   +++S
Sbjct:   135 KRNRVKKVISATTTTHSAIEECTSSLSSSAAS 166

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2146663 BHLH101 "AT5G04150" [Arabidopsis thaliana (taxid:3702)]

 Score = 125 (49.1 bits), Expect = 7.9e-07, P = 7.9e-07
 Identities = 36/154 (23%), Positives = 75/154 (48%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
             K+     E++RR ++  LYS+L++LLP    K +LS+P  V   + YI   + +L+   +
Sbjct:    67 KLNHNASERDRRRKLNALYSSLRALLPLSDQKRKLSIPMTVARVVKYIPEQKQELQRLSR 126

Query:    86 RKESLQGR--ERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFY 143
             RKE L  R   ++H       +A + +  S  +  I  + + ++ E+ +           
Sbjct:   127 RKEELLKRISRKTHQ-EQLRNKAMMDSIDSSSSQRIAANWL-TDTEIAVQIATSKWTSVS 184

Query:   144 EVIRILHQDGAEILNAKFSVVGNT-IFHVIHAEV 176
             +++  L ++G  +++   SV     IF+ +H ++
Sbjct:   185 DMLLRLEENGLNVISVSSSVSSTARIFYTLHLQM 218

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0055072 "iron ion homeostasis" evidence=IGI

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

 Score = 125 (49.1 bits), Expect = 9.9e-07, P = 9.9e-07
 Identities = 40/158 (25%), Positives = 74/158 (46%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
             K+     E++RR ++ +L+S+L+S LP     ++LS+P  V  ++ YI  L+ ++K+  K
Sbjct:    78 KLNHNASERDRRRKINSLFSSLRSCLPASGQSKKLSIPATVSRSLKYIPELQEQVKKLIK 137

Query:    86 RKESLQGRERSHACISDGTEARLMTSSSPKA-----PEIEIHEMGSN-LEVILTSGVDDQ 139
             +KE L  +      IS            PKA       +    +G N + V ++S     
Sbjct:   138 KKEELLVQ------ISGQRNTECYVKQPPKAVANYISTVSATRLGDNEVMVQISSSKIHN 191

Query:   140 FIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEV 176
             F    V+  L +D   +++   S   G  +F+ +H +V
Sbjct:   192 FSISNVLSGLEEDRFVLVDMSSSRSQGERLFYTLHLQV 229

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

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0055072 "iron ion homeostasis" evidence=IGI

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

 Score = 120 (47.3 bits), Expect = 1.2e-06, P = 1.2e-06
 Identities = 38/156 (24%), Positives = 85/156 (54%)

Query:    21 SSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL 80
             +SS  + +R   EK+RR +MK+L+S L S +   P+++ L +P  +D+A +Y+  L+  +
Sbjct:    11 NSSSLREQRNLREKDRRMRMKHLFSILSSHV--SPTRK-LPVPHLIDQATSYMIQLKENV 67

Query:    81 KECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVD-DQ 139
                K++K +L   E  +  + +G+   L+       P++ I    S +E+ L   ++  +
Sbjct:    68 NYLKEKKRTLLQGELGN--LYEGSF--LL-------PKLSIRSRDSTIEMNLIMDLNMKR 116

Query:   140 FIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE 175
              + +E++ I  ++GA++++A    + +   + I A+
Sbjct:   117 VMLHELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQ 152

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0006865 "amino acid transport" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	179
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	4e-09
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-07
smart00353	53	smart00353, HLH, helix loop helix domain	7e-06

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

 Score = 49.8 bits (120), Expect = 4e-09
 Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 32 IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLE 77
           E+ RRD++ + +  L+ LLP  P+K +LS  + +  AI YIK L+
Sbjct: 8  RERRRRDRINDAFEELRELLPTPPNK-KLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 45.3 bits (108), Expect = 3e-07
 Identities = 17/50 (34%), Positives = 33/50 (66%)

Query: 32 IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK 81
           E+ RR+++ + +  L+SLLP  P  ++LS  + + +A++YIK L+  L+
Sbjct: 11 RERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 41.4 bits (98), Expect = 7e-06
 Identities = 18/51 (35%), Positives = 31/51 (60%)

Query: 32 IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKE 82
           E+ RR ++   +  L+SLLP  P  ++LS  + +  AI YIK L+ +L++
Sbjct: 3  RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	179
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.52
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.5
smart00353	53	HLH helix loop helix domain.	99.43
KOG1318	411	consensus Helix loop helix transcription factor EB	98.97
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.89
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.84
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.43
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.29
KOG0561	373	consensus bHLH transcription factor [Transcription	98.28
PLN03217	93	transcription factor ATBS1; Provisional	98.28
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.27
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.65
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.59
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.55
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.54
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.47
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.26
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.23
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.21
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	97.2
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.15
KOG3898	254	consensus Transcription factor NeuroD and related	97.01
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.95
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	96.84
KOG3910	632	consensus Helix loop helix transcription factor [T	96.24
PRK00275	895	glnD PII uridylyl-transferase; Provisional	96.2
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.16
KOG4395	285	consensus Transcription factor Atonal, contains HT	96.15
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.13
PRK04374	869	PII uridylyl-transferase; Provisional	96.05
PRK05007	884	PII uridylyl-transferase; Provisional	95.97
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	95.66
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	95.63
PRK03059	856	PII uridylyl-transferase; Provisional	95.52
PRK05092	931	PII uridylyl-transferase; Provisional	95.43
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	95.26
PRK03381	774	PII uridylyl-transferase; Provisional	95.19
PRK03381	774	PII uridylyl-transferase; Provisional	95.18
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.89
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.47
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	94.35
PRK05007	884	PII uridylyl-transferase; Provisional	94.3
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.0
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	93.98
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	93.91
PRK00194	90	hypothetical protein; Validated	93.87
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	93.71
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	93.71
PRK03059	856	PII uridylyl-transferase; Provisional	93.66
PRK05092	931	PII uridylyl-transferase; Provisional	93.64
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	93.25
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	93.14
PRK00275	895	glnD PII uridylyl-transferase; Provisional	92.97
PRK04374	869	PII uridylyl-transferase; Provisional	92.64
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	91.93
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	91.44
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	91.18
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	91.03
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	90.52
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	90.37
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	89.88
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	89.01
cd02116	60	ACT ACT domains are commonly involved in specifica	88.91
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	88.16
PRK04435	147	hypothetical protein; Provisional	88.1
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	87.85
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	87.25
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	86.88
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	86.27
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	86.14
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	84.64
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	84.42
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	84.29
PRK08577	136	hypothetical protein; Provisional	84.07
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	83.95
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	83.92
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	83.27
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	82.77
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	82.13
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	81.29
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	81.14
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	81.06

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

Probab=99.52  E-value=3.6e-14  Score=92.26  Aligned_cols=53  Identities=32%  Similarity=0.572  Sum_probs=48.3

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCCCCChhHHHHHHHHHHHHHH
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQ--PSKEELSLPDQVDEAINYIKMLE   77 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~--~~~~k~S~~~~l~~Ai~YIk~L~   77 (179)
                      +|..|+..||+||..||+.|..|+.+||..  ....|.+.++||..||+||++||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            578999999999999999999999999996  25567888999999999999997

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

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

Probab=99.50  E-value=7.9e-14  Score=91.46  Aligned_cols=57  Identities=30%  Similarity=0.577  Sum_probs=50.6

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      .++..|+..||+||.+||..|..|+++||......|.+.++||..|++||+.|++.+
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            478899999999999999999999999999854456666777999999999999875

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

>smart00353 HLH helix loop helix domain

Probab=99.43  E-value=4.5e-13  Score=86.06  Aligned_cols=52  Identities=35%  Similarity=0.622  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 030331           30 KTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (179)
Q Consensus        30 ~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~   81 (179)
                      +..||+||.+||+.|..|+++||......|.+.++||..|++||+.|+++++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999999976544566666779999999999999875

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

Probab=98.97  E-value=1.5e-09  Score=96.08  Aligned_cols=59  Identities=19%  Similarity=0.368  Sum_probs=50.9

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC-CCCChhHHHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK-EELSLPDQVDEAINYIKMLETKLKE   82 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~-~k~S~~~~l~~Ai~YIk~L~~~v~~   82 (179)
                      .+|..||++||+||.+||+++..|..|||..... .|+.+..||..+++||+.||+..++
T Consensus       232 ~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~  291 (411)
T KOG1318|consen  232 RKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR  291 (411)
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999988432 3566667799999999999887663

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

Probab=98.89  E-value=9e-09  Score=85.25  Aligned_cols=70  Identities=24%  Similarity=0.383  Sum_probs=57.4

Q ss_pred             CCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030331           21 SSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESL   90 (179)
Q Consensus        21 ~~~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~   90 (179)
                      ...+.|..||+.||+||.+++++|..|+.+||......+-....||+.|..||+.|+.+.......++++
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l  124 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDL  124 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHH
Confidence            4568999999999999999999999999999987544322267789999999999988776666555544

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.84  E-value=8.8e-09  Score=82.21  Aligned_cols=67  Identities=25%  Similarity=0.458  Sum_probs=58.8

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCC----CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKE----ELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~----k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~   91 (179)
                      +|..|-.+||+||+.||..|+.|..|||.....+    |.|.+-||..+|+||..|.+++..-+++...|.
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~  132 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR  132 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4889999999999999999999999999987766    899999999999999999888777666555443

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

Probab=98.43  E-value=1.1e-07  Score=79.75  Aligned_cols=58  Identities=24%  Similarity=0.425  Sum_probs=51.2

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC-----CCCChhHHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK-----EELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~-----~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      ..+|..|-..||+||.+||+.+..|+.|||...++     .|.-+++||.-+++|++.|+...
T Consensus        30 ~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~   92 (250)
T KOG4304|consen   30 QYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ   92 (250)
T ss_pred             HHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence            46889999999999999999999999999987665     46777888999999999998754

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

Probab=98.29  E-value=1.4e-06  Score=71.94  Aligned_cols=62  Identities=26%  Similarity=0.469  Sum_probs=55.4

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCC-CCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPS-KEELSLPDQVDEAINYIKMLETKLKECK   84 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~-~~k~S~~~~l~~Ai~YIk~L~~~v~~L~   84 (179)
                      ...+..+|..||+|-+.+|..|..||.+||.... ..|.|+.++|..||.||+.|++-++.-.
T Consensus       107 ~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~  169 (228)
T KOG4029|consen  107 SAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE  169 (228)
T ss_pred             hhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence            3577889999999999999999999999999887 7789999999999999999998765544

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.28  E-value=6.2e-07  Score=76.35  Aligned_cols=59  Identities=24%  Similarity=0.370  Sum_probs=50.0

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKEC   83 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L   83 (179)
                      -+|..-|--||+|-+-||..|..||+|||... ..|.|++.||..+.+||.+|+..--+|
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~e-GEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKE-GEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCccc-chhhHHHHHHHHHHHHHHHHHhccccc
Confidence            46677888999999999999999999999743 458888999999999999997754433

>PLN03217 transcription factor ATBS1; Provisional

Probab=98.28  E-value=2.4e-06  Score=60.04  Aligned_cols=55  Identities=25%  Similarity=0.468  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHhcCCCCCC---CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           38 DQMKNLYSTLKSLLPNQPS---KEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        38 ~~mn~~~~~LrsllP~~~~---~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      ++|+++...|+.|||....   .+|+|-+.+|.++.+||+.|+.++.+|.++..+|..
T Consensus        20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~   77 (93)
T PLN03217         20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLA   77 (93)
T ss_pred             HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6899999999999998643   479999999999999999999999999999998875

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

Probab=98.27  E-value=8.7e-07  Score=84.27  Aligned_cols=53  Identities=25%  Similarity=0.540  Sum_probs=46.6

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCC----CCCCCChhHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQP----SKEELSLPDQVDEAINYIKMLETK   79 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~----~~~k~S~~~~l~~Ai~YIk~L~~~   79 (179)
                      ..|..|+.+||+||++||..+..|.+|||...    |+||..|   |..||.+|+.+++.
T Consensus        19 ~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tV---Lr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   19 KKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTV---LRMAVDHLRLIKEQ   75 (803)
T ss_pred             hccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHH---HHHHHHHHHHHhhh
Confidence            35899999999999999999999999999875    5566555   99999999999884

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

Probab=97.65  E-value=0.00036  Score=47.94  Aligned_cols=45  Identities=24%  Similarity=0.257  Sum_probs=38.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      |.|.+. +++|+|.+|.++|.++||+|..|.|++.|+++.-+|.+.
T Consensus         4 iev~a~-DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~   48 (72)
T cd04895           4 VKVDSA-RKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVT   48 (72)
T ss_pred             EEEEEC-CcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEE
Confidence            344454 689999999999999999999999999999977777653

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=97.59  E-value=0.00055  Score=47.07  Aligned_cols=46  Identities=15%  Similarity=0.160  Sum_probs=39.0

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAE  175 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~v~~ti~~k  175 (179)
                      .+.+.|. +++|+|+++..+|..+|++|++|.+++ .+++++-+|.+.
T Consensus         2 ~~ei~~~-Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~   48 (76)
T cd04927           2 LLKLFCS-DRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFIT   48 (76)
T ss_pred             EEEEEEC-CCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEe
Confidence            3445564 689999999999999999999999986 889988888764

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

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

Probab=97.55  E-value=0.00073  Score=45.74  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=38.0

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe-CCEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAE  175 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~-~~~v~~ti~~k  175 (179)
                      +|.+.|. +++|+|+++..+|..+|++|++|.+.+. ++.++-+|.+.
T Consensus         3 ~i~v~~~-Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~   49 (73)
T cd04900           3 EVFIYTP-DRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVL   49 (73)
T ss_pred             EEEEEec-CCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEE
Confidence            4555554 7899999999999999999999999877 68877777663

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.

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

Probab=97.54  E-value=0.00042  Score=57.92  Aligned_cols=68  Identities=22%  Similarity=0.331  Sum_probs=53.2

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030331           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESL   90 (179)
Q Consensus        22 ~~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~   90 (179)
                      +..+|..--+.||+|=.++|+.|.+|..-.-.. +..+..+.+||..||.||..||.-++++.+....+
T Consensus       115 svDRRKAATMRERRRLkKVNEAFE~LKRrT~~N-PNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  115 SVDRRKAATMRERRRLKKVNEAFETLKRRTSSN-PNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-ccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            346777888999999999999999997765222 22356667889999999999999988887654433

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

Probab=97.47  E-value=0.00082  Score=46.52  Aligned_cols=45  Identities=13%  Similarity=0.222  Sum_probs=38.3

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      |.+.|. ++||+|.+|..+|-++|++|.+|.|++.|+++.-+|.+.
T Consensus         4 veV~~~-DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~   48 (75)
T cd04897           4 VTVQCR-DRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIR   48 (75)
T ss_pred             EEEEeC-CcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEE
Confidence            344564 789999999999999999999999999999977666653

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.

>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=97.26  E-value=0.0025  Score=43.12  Aligned_cols=46  Identities=20%  Similarity=0.349  Sum_probs=38.6

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .|.+.+. +++|+|.+|..+|.++|++|++|.+.+.++.++.+|++.
T Consensus         3 ri~V~~~-D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~   48 (72)
T cd04926           3 RLELRTE-DRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVT   48 (72)
T ss_pred             EEEEEEC-CccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEE
Confidence            4555554 689999999999999999999999988888877777764

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

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

Probab=97.23  E-value=0.0019  Score=44.65  Aligned_cols=43  Identities=19%  Similarity=0.314  Sum_probs=37.6

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCcEEEEEEEE--EeCCEEEEEEEE
Q 030331          131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFS--VVGNTIFHVIHA  174 (179)
Q Consensus       131 ~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs--~~~~~v~~ti~~  174 (179)
                      .|.|. +++|+|.+|.++|..+|++|.+|-|+  +.|+++.-+|.+
T Consensus         4 ev~a~-DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv   48 (75)
T cd04896           4 QIRCV-DQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV   48 (75)
T ss_pred             EEEeC-CcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE
Confidence            44564 68999999999999999999999999  999997777665

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.

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.21  E-value=0.00021  Score=68.88  Aligned_cols=67  Identities=25%  Similarity=0.375  Sum_probs=55.7

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~   91 (179)
                      ..+|..||.+|++=|..||+++..|+.++|....  |...+..|..||+||++|+...+.+......+.
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~a--Kl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEA--KLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHh--hhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            4789999999999999999999999999997643  344455699999999999988777776655544

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

Probab=97.20  E-value=0.0032  Score=42.77  Aligned_cols=46  Identities=15%  Similarity=0.231  Sum_probs=37.9

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAE  175 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~v~~ti~~k  175 (179)
                      +|.|.|. +++++|+++..+|..+||+|++|.+.+ .+|.++-+|.+.
T Consensus         3 eI~V~~~-Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~   49 (68)
T cd04928           3 EITFAAG-DKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVT   49 (68)
T ss_pred             EEEEEEC-CCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEe
Confidence            4555554 689999999999999999999999964 577888887764

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=97.15  E-value=0.0037  Score=42.54  Aligned_cols=44  Identities=20%  Similarity=0.195  Sum_probs=38.2

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       131 ~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .+.+ .+++|+|.+|..+|..+|+.|++|.+.+.|+.++.+|.+.
T Consensus         4 ~v~~-~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~   47 (74)
T cd04925           4 ELTG-TDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVR   47 (74)
T ss_pred             EEEE-CCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEE
Confidence            3444 4789999999999999999999999999999988888764

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.

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

Probab=97.01  E-value=0.00054  Score=57.71  Aligned_cols=57  Identities=19%  Similarity=0.348  Sum_probs=50.5

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETK   79 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~   79 (179)
                      ..+|..-|..||+|-..+|+.|+.||.++|......|.++..+|.-|-+||..|++-
T Consensus        70 ~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   70 TLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            457788899999999999999999999999866666888888899999999999865

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.95  E-value=0.0011  Score=51.68  Aligned_cols=55  Identities=20%  Similarity=0.434  Sum_probs=48.2

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETK   79 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~   79 (179)
                      .++.-||..||+|=..+|+.|..||.++|-.+ -||.|....|.-|.-||..|-+-
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlP-sdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLP-SDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCC-ccccccccchhhcccCCchhhhc
Confidence            57889999999999999999999999999754 46788888899999999888654

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

Probab=96.84  E-value=0.012  Score=38.78  Aligned_cols=44  Identities=27%  Similarity=0.354  Sum_probs=37.7

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       131 ~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .+.+ .+++|+|.+|+.+|.++++.|.++.+.+.++.++.+|+++
T Consensus         4 ~v~~-~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~   47 (70)
T cd04899           4 ELTA-LDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVT   47 (70)
T ss_pred             EEEE-cCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEE
Confidence            3444 4679999999999999999999999998888888888775

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.24  E-value=0.0041  Score=56.56  Aligned_cols=62  Identities=15%  Similarity=0.230  Sum_probs=49.4

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCC-CChhHHHHHHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEE-LSLPDQVDEAINYIKMLETKLKECK   84 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k-~S~~~~l~~Ai~YIk~L~~~v~~L~   84 (179)
                      +.+|+.+|+.||-|-..||+.|..|-.+.-...+.+| .++.-||..|+.-|-.|+|+|.+-.
T Consensus       524 kERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN  586 (632)
T KOG3910|consen  524 KERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN  586 (632)
T ss_pred             HHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence            3678999999999999999999999987644333322 3555669999999999999987643

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=96.20  E-value=0.036  Score=54.35  Aligned_cols=60  Identities=15%  Similarity=0.146  Sum_probs=46.6

Q ss_pred             CCCeEEEEEeCC-e-eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          115 KAPEIEIHEMGS-N-LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       115 ~~p~V~V~~~~~-~-v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      ..|.|.+....+ + ..|. +++.+++|+|++|..+|..+||+|++|.|+|.|+++.-+|.+.
T Consensus       800 ~~~~V~i~~~~~~~~T~i~-V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~  861 (895)
T PRK00275        800 FPTQVTISNDAQRPVTVLE-IIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFIT  861 (895)
T ss_pred             CCCEEEEEECCCCCeEEEE-EEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEE
Confidence            345666655433 3 3444 4455789999999999999999999999999999988888764

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

Probab=96.16  E-value=0.057  Score=36.74  Aligned_cols=48  Identities=19%  Similarity=0.320  Sum_probs=38.1

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV  176 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv  176 (179)
                      +.|++++ .+++|++..|..+|.++|..+++++.++.++.+..++.+.+
T Consensus         3 ~vItv~G-~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~   50 (76)
T PF13740_consen    3 LVITVVG-PDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSI   50 (76)
T ss_dssp             EEEEEEE-E--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEe-cCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEe
Confidence            4555555 46899999999999999999999999999999777776654

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

Probab=96.15  E-value=0.0099  Score=49.89  Aligned_cols=57  Identities=21%  Similarity=0.366  Sum_probs=51.8

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      .+|..-|..||+|-..+|..|+.||..+|......|.|.-.+|..|-.||--|-..+
T Consensus       173 ~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  173 HRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             hhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            467778999999999999999999999999988889999999999999998887654

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

Probab=96.13  E-value=0.06  Score=34.90  Aligned_cols=45  Identities=22%  Similarity=0.333  Sum_probs=36.3

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      +.+.|. +++|+|.+++.+|.++++.|.++.+.+.++....+|++.
T Consensus         3 l~i~~~-d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~   47 (70)
T cd04873           3 VEVYAP-DRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVT   47 (70)
T ss_pred             EEEEeC-CCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEE
Confidence            445554 679999999999999999999999988777666666553

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

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.05  E-value=0.046  Score=53.45  Aligned_cols=60  Identities=17%  Similarity=0.269  Sum_probs=46.6

Q ss_pred             CCCeEEEEEeCC-e-eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          115 KAPEIEIHEMGS-N-LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       115 ~~p~V~V~~~~~-~-v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .+|.|.+....+ + ..|.|++ .+++|+|++|..+|..+|++|++|.|+|.|+++.-+|.++
T Consensus       782 ~~~~V~~~~~~~~~~t~leI~a-~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~  843 (869)
T PRK04374        782 FAPRVEFSESAGGRRTRISLVA-PDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQIT  843 (869)
T ss_pred             CCCeEEEeecCCCCeEEEEEEe-CCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEE
Confidence            345666655333 3 3444444 5789999999999999999999999999999988887764

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.97  E-value=0.034  Score=54.43  Aligned_cols=59  Identities=14%  Similarity=0.213  Sum_probs=44.2

Q ss_pred             CCeEEEEEeCC--eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          116 APEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~~~--~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      +|.|.+....+  --.|.|++ .+++|+|++|.++|.++|++|.+|-|+|.|+++.-+|.+.
T Consensus       795 ~~~V~~d~~~s~~~TvlEV~a-~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~  855 (884)
T PRK05007        795 PTEVSFLPTHTDRRSYMELIA-LDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILA  855 (884)
T ss_pred             CCEEEEccCCCCCeEEEEEEe-CCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEE
Confidence            44555543222  23344445 5789999999999999999999999999999977776653

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

Probab=95.66  E-value=0.095  Score=35.75  Aligned_cols=47  Identities=19%  Similarity=0.333  Sum_probs=40.0

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV  176 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv  176 (179)
                      .|.++|. +++|+..+|-..|.++|..+++++....++.+++.+.+.+
T Consensus         3 iltv~g~-Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~   49 (77)
T cd04893           3 VISALGT-DRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEG   49 (77)
T ss_pred             EEEEEeC-CCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEe
Confidence            4555664 6899999999999999999999999998998888776654

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

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

Probab=95.63  E-value=0.15  Score=32.61  Aligned_cols=36  Identities=25%  Similarity=0.192  Sum_probs=31.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCC
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGN  166 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~  166 (179)
                      |.+.|. +++|.|.++..+|.++|+.|.++...+.++
T Consensus         3 v~v~~~-drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    3 VRVIVP-DRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             EEEEEE-TSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             EEEEcC-CCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            455565 689999999999999999999999988776

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 ....

>PRK03059 PII uridylyl-transferase; Provisional

Probab=95.52  E-value=0.1  Score=51.04  Aligned_cols=58  Identities=14%  Similarity=0.311  Sum_probs=44.7

Q ss_pred             CCeEEEEEeCC--eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEE
Q 030331          116 APEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHA  174 (179)
Q Consensus       116 ~p~V~V~~~~~--~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~  174 (179)
                      +|.|.+....+  ...|.|++ .+++|+|++|..+|..+|++|++|.|+|.|+++.-+|.+
T Consensus       773 ~~~V~~~~~~~~~~T~i~V~a-~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V  832 (856)
T PRK03059        773 TPRVDLRPDERGQYYILSVSA-NDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI  832 (856)
T ss_pred             CceEEEEEcCCCCEEEEEEEe-CCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            34555544322  34444455 578999999999999999999999999999998888776

>PRK05092 PII uridylyl-transferase; Provisional

Probab=95.43  E-value=0.11  Score=51.18  Aligned_cols=59  Identities=19%  Similarity=0.280  Sum_probs=45.8

Q ss_pred             CCeEEEEEeCC--eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          116 APEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~~~--~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .|.|.+....+  ...|.|.+ .+++|+|.+|..+|.++|++|.+|.+.|.++++.-+|.+.
T Consensus       830 ~~~V~~~~~~s~~~t~i~I~~-~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~  890 (931)
T PRK05092        830 PPRVTIDNEASNRFTVIEVNG-RDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVT  890 (931)
T ss_pred             CCEEEEeeCCCCCeEEEEEEE-CCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEe
Confidence            45666654333  34444455 5789999999999999999999999999999988777764

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

Probab=95.26  E-value=0.19  Score=34.00  Aligned_cols=48  Identities=13%  Similarity=0.230  Sum_probs=35.9

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe--CCEEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEV  176 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~--~~~v~~ti~~kv  176 (179)
                      +.+.+.+. +++|+|.+|..++.+.|+.|.++++...  ++....+|.++|
T Consensus         7 ~~l~i~~~-dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V   56 (80)
T PF13291_consen    7 VRLRIEAE-DRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEV   56 (80)
T ss_dssp             EEEEEEEE---TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEE
T ss_pred             EEEEEEEE-cCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEE
Confidence            33444553 5799999999999999999999999874  566666777665

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.19  E-value=0.15  Score=49.28  Aligned_cols=58  Identities=16%  Similarity=0.256  Sum_probs=44.4

Q ss_pred             CeEEEEEeCC--eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          117 PEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       117 p~V~V~~~~~--~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      |.|.+....+  ...|.|.+ .+++|+|++|..+|..+|++|.+|.++|.|++++-+|.+.
T Consensus       695 ~~v~~~~~~~~~~t~i~V~a-~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~  754 (774)
T PRK03381        695 PRVLWLDGASPDATVLEVRA-ADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVT  754 (774)
T ss_pred             cEEEEEECCCCCeEEEEEEe-CCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEE
Confidence            3455544332  24444444 5789999999999999999999999999999988777764

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.18  E-value=0.14  Score=49.42  Aligned_cols=59  Identities=12%  Similarity=0.093  Sum_probs=46.1

Q ss_pred             CCeEEEEEe-CCeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          116 APEIEIHEM-GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~-~~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .|.|.+... .+..+|.|+| .+++|+|++|..+|..+|++|++|.+.+.+|.++-+|.+.
T Consensus       587 ~~~v~~~~~~~~~~~V~V~~-~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~  646 (774)
T PRK03381        587 GVHVEIAPADPHMVEVTVVA-PDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVS  646 (774)
T ss_pred             CCEEEEeeCCCCeEEEEEEe-cCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEE
Confidence            345555432 3556776665 4789999999999999999999999998888888887764

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=94.89  E-value=0.11  Score=50.80  Aligned_cols=59  Identities=17%  Similarity=0.243  Sum_probs=43.9

Q ss_pred             CCeEEEEEeCC-e-eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          116 APEIEIHEMGS-N-LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~~~-~-v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      +|.|.+....+ . -.|.|.+ .+++|+|.+|.++|.++|++|.+|-|+|.|+++.-+|.+.
T Consensus       770 ~~~V~~dn~~s~~~T~iev~a-~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~  830 (854)
T PRK01759        770 KTEVRFLNEEKQEQTEMELFA-LDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILT  830 (854)
T ss_pred             CCEEEEccCCCCCeEEEEEEe-CCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEE
Confidence            45555543222 2 3344445 4789999999999999999999999999999977666653

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=94.47  E-value=0.3  Score=47.77  Aligned_cols=59  Identities=12%  Similarity=0.170  Sum_probs=45.6

Q ss_pred             CCeEEEEEeC--CeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCEEEEEEEEE
Q 030331          116 APEIEIHEMG--SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~~--~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~v~~ti~~k  175 (179)
                      .|.|.+....  +..+|.|.| .+++|+|++|..+|..+||+|++|.+.+ .+|.++-+|.+.
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~-~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~  725 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYC-QDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVT  725 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEe-cCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEe
Confidence            5666665433  345666555 4789999999999999999999999866 788988887764

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

Probab=94.35  E-value=0.28  Score=32.83  Aligned_cols=46  Identities=20%  Similarity=0.152  Sum_probs=33.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEEe
Q 030331          131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEVC  177 (179)
Q Consensus       131 ~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv~  177 (179)
                      .+.| .+++|++.+|...|-++|+.+++.+..+..+.-.+.+.++++
T Consensus         3 ~v~g-~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~   48 (74)
T cd04875           3 TLSC-PDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFE   48 (74)
T ss_pred             EEEc-CCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEE
Confidence            4455 468999999999999999999999887532222244444444

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.

>PRK05007 PII uridylyl-transferase; Provisional

Probab=94.30  E-value=0.32  Score=47.71  Aligned_cols=60  Identities=13%  Similarity=0.207  Sum_probs=44.4

Q ss_pred             CCCeEEEEEeC--CeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeC-CEEEEEEEEE
Q 030331          115 KAPEIEIHEMG--SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAE  175 (179)
Q Consensus       115 ~~p~V~V~~~~--~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~-~~v~~ti~~k  175 (179)
                      ..|.|.+....  +..+|.|.| .+++|+|++|..+|..+||+|++|.|.+.+ |.++-+|.+.
T Consensus       687 ~~p~V~i~~~~~~~~t~V~V~a-~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~  749 (884)
T PRK05007        687 DKPLVLLSKQATRGGTEIFIWS-PDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVL  749 (884)
T ss_pred             CCCeEEEEecCCCCeEEEEEEe-cCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEE
Confidence            35666665433  355666555 578999999999999999999999987654 5876666653

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.00  E-value=0.36  Score=47.07  Aligned_cols=59  Identities=15%  Similarity=0.170  Sum_probs=44.9

Q ss_pred             CCeEEEEEe--CCeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEE-EeCCEEEEEEEEE
Q 030331          116 APEIEIHEM--GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~--~~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs-~~~~~v~~ti~~k  175 (179)
                      .|.|.+...  ....+|.|.+ .+++|+|++|..+|..+||+|++|.+. +.++.++-+|.++
T Consensus       655 ~~~v~~~~~~~~~~t~i~V~~-~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~  716 (850)
T TIGR01693       655 GPLALIDGTRPSGGTEVFIYA-PDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQ  716 (850)
T ss_pred             CCEEEEeccCCCCeEEEEEEe-CCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEE
Confidence            455554321  2345566555 468999999999999999999999997 7788888887775

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.

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

Probab=93.98  E-value=0.15  Score=49.26  Aligned_cols=60  Identities=15%  Similarity=0.233  Sum_probs=45.5

Q ss_pred             CCCeEEEEEeCC--eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          115 KAPEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       115 ~~p~V~V~~~~~--~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      ..|.|.+....+  .-.+.+.+ .+++|+|..|-.+|..++|++.+|.|+|+|.++.-+|.+.
T Consensus       777 i~p~v~i~~t~~~~~t~lEv~a-lDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt  838 (867)
T COG2844         777 IPPRVTILPTASNDKTVLEVRA-LDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVT  838 (867)
T ss_pred             cCCceeeccccCCCceEEEEEe-CCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEe
Confidence            456777655433  23444444 4789999999999999999999999999999966655543

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=93.91  E-value=0.3  Score=47.55  Aligned_cols=59  Identities=22%  Similarity=0.263  Sum_probs=44.5

Q ss_pred             CCeEEEEEeCC-e-eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          116 APEIEIHEMGS-N-LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~~~-~-v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      +|.|.+....+ . -.|.|.| .++||+|.+|.++|..+|++|.+|.++|.++++.-+|.+.
T Consensus       766 ~~~V~~d~~~s~~~t~~~v~~-~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~  826 (850)
T TIGR01693       766 PPRVTILNTASRKATIMEVRA-LDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVT  826 (850)
T ss_pred             CCeEEEccCCCCCeEEEEEEE-CCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEE
Confidence            44565544333 2 3344445 5789999999999999999999999999999877666664

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.

>PRK00194 hypothetical protein; Validated

Probab=93.87  E-value=0.2  Score=34.84  Aligned_cols=47  Identities=13%  Similarity=0.159  Sum_probs=37.2

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      +.|.+.|. +++|++.+|...|-++|+.|++.+..+.++.++..+.+.
T Consensus         4 ~~ltv~g~-DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~   50 (90)
T PRK00194          4 AIITVIGK-DKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVD   50 (90)
T ss_pred             EEEEEEcC-CCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEE
Confidence            45566665 689999999999999999999999887777655555443

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

Probab=93.71  E-value=0.2  Score=34.78  Aligned_cols=46  Identities=13%  Similarity=0.129  Sum_probs=37.2

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      .|.+.|. +++|+++.|.+.|-++|+.+++.+..+.++.++..+.+.
T Consensus         3 vl~i~g~-D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~   48 (88)
T cd04872           3 VITVVGK-DRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVD   48 (88)
T ss_pred             EEEEEcC-CCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEE
Confidence            4555665 689999999999999999999999888777666555544

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=93.71  E-value=0.52  Score=31.72  Aligned_cols=35  Identities=23%  Similarity=0.181  Sum_probs=30.2

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeC
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG  165 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~  165 (179)
                      |.+.|. +++|++.+|-+.|.++|+.|.+.+..+.+
T Consensus         2 l~v~g~-D~~Giv~~it~~l~~~~~nI~~~~~~~~~   36 (81)
T cd04869           2 VEVVGN-DRPGIVHEVTQFLAQRNINIEDLSTETYS   36 (81)
T ss_pred             EEEEeC-CCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence            344564 68999999999999999999999998876

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=93.66  E-value=0.31  Score=47.64  Aligned_cols=59  Identities=17%  Similarity=0.304  Sum_probs=45.4

Q ss_pred             CCeEEEEEe--CCeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEE-EEeCCEEEEEEEEE
Q 030331          116 APEIEIHEM--GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKF-SVVGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~--~~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~v-s~~~~~v~~ti~~k  175 (179)
                      .|-|-++..  .+..+|.|.|. +++|+|+++..+|..+||+|++|.+ ++.+|.++-||.+.
T Consensus       665 ~~~v~~~~~~~~~~~~v~i~~~-d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~  726 (856)
T PRK03059        665 TPIVRARLSPAGEGLQVMVYTP-DQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVL  726 (856)
T ss_pred             CCeEEEEecCCCCeEEEEEEec-CCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEe
Confidence            344445443  34677776664 6899999999999999999999999 45678888888764

>PRK05092 PII uridylyl-transferase; Provisional

Probab=93.64  E-value=0.57  Score=46.21  Aligned_cols=59  Identities=15%  Similarity=0.199  Sum_probs=45.6

Q ss_pred             CCeEEEEEeC--CeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCEEEEEEEEE
Q 030331          116 APEIEIHEMG--SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAE  175 (179)
Q Consensus       116 ~p~V~V~~~~--~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~v~~ti~~k  175 (179)
                      .+.|.++...  +..+|.|+|. +++|+|.+|..+|..+|++|++|.+.+ .++.++-+|.++
T Consensus       719 ~~~v~~~~~~~~~~t~v~I~~~-Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~  780 (931)
T PRK05092        719 PLATEVRPDPARGVTEVTVLAA-DHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQ  780 (931)
T ss_pred             CcEEEEEecCCCCeEEEEEEeC-CCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEE
Confidence            4566665533  4677777665 689999999999999999999999876 577777777664

>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains

Probab=93.25  E-value=0.93  Score=29.80  Aligned_cols=40  Identities=13%  Similarity=0.161  Sum_probs=32.0

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeC-CEEEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAEV  176 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~-~~v~~ti~~kv  176 (179)
                      +++|.|.+|+.++.+.|..|.+.++.... +.....|.+++
T Consensus         8 d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev   48 (74)
T cd04887           8 NRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDA   48 (74)
T ss_pred             CCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEc
Confidence            57999999999999999999999987764 55555555544

The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=93.14  E-value=0.71  Score=29.52  Aligned_cols=39  Identities=13%  Similarity=0.181  Sum_probs=30.1

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEe-----CCEEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVV-----GNTIFHVIHAE  175 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~-----~~~v~~ti~~k  175 (179)
                      +++|.|.+|+.+|.+.|++|.+.+....     .+...+.|.++
T Consensus         7 d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~   50 (73)
T cd04886           7 DRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLE   50 (73)
T ss_pred             CCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEE
Confidence            5799999999999999999999987654     24444444444

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.

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=92.97  E-value=0.69  Score=45.52  Aligned_cols=49  Identities=10%  Similarity=0.155  Sum_probs=40.1

Q ss_pred             CeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEE-EEeCCEEEEEEEEE
Q 030331          126 SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKF-SVVGNTIFHVIHAE  175 (179)
Q Consensus       126 ~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~v-s~~~~~v~~ti~~k  175 (179)
                      +..+|.|.|. +++|+|+++..+|..+|++|++|.+ ++.+|.++-+|.+.
T Consensus       703 ~~t~V~V~~~-DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~  752 (895)
T PRK00275        703 GGTQIFIYAP-DQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVL  752 (895)
T ss_pred             CeEEEEEEeC-CCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEe
Confidence            4567776664 6899999999999999999999998 55567777777664

>PRK04374 PII uridylyl-transferase; Provisional

Probab=92.64  E-value=0.86  Score=44.74  Aligned_cols=49  Identities=27%  Similarity=0.349  Sum_probs=41.3

Q ss_pred             CeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCEEEEEEEEE
Q 030331          126 SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAE  175 (179)
Q Consensus       126 ~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~v~~ti~~k  175 (179)
                      +..+|.|.|. +++|+|++|..+|..+|++|++|.+.+ .+|.++-+|.+.
T Consensus       689 ~~~~v~v~~~-d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~  738 (869)
T PRK04374        689 DALEVFVYSP-DRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVL  738 (869)
T ss_pred             CeEEEEEEeC-CCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEe
Confidence            4677776664 689999999999999999999999965 678888888764

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

Probab=91.93  E-value=0.86  Score=30.60  Aligned_cols=39  Identities=21%  Similarity=0.267  Sum_probs=32.7

Q ss_pred             EcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEE
Q 030331          134 SGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVI  172 (179)
Q Consensus       134 c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti  172 (179)
                      .+.+++|+..++.++|-++|+.+.+.+.++.++.+...+
T Consensus         5 ~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~   43 (75)
T cd04870           5 TGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGI   43 (75)
T ss_pred             EcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEE
Confidence            356789999999999999999999999888887644443

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.

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

Probab=91.44  E-value=1.7  Score=27.77  Aligned_cols=34  Identities=9%  Similarity=0.226  Sum_probs=28.2

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV  164 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~  164 (179)
                      +.+.+. +++|.|.+++..|.++++.|.+.+..+.
T Consensus         3 l~i~~~-d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04874           3 LSIIAE-DKPGVLRDLTGVIAEHGGNITYTQQFIE   36 (72)
T ss_pred             EEEEeC-CCCChHHHHHHHHHhCCCCEEEEEEecc
Confidence            444554 5789999999999999999999887765

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.

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

Probab=91.18  E-value=1.2  Score=29.73  Aligned_cols=42  Identities=17%  Similarity=0.197  Sum_probs=31.7

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIH  173 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~  173 (179)
                      +.+.+. +++|+|.+|+.++.+++..+.+.++.+. +.+.+++.
T Consensus         3 l~I~~~-dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~l~i~   44 (74)
T cd04877           3 LEITCE-DRLGITQEVLDLLVEHNIDLRGIEIDPK-GRIYLNFP   44 (74)
T ss_pred             EEEEEE-ccchHHHHHHHHHHHCCCceEEEEEecC-CeEEEEeE
Confidence            344454 5789999999999999999999998764 44444443

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

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

Probab=91.03  E-value=1.5  Score=29.14  Aligned_cols=40  Identities=3%  Similarity=0.043  Sum_probs=31.2

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeCC-EEEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVGN-TIFHVIHAEV  176 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~-~v~~ti~~kv  176 (179)
                      +++|.|.+++..|.++|+.+++..+.+..+ .--|.|.+.+
T Consensus         8 d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~   48 (75)
T cd04880           8 NKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDF   48 (75)
T ss_pred             CcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEE
Confidence            579999999999999999999998877654 3345544443

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

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

Probab=90.52  E-value=1.7  Score=28.57  Aligned_cols=44  Identities=11%  Similarity=0.079  Sum_probs=31.4

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe-CCEEEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHA  174 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~-~~~v~~ti~~  174 (179)
                      +.+.+. +++|.+.+|+..|.++|+.|...+.+.. ++.....|.+
T Consensus         3 l~i~~~-d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v   47 (76)
T cd04888           3 LSLLLE-HRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISI   47 (76)
T ss_pred             EEEEec-CCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEE
Confidence            344443 4689999999999999999999987543 3443344443

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.

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

Probab=90.37  E-value=2.3  Score=25.96  Aligned_cols=42  Identities=7%  Similarity=0.091  Sum_probs=30.9

Q ss_pred             EEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeC-CEEEEEEEE
Q 030331          132 LTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHA  174 (179)
Q Consensus       132 i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~-~~v~~ti~~  174 (179)
                      +.+. ++++.+.+++..|.++++++.+..+...+ +...+.|..
T Consensus         3 v~~~-~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~   45 (71)
T cd04876           3 VEAI-DRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTL   45 (71)
T ss_pred             EEEe-ccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEE
Confidence            3443 46899999999999999999999887655 433333433

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

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

Probab=89.88  E-value=0.27  Score=46.76  Aligned_cols=47  Identities=21%  Similarity=0.408  Sum_probs=40.8

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCC----CCCCCChhHHHHHHHHHHH
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQP----SKEELSLPDQVDEAINYIK   74 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~----~~~k~S~~~~l~~Ai~YIk   74 (179)
                      +|++-..+-|-||.+-|+-|+.|.-+||...    ..||+||   +.-||.|++
T Consensus        46 rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSi---mRLtISyLR   96 (768)
T KOG3558|consen   46 RKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASI---MRLTISYLR   96 (768)
T ss_pred             HhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHH---HHHHHHHHH
Confidence            4677778889999999999999999999653    3589888   999999987

>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=89.01  E-value=2.6  Score=28.49  Aligned_cols=41  Identities=10%  Similarity=0.139  Sum_probs=32.7

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeCC-EEEEEEEEEEe
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVGN-TIFHVIHAEVC  177 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~-~v~~ti~~kv~  177 (179)
                      +++|.|.+++..|.++|+.+++..+.+..+ .-.|+|.++++
T Consensus        10 d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~   51 (80)
T cd04905          10 NKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE   51 (80)
T ss_pred             CCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE
Confidence            579999999999999999999998776543 45566666554

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

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

Probab=88.91  E-value=3  Score=23.95  Aligned_cols=32  Identities=16%  Similarity=0.267  Sum_probs=26.8

Q ss_pred             EEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe
Q 030331          132 LTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV  164 (179)
Q Consensus       132 i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~  164 (179)
                      +.|. +.++.+.+++..|...++.+...+....
T Consensus         3 i~~~-~~~~~l~~i~~~l~~~~~~i~~~~~~~~   34 (60)
T cd02116           3 VSGP-DRPGLLAKVLSVLAEAGINITSIEQRTS   34 (60)
T ss_pred             EEec-CCCchHHHHHHHHHHCCCcEEEEEeEEc
Confidence            4454 4679999999999999999999988664

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

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=88.16  E-value=0.49  Score=42.67  Aligned_cols=43  Identities=26%  Similarity=0.456  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCC----CCCCCChhHHHHHHHHHHHH
Q 030331           30 KTIEKNRRDQMKNLYSTLKSLLPNQP----SKEELSLPDQVDEAINYIKM   75 (179)
Q Consensus        30 ~~~ER~RR~~mn~~~~~LrsllP~~~----~~~k~S~~~~l~~Ai~YIk~   75 (179)
                      +.+-|.||++-|--|..|..+||...    ..||+|+   +.-|..|||-
T Consensus         6 KnaA~tRRekEN~EF~eLAklLPLa~AItsQlDKasi---iRLtTsYlKm   52 (598)
T KOG3559|consen    6 KNAARTRREKENYEFYELAKLLPLASAITSQLDKASI---IRLTTSYLKM   52 (598)
T ss_pred             hhHHHHHHHhhcchHHHHHhhccchhhhhhccchhhh---hhHHHHHHHH
Confidence            44679999999999999999999763    3578887   9999999974

>PRK04435 hypothetical protein; Provisional

Probab=88.10  E-value=3.9  Score=31.44  Aligned_cols=51  Identities=18%  Similarity=0.260  Sum_probs=37.4

Q ss_pred             CCeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCEEEEEEEEEE
Q 030331          125 GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAEV  176 (179)
Q Consensus       125 ~~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~v~~ti~~kv  176 (179)
                      +..+.+.+.+. +++|.|++|+..|.+.|+.|+..+.+. .++....+|.+.+
T Consensus        67 ~r~vtL~i~l~-Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVev  118 (147)
T PRK04435         67 GKIITLSLLLE-DRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDT  118 (147)
T ss_pred             CcEEEEEEEEe-cCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEe
Confidence            44566666554 468999999999999999999998754 3565555555543

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

Probab=87.85  E-value=3.3  Score=26.05  Aligned_cols=38  Identities=18%  Similarity=0.183  Sum_probs=30.5

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeC--CEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHA  174 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~--~~v~~ti~~  174 (179)
                      +++|.+.+++..|.+.|+.|.+..+...+  +...++|.+
T Consensus         8 d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v   47 (71)
T cd04879           8 DVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV   47 (71)
T ss_pred             CCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc
Confidence            56899999999999999999999987654  555555544

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

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

Probab=87.25  E-value=1.8  Score=42.14  Aligned_cols=55  Identities=16%  Similarity=0.222  Sum_probs=45.3

Q ss_pred             EEEEeCCeeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEE-EEeCCEEEEEEEEE
Q 030331          120 EIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKF-SVVGNTIFHVIHAE  175 (179)
Q Consensus       120 ~V~~~~~~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~v-s~~~~~v~~ti~~k  175 (179)
                      .++...++.+|.|.|. +++.+|+.+..++...|++|++|.+ ++-+|..+-||.+.
T Consensus       677 ~~r~~~~~teV~V~a~-d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~  732 (867)
T COG2844         677 SVRPHSGGTEVFVYAP-DRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVL  732 (867)
T ss_pred             eecccCCceEEEEEcC-CCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEe
Confidence            3444557899998886 5799999999999999999999998 56678888887654

>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=86.88  E-value=3.6  Score=25.59  Aligned_cols=38  Identities=16%  Similarity=0.059  Sum_probs=30.1

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeC-CEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHA  174 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~-~~v~~ti~~  174 (179)
                      +++|.|.+++..|.+.|+.|.+..+...+ +..+..|..
T Consensus         7 d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v   45 (56)
T cd04889           7 NKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIF   45 (56)
T ss_pred             CCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEE
Confidence            57999999999999999999888876654 555554443

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

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

Probab=86.27  E-value=3  Score=26.30  Aligned_cols=38  Identities=18%  Similarity=0.198  Sum_probs=29.0

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeC--CEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHA  174 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~--~~v~~ti~~  174 (179)
                      +++|.|.+++..|.++|+.|.+.......  +...+.|..
T Consensus         8 d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~v   47 (65)
T cd04882           8 DKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRT   47 (65)
T ss_pred             CCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEe
Confidence            57999999999999999999888765443  444455544

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.

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=86.14  E-value=0.78  Score=42.72  Aligned_cols=39  Identities=28%  Similarity=0.526  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCC----CCCCCCChhHHHHHHHHHHH
Q 030331           33 EKNRRDQMKNLYSTLKSLLPNQ----PSKEELSLPDQVDEAINYIK   74 (179)
Q Consensus        33 ER~RR~~mn~~~~~LrsllP~~----~~~~k~S~~~~l~~Ai~YIk   74 (179)
                      -++-|+++|.-++.|.+|||..    .|.||.|+   |.-++.|++
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSV---LRLSVSyLr   75 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSV---LRLSVSYLR   75 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhh---hhhhHHHHH
Confidence            4566899999999999999975    46788888   999999975

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

Probab=84.64  E-value=6.9  Score=25.28  Aligned_cols=31  Identities=16%  Similarity=0.136  Sum_probs=26.8

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeCCE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVGNT  167 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~  167 (179)
                      +++|.|.+|++.|.+.|+.|.+..+...++.
T Consensus        10 d~pG~La~v~~~l~~~~inI~~i~~~~~~~~   40 (66)
T cd04908          10 NKPGRLAAVTEILSEAGINIRALSIADTSEF   40 (66)
T ss_pred             CCCChHHHHHHHHHHCCCCEEEEEEEecCCC
Confidence            5799999999999999999999987665554

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=84.42  E-value=6.6  Score=24.71  Aligned_cols=38  Identities=21%  Similarity=0.209  Sum_probs=28.8

Q ss_pred             CCCCchHHHHHHHHHhCCcEEEEEEEEEe--CCEEEEEEE
Q 030331          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIH  173 (179)
Q Consensus       136 ~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~--~~~v~~ti~  173 (179)
                      .+++|.+.+++..|.++++.+.+......  ++.....|.
T Consensus         7 ~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~   46 (71)
T cd04903           7 KDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIE   46 (71)
T ss_pred             CCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEE
Confidence            35789999999999999999999887652  344443443

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.

>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=84.29  E-value=6.1  Score=25.39  Aligned_cols=34  Identities=21%  Similarity=0.201  Sum_probs=27.9

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV  164 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~  164 (179)
                      +.+.+. +++|.+.+++..|.+.++.+.+.+....
T Consensus         3 l~i~~~-d~~g~l~~i~~~l~~~~i~I~~~~~~~~   36 (79)
T cd04881           3 LRLTVK-DKPGVLAKITGILAEHGISIESVIQKEA   36 (79)
T ss_pred             EEEEeC-CCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence            455554 5789999999999999999999987654

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.

>PRK08577 hypothetical protein; Provisional

Probab=84.07  E-value=9.2  Score=28.70  Aligned_cols=38  Identities=18%  Similarity=0.307  Sum_probs=30.9

Q ss_pred             eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeC
Q 030331          127 NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG  165 (179)
Q Consensus       127 ~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~  165 (179)
                      .+.+.+.+. +++|.|.+++..|.++++.+.+.+..+..
T Consensus        56 ~~~I~V~~~-Dr~GvLa~I~~~l~~~~inI~~i~~~~~~   93 (136)
T PRK08577         56 LVEIELVVE-DRPGVLAKITGLLAEHGVDILATECEELK   93 (136)
T ss_pred             EEEEEEEEc-CCCCHHHHHHHHHHHCCCCEEEEEEEEec
Confidence            455666664 57899999999999999999999876653

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

Probab=83.95  E-value=4.8  Score=26.97  Aligned_cols=41  Identities=2%  Similarity=0.016  Sum_probs=32.8

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeCCE-EEEEEEEEEe
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVGNT-IFHVIHAEVC  177 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~-v~~ti~~kv~  177 (179)
                      +++|.|.++|..|...|+.+.+..+-+..+. --|.|.+.++
T Consensus         9 ~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~   50 (74)
T cd04904           9 EEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCE   50 (74)
T ss_pred             CCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEE
Confidence            4799999999999999999999998776554 3466655554

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

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=83.92  E-value=0.92  Score=35.58  Aligned_cols=53  Identities=15%  Similarity=0.266  Sum_probs=36.2

Q ss_pred             chhhhhhH-HHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHH
Q 030331           24 PTKIERKT-IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLE   77 (179)
Q Consensus        24 ~~r~~h~~-~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~   77 (179)
                      +.+..-+. .||.|-.++++.|.-|+.|+|..+...|.-+ ..|.-+.+||..|.
T Consensus        20 ~~~~~~r~~~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~-ktlr~~~~~~~~~d   73 (173)
T KOG4447|consen   20 SEEECDRQRKERGRKRRLSDASTLLGKLEPGSPADGKRGK-KTLRIGTDSIQSLD   73 (173)
T ss_pred             hhhhhhhhHHHHhHHhhhhhhhhhccccCCCCCCcccccc-cccccCCCchhhHH
Confidence            34444343 5999999999999999999998865433222 22666666666554

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

Probab=83.27  E-value=3.6  Score=26.58  Aligned_cols=40  Identities=20%  Similarity=0.252  Sum_probs=31.6

Q ss_pred             CCCCchHHHHHHHHHhCCcEEEEEEEEE--eCCEEEEEEEEE
Q 030331          136 VDDQFIFYEVIRILHQDGAEILNAKFSV--VGNTIFHVIHAE  175 (179)
Q Consensus       136 ~~~~~~l~~vl~~Le~~gL~Vv~a~vs~--~~~~v~~ti~~k  175 (179)
                      .+++|.+.++...|.++|+.+.+..+..  .++...+.|.++
T Consensus         7 ~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~   48 (73)
T cd04902           7 TDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVD   48 (73)
T ss_pred             CCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeC
Confidence            4679999999999999999998887654  346666666654

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

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

Probab=82.77  E-value=10  Score=24.77  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=25.2

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEe
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVV  164 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~  164 (179)
                      +++|.|.+++..|.++|+.|++......
T Consensus         8 d~pG~L~~l~~~i~~~g~nI~~i~~~~~   35 (72)
T cd04884           8 DKPGTLKPVVDTLREFNARIISILTAFE   35 (72)
T ss_pred             CCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence            5799999999999999999999987654

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

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

Probab=82.13  E-value=10  Score=23.82  Aligned_cols=39  Identities=10%  Similarity=0.094  Sum_probs=30.1

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEe--CCEEEEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAE  175 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~--~~~v~~ti~~k  175 (179)
                      +++|.|.+++..|.++++.+.+.+..+.  ++...+.|...
T Consensus         9 d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~   49 (72)
T cd04878           9 NEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVE   49 (72)
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEE
Confidence            5689999999999999999999988664  34444444443

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

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

Probab=81.29  E-value=12  Score=24.12  Aligned_cols=46  Identities=11%  Similarity=0.169  Sum_probs=32.4

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe--CCEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAE  175 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~--~~~v~~ti~~k  175 (179)
                      .+.+... +++|.|.+++..|.++|+.+.+......  ++...+.|+..
T Consensus         3 ~~~v~~~-d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~   50 (72)
T cd04883           3 QIEVRVP-DRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQ   50 (72)
T ss_pred             EEEEEEC-CCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEe
Confidence            3444443 5689999999999999999998865433  34555556554

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.

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

Probab=81.14  E-value=8.5  Score=27.21  Aligned_cols=47  Identities=6%  Similarity=0.034  Sum_probs=34.5

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCE-EEEEEEEEEe
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNT-IFHVIHAEVC  177 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~-v~~ti~~kv~  177 (179)
                      +.+.. .+++|.|.++|..|...|+.+.+..+-+..+. --|.|.+.++
T Consensus        17 lif~l-~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDie   64 (90)
T cd04931          17 LIFSL-KEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLD   64 (90)
T ss_pred             EEEEc-CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEE
Confidence            33334 35799999999999999999999998776443 3455555544

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.

>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=81.06  E-value=9.1  Score=25.95  Aligned_cols=42  Identities=5%  Similarity=0.040  Sum_probs=32.4

Q ss_pred             CCCCchHHHHHHHHHhCCcEEEEEEEEEeCCE-EEEEEEEEEe
Q 030331          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGNT-IFHVIHAEVC  177 (179)
Q Consensus       136 ~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~-v~~ti~~kv~  177 (179)
                      .+++|.|.++|..|+..|+.+.+..+-+..+. --|.|.+.++
T Consensus         8 ~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e   50 (74)
T cd04929           8 KNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCE   50 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEE
Confidence            35699999999999999999999998775433 4455555544

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	179
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	9e-07
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	4e-06
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	6e-06
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	6e-05

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Length = 88

 Score = 46.2 bits (110), Expect = 1e-07
 Identities = 12/64 (18%), Positives = 32/64 (50%)

Query: 30 KTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKES 89
            +E+ RR+++K  +  L+  +P   + E+      + +A  YI  ++ + ++    ++ 
Sbjct: 11 NVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL 70

Query: 90 LQGR 93
          L+ R
Sbjct: 71 LRKR 74

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

 Score = 44.0 bits (104), Expect = 9e-07
 Identities = 17/67 (25%), Positives = 31/67 (46%)

Query: 25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECK 84
          ++     +EKNRR  ++     LK L+P  P     +    + +A  +IK LE   ++  
Sbjct: 1  SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV 60

Query: 85 KRKESLQ 91
           + + LQ
Sbjct: 61 HQIDQLQ 67

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

 Score = 42.0 bits (99), Expect = 4e-06
 Identities = 15/68 (22%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 28 ERKT----IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKEC 83
          +++     +E+ RRD +K+ + +L+  +P+    E+ S    +D+A  YI+ +  K    
Sbjct: 1  DKRAHHNALERKRRDHIKDSFHSLRDSVPS-LQGEKASRAQILDKATEYIQYMRRKNHTH 59

Query: 84 KKRKESLQ 91
          ++  + L+
Sbjct: 60 QQDIDDLK 67

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

 Score = 41.6 bits (98), Expect = 6e-06
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 20 SSSSPTKIERKT----IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKM 75
               +  +++     +E+ RRD +K+ + +L+  +P     E+ S    +D+A  YI+ 
Sbjct: 3  DIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVP-SLQGEKASRAQILDKATEYIQY 61

Query: 76 LETKLKECKKRKESLQ 91
          +  K    ++  + L+
Sbjct: 62 MRRKNHTHQQDIDDLK 77

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

 Score = 38.9 bits (91), Expect = 6e-05
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 25 TKIERKT----IEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL 80
          ++ E++T    IEK  R  + +    LK L+    ++ +L+    + +AI+YI+ L+   
Sbjct: 2  SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSN 59

Query: 81 KECKKRKESLQGRERS 96
          ++ K+   SL+     
Sbjct: 60 QKLKQENLSLRTAVHK 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	179
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.72
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.69
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.68
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.67
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.67
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.63
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.59
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.57
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.57
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.55
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.53
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.47
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.43
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.14
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.91
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.77
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.75
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.5
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	95.66
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	93.68
2nyi_A	195	Unknown protein; protein structure initiative, PSI	90.66
1u8s_A	192	Glycine cleavage system transcriptional repressor,	87.87
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	87.16
3he4_B	46	Synzip5; heterodimeric coiled-coil, de novo protei	81.76

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

Probab=99.72  E-value=3.5e-17  Score=113.83  Aligned_cols=68  Identities=25%  Similarity=0.331  Sum_probs=62.7

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      .|..||..||+||..||++|..|+++||......|.|.++||..|++||++|+++.+.|..+++.+..
T Consensus         1 ~R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A            1 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999999999877788999999999999999999999999998877653

>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=99.69  E-value=3.9e-17  Score=114.07  Aligned_cols=67  Identities=24%  Similarity=0.379  Sum_probs=59.3

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      .+|..|+.+||+||.+||+.|..|+++||..  ..|.+.++||.+||+||++|+++++.|+.+.+.+..
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~--~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   71 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGT--EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS--SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999985  235555666999999999999999999999887765

>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=99.68  E-value=1.5e-16  Score=112.49  Aligned_cols=68  Identities=16%  Similarity=0.318  Sum_probs=60.8

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~   91 (179)
                      .+|..||..||+||..||+.|..|+++||......|.|.++||..||+||+.|+++.+.+..+++.+.
T Consensus         5 ~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A            5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999887667888888899999999999999988877666554

>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=99.67  E-value=1.2e-16  Score=110.93  Aligned_cols=68  Identities=22%  Similarity=0.463  Sum_probs=61.9

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~   91 (179)
                      ..+|..|+..||+||..||+.|..|+++||.... .|.|.++||..||+||+.|++++++|+.+.+.+.
T Consensus        10 ~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~-~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A           10 ADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQG-EKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTT-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999998653 4788888899999999999999999999988775

>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=99.67  E-value=1.7e-16  Score=110.81  Aligned_cols=67  Identities=22%  Similarity=0.456  Sum_probs=59.8

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      +|..||..||+||..||+.|..|+++||... ..|.|.++||..||+||+.|+++++.|+.+++.+..
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~   68 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999754 346788888999999999999999999988877654

>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=99.63  E-value=6.7e-17  Score=107.55  Aligned_cols=56  Identities=25%  Similarity=0.344  Sum_probs=49.5

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCC----CCCCChhHHHHHHHHHHHHHHHHH
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPS----KEELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~----~~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      +|.+|+.+||+||.+||..|..|++|||...+    ..|.|+++||+.||+||++||+++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999997643    247778888999999999999865

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

Probab=99.59  E-value=4e-16  Score=107.44  Aligned_cols=61  Identities=15%  Similarity=0.273  Sum_probs=50.5

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC-ChhHHHHHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEEL-SLPDQVDEAINYIKMLETKLKECK   84 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~-S~~~~l~~Ai~YIk~L~~~v~~L~   84 (179)
                      .+|..||..||+||..||+.|..|+.+||...+.+|. |+.+||..||+||+.|++++++++
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999965455666 788899999999999999998764

>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=99.57  E-value=5.7e-16  Score=103.42  Aligned_cols=57  Identities=21%  Similarity=0.397  Sum_probs=48.8

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC---CCCChhHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK---EELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~---~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      .+|..|+.+||+||..||+.|..|++|||.....   .|.+.++||.+||+||++||++.
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4788999999999999999999999999987642   24555556999999999999764

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

Probab=99.57  E-value=5.2e-15  Score=109.85  Aligned_cols=65  Identities=18%  Similarity=0.329  Sum_probs=52.5

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC-CCCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK-EELSLPDQVDEAINYIKMLETKLKECKKRKE   88 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~-~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~   88 (179)
                      .+|..|+.+||+||.+||+.|..|++|||...+. .|.+.++||..||+||+.||++++.|+....
T Consensus        26 ~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~   91 (118)
T 4ati_A           26 QKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   91 (118)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999987654 4778888899999999999999999987543

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

Probab=99.55  E-value=1.2e-14  Score=95.74  Aligned_cols=58  Identities=22%  Similarity=0.357  Sum_probs=54.0

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~   81 (179)
                      ++|..||..||+|+..||+.|..||.+||..+...|.|+.+||..||+||..|++.++
T Consensus         1 ~rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            1 SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            4788999999999999999999999999998877899999999999999999998753

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

Probab=99.53  E-value=7.7e-15  Score=99.58  Aligned_cols=59  Identities=22%  Similarity=0.401  Sum_probs=49.7

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKEC   83 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L   83 (179)
                      ..+|..|+.+||+||.+||+.|..|++|||...  .|.++++||..||+||++||+++.=|
T Consensus         6 ~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~--~K~dK~sIL~~aI~yik~Lq~~~~~~   64 (71)
T 4h10_B            6 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNA--RKMDKSTVLQKSIDFLRKHKEITAWL   64 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCC--SCCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCC--CCCcHHHHHHHHHHHHHHHHHhhhHH
Confidence            368999999999999999999999999999542  24444555999999999999987654

>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B*

Probab=99.47  E-value=3.3e-14  Score=95.79  Aligned_cols=57  Identities=23%  Similarity=0.367  Sum_probs=52.0

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      ..+|..||..||+|+..||+.|..||.+||..+ ..|.|+.+||..||+||..|++.+
T Consensus        10 ~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~-~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCT-TSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999999999754 568999999999999999999864

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

Probab=99.43  E-value=3.3e-14  Score=97.07  Aligned_cols=56  Identities=27%  Similarity=0.371  Sum_probs=45.9

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCCChhHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQP-SKEELSLPDQVDEAINYIKMLET   78 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~-~~~k~S~~~~l~~Ai~YIk~L~~   78 (179)
                      ..+|..|+.+||+||++||+.|..|++|||... ...|.++++||..||+||+.|+.
T Consensus         7 ~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            7 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999652 12244445559999999999863

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

Probab=99.14  E-value=8.6e-12  Score=83.42  Aligned_cols=49  Identities=29%  Similarity=0.432  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHH
Q 030331           30 KTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLET   78 (179)
Q Consensus        30 ~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~   78 (179)
                      ++.||+|+..||+.|..||.+||..+...|.|+.+||..||+||..||+
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            3559999999999999999999999888899999999999999999984

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

Probab=98.91  E-value=7.6e-10  Score=94.92  Aligned_cols=54  Identities=26%  Similarity=0.519  Sum_probs=39.5

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCC-CCCCCCCCChhHHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLP-NQPSKEELSLPDQVDEAINYIKMLETK   79 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP-~~~~~~k~S~~~~l~~Ai~YIk~L~~~   79 (179)
                      ..+|..|+.+||+||++||..|..|++||| ...++||++|   |..||+||+.|+.-
T Consensus        10 ~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~i---l~~~~~~~~~~~~~   64 (361)
T 4f3l_A           10 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTV---LQKSIDFLRKHKET   64 (361)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHH---HHHHHHHHHHHHHH
T ss_pred             chhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHH---HHHHHHHHHHHHhh
Confidence            468899999999999999999999999999 3346666666   99999999999864

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

Probab=98.77  E-value=3.9e-09  Score=91.47  Aligned_cols=53  Identities=28%  Similarity=0.456  Sum_probs=47.3

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCC----CCCCCCCCChhHHHHHHHHHHHHHHH
Q 030331           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLP----NQPSKEELSLPDQVDEAINYIKMLET   78 (179)
Q Consensus        23 ~~~r~~h~~~ER~RR~~mn~~~~~LrsllP----~~~~~~k~S~~~~l~~Ai~YIk~L~~   78 (179)
                      ..+|.+|+.+||+||.+||..|..|++|||    ...+.||+||   |..||+||+.|+.
T Consensus        11 ~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~i---l~~~~~~l~~~~~   67 (387)
T 4f3l_B           11 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTV---LRMAVQHMKTLRG   67 (387)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHH---HHHHHHHHHHHHC
T ss_pred             hhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHH---HHHHHHHHHHhhc
Confidence            458999999999999999999999999999    4556777776   9999999999974

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

Probab=98.75  E-value=1.9e-08  Score=71.70  Aligned_cols=51  Identities=27%  Similarity=0.400  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 030331           31 TIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (179)
Q Consensus        31 ~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~   81 (179)
                      ..||.|-..||+.|..||.+||..+...|.|+.++|.-||+||..|++-++
T Consensus        31 ~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~   81 (97)
T 4aya_A           31 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALD   81 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHh
Confidence            446889999999999999999998777899999999999999999998764

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

Probab=98.50  E-value=4.1e-07  Score=62.96  Aligned_cols=52  Identities=15%  Similarity=0.317  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHhcCCCCC-CCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030331           37 RDQMKNLYSTLKSLLPNQP-SKEELSLPDQVDEAINYIKMLETKLKECKKRKE   88 (179)
Q Consensus        37 R~~mn~~~~~LrsllP~~~-~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~   88 (179)
                      |..||+.+..|..|||... +..|++..+||..|++||+.||+..+.+.+.-.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~   56 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   56 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7889999999999999753 455888899999999999999998887776443

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

Probab=95.66  E-value=0.11  Score=34.68  Aligned_cols=48  Identities=13%  Similarity=0.043  Sum_probs=38.3

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV  176 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv  176 (179)
                      +.+.+.|. +++|++.+|..+|-+.|..|++.+..+.++..+..+.+++
T Consensus         6 ~~l~v~~~-DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~   53 (91)
T 1zpv_A            6 AIITVVGK-DKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSS   53 (91)
T ss_dssp             EEEEEEES-CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEEC-CCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEe
Confidence            45566665 6899999999999999999999999887776555555543

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

Probab=93.68  E-value=0.41  Score=31.37  Aligned_cols=47  Identities=4%  Similarity=0.012  Sum_probs=34.6

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAE  175 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~k  175 (179)
                      +.+.+.+. +++|.|.+|..+|.+.|+.|.+.+..+.++....+|.++
T Consensus         6 ~~l~v~~~-Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~   52 (88)
T 2ko1_A            6 AGIRIVGE-DKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIF   52 (88)
T ss_dssp             EEEEEEEE-CCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEE
T ss_pred             EEEEEEEE-CCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEE
Confidence            33444443 679999999999999999999999987666333344433

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

Probab=90.66  E-value=1.3  Score=34.13  Aligned_cols=37  Identities=22%  Similarity=0.304  Sum_probs=32.2

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeC
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG  165 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~  165 (179)
                      ..|.+.|. +++|++..|-.+|-++|+.|+++...+.+
T Consensus        94 ~iltv~g~-DrpGiva~Vt~~La~~g~nI~~~~~~t~~  130 (195)
T 2nyi_A           94 YELYVEGP-DSEGIVEAVTAVLAKKGANIVELETETLP  130 (195)
T ss_dssp             EEEEEEEE-CCTTHHHHHHHHHHHTTCEEEEEEEEEEE
T ss_pred             EEEEEEeC-CCcCHHHHHHHHHHHcCCCEEEceeeecc
Confidence            45666775 68999999999999999999999998776

>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=87.87  E-value=2.7  Score=31.92  Aligned_cols=37  Identities=14%  Similarity=0.138  Sum_probs=31.2

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeC
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG  165 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~  165 (179)
                      ..|.+.|. +++|++.+|..+|-++|+.|.++...+.+
T Consensus        94 ~~l~v~~~-D~~Gil~~v~~~l~~~~~nI~~~~~~t~~  130 (192)
T 1u8s_A           94 VEVYVESD-DKLGLTEKFTQFFAQRQIGMASLSAQTIS  130 (192)
T ss_dssp             EEEEEEES-CCTTHHHHHHHHHHHTTCCEEEEEEEEEC
T ss_pred             EEEEEEeC-CCccHHHHHHHHHHHcCCcHHHhhhhccc
Confidence            44555664 68999999999999999999999988765

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

Probab=87.16  E-value=2.5  Score=35.83  Aligned_cols=48  Identities=17%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV  176 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv  176 (179)
                      +.|+++|. +++|+...|...|-++|..|++++-...++.++-.+.+.+
T Consensus        13 ~~lt~~g~-Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~   60 (415)
T 3p96_A           13 VLITVTGV-DQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCC   60 (415)
T ss_dssp             EEEEEEEE-CCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEcC-CCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEe
Confidence            55677775 6899999999999999999999999988888766665543

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

Probab=81.76  E-value=2.1  Score=25.03  Aligned_cols=27  Identities=44%  Similarity=0.520  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030331           65 QVDEAINYIKMLETKLKECKKRKESLQ   91 (179)
Q Consensus        65 ~l~~Ai~YIk~L~~~v~~L~~~~~~~~   91 (179)
                      ++.+--+||++|+++-.+|..-++-+.
T Consensus         4 tvkelknyiqeleernaelknlkehlk   30 (46)
T 3he4_B            4 TVKELKNYIQELEERNAELKNLKEHLK   30 (46)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhHHHHhHHHHHH
Confidence            378888999999999999988776554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	179
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	4e-11
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-09
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	1e-08
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-06
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-06
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-06
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-05
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-04

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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

 Score = 54.5 bits (131), Expect = 4e-11
 Identities = 12/71 (16%), Positives = 33/71 (46%)

Query: 26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
          +     +E+ RR+++K  +  L+  +P   + E+      + +A  YI  ++ + ++   
Sbjct: 7  RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS 66

Query: 86 RKESLQGRERS 96
           ++ L+ R   
Sbjct: 67 EEDLLRKRREQ 77

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

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

 Score = 50.3 bits (120), Expect = 1e-09
 Identities = 18/72 (25%), Positives = 33/72 (45%)

Query: 25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECK 84
          ++     +EKNRR  ++     LK L+P  P     +    + +A  +IK LE   ++  
Sbjct: 1  SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV 60

Query: 85 KRKESLQGRERS 96
           + + LQ  +R 
Sbjct: 61 HQIDQLQREQRH 72

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

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

 Score = 47.6 bits (113), Expect = 1e-08
 Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 14 MKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYI 73
          M+ K+ ++++  +      E+ R  ++   + TLK    + P++  L   + +  AI YI
Sbjct: 1  MELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQ-RLPKVEILRNAIRYI 59

Query: 74 KMLETKLKE 82
          + L+  L++
Sbjct: 60 EGLQALLRD 68

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

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

 Score = 42.5 bits (100), Expect = 1e-06
 Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
          +     +E+ RRD +K+ + +L+  +P+    E+ S    +D+A  YI+ +  K    ++
Sbjct: 3  RAHHNALERKRRDHIKDSFHSLRDSVPSLQG-EKASRAQILDKATEYIQYMRRKNHTHQQ 61

Query: 86 RKESLQGRERS 96
            + L+ +   
Sbjct: 62 DIDDLKRQNAL 72

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

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

 Score = 41.8 bits (98), Expect = 1e-06
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEE----LSLPDQVDEAINYIKMLETKLK 81
          +   K  E+ RR+++      L SL+P +  ++      S    V+ A  YI+ L+    
Sbjct: 3  RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

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

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

 Score = 42.2 bits (99), Expect = 1e-06
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 21 SSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL 80
          S    +     IEK  R  + +    LK L+    +K  L+    + +AI+YI+ L+   
Sbjct: 2  SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAK--LNKSAVLRKAIDYIRFLQHSN 59

Query: 81 KECKKRKESLQGRERS 96
          ++ K+   SL+     
Sbjct: 60 QKLKQENLSLRTAVHK 75

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

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

 Score = 39.3 bits (92), Expect = 1e-05
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 37 RDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQGRERS 96
          R  + +    LK L+    +K  +     + +AI+YIK L+    + ++    L+   + 
Sbjct: 1  RSSINDKIIELKDLVMGTDAK--MHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQK 58

Query: 97 H 97
          +
Sbjct: 59 N 59

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

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

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEE---LSLPDQVDEAINYIKMLETK 79
          + +   +E+ RRD++ N    L  ++P+   +      S    + +A +YI+ L   
Sbjct: 6  RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS 62

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	179
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.71
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.69
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.64
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.6
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.49
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.04
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	95.71
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	92.16
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	90.87
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	88.55
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	87.24
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	84.23

>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=99.71  E-value=1.8e-17  Score=113.16  Aligned_cols=67  Identities=25%  Similarity=0.329  Sum_probs=61.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        26 r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      |..||..||+||..||+.|..|+++||......|.|.++||..||+||+.|+++++.|..+++.+..
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~   68 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999998877778899999999999999999999999988877653

>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=99.69  E-value=3.3e-17  Score=113.91  Aligned_cols=69  Identities=16%  Similarity=0.308  Sum_probs=62.9

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      .+|..||.+||+||+.||+.|..|+++||......|.|.++||..|++||+.|+++++.|..+++.+..
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   73 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK   73 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478899999999999999999999999998777778899999999999999999999999988776653

>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=99.65  E-value=2.1e-16  Score=108.03  Aligned_cols=67  Identities=24%  Similarity=0.370  Sum_probs=59.2

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      .+|..|+.+||+||.+||+.|..|+++||...  .|.|.++||..||+||+.|+++++.|..+...+..
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~--~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~   71 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999743  35667777999999999999999999988877653

>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=99.64  E-value=4.8e-17  Score=108.21  Aligned_cols=59  Identities=22%  Similarity=0.375  Sum_probs=52.7

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 030331           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (179)
Q Consensus        22 ~~~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~   81 (179)
                      +..+|..||..||+||..||+.|..|+++||..+. +|.|.++||..||+||++||+.++
T Consensus         9 ~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~-~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPN-QRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTT-SCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHhh
Confidence            45788999999999999999999999999998754 478888889999999999998764

>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=99.64  E-value=3.6e-16  Score=107.44  Aligned_cols=67  Identities=22%  Similarity=0.456  Sum_probs=59.2

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      +|..|+..||+||.+||+.|..|+++||..+ ..|.|.++||..||+||+.|+++++.|..+.+.+..
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~-~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   68 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999643 347788888999999999999999999988776543

>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=99.60  E-value=2.3e-16  Score=103.26  Aligned_cols=56  Identities=25%  Similarity=0.361  Sum_probs=48.1

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCCCCChhHHHHHHHHHHHHHHHHH
Q 030331           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQ----PSKEELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        25 ~r~~h~~~ER~RR~~mn~~~~~LrsllP~~----~~~~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      +|..|+.+||+||.+||+.|..|+++||..    ....|.|.++||..||+||++||+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            578999999999999999999999999952    23346667777999999999999865

>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=99.49  E-value=5e-15  Score=97.36  Aligned_cols=57  Identities=21%  Similarity=0.397  Sum_probs=48.0

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC---CCCChhHHHHHHHHHHHHHHHHH
Q 030331           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK---EELSLPDQVDEAINYIKMLETKL   80 (179)
Q Consensus        24 ~~r~~h~~~ER~RR~~mn~~~~~LrsllP~~~~~---~k~S~~~~l~~Ai~YIk~L~~~v   80 (179)
                      .+|..|+..||+||..||+.|..|+++||.....   .|.|.++||..|++||+.||++.
T Consensus         4 ~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            4678899999999999999999999999976422   35566666999999999998753

>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=99.37  E-value=2.1e-13  Score=88.35  Aligned_cols=53  Identities=21%  Similarity=0.305  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHhcCCCCC-CCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 030331           37 RDQMKNLYSTLKSLLPNQP-SKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (179)
Q Consensus        37 R~~mn~~~~~LrsllP~~~-~~~k~S~~~~l~~Ai~YIk~L~~~v~~L~~~~~~~~~   92 (179)
                      |.+||++|..|+++||+.. +.+|+++   |.+||+||+.|+++++.|+.+...+..
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~i---L~~Ai~YI~~Lq~~~~~L~~e~~~L~~   54 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGV---LRKAIDYIKYLQQVNHKLRQENMVLKL   54 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999864 5566666   999999999999999999998887754

>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=96.04  E-value=0.026  Score=36.73  Aligned_cols=48  Identities=21%  Similarity=0.365  Sum_probs=40.8

Q ss_pred             eEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEE
Q 030331          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV  176 (179)
Q Consensus       128 v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv  176 (179)
                      +.|+++|. +++|++.+|..+|-+.|..|++++...+++.+.+.+.+.+
T Consensus         6 ~vitv~G~-DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~   53 (86)
T d1u8sa1           6 LVITAVGT-DRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG   53 (86)
T ss_dssp             EEEEEEEE-CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEeC-CCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEc
Confidence            55666664 7899999999999999999999999999998777766654

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

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

Probab=95.71  E-value=0.049  Score=34.99  Aligned_cols=47  Identities=13%  Similarity=0.052  Sum_probs=38.7

Q ss_pred             EEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEEEEEE
Q 030331          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEV  176 (179)
Q Consensus       129 ~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti~~kv  176 (179)
                      .|+++|. +++|++..|-..|-++|..+++++-.+.++.++..+.+.+
T Consensus         4 vitv~g~-DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~   50 (83)
T d1zpva1           4 IITVVGK-DKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSS   50 (83)
T ss_dssp             EEEEEES-CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEcC-CCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEE
Confidence            4566775 7899999999999999999999999888887666655543

>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=92.16  E-value=0.54  Score=30.45  Aligned_cols=37  Identities=14%  Similarity=0.139  Sum_probs=31.4

Q ss_pred             eeEEEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEe
Q 030331          127 NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV  164 (179)
Q Consensus       127 ~v~I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~  164 (179)
                      .++|.|.|. +++|++.+|-..|-++|+.|.+.+..+.
T Consensus         6 tv~v~v~g~-DrpGIV~~it~~la~~~~nI~~l~t~~~   42 (93)
T d1u8sa2           6 TVEVYVESD-DKLGLTEKFTQFFAQRQIGMASLSAQTI   42 (93)
T ss_dssp             EEEEEEEES-CCTTHHHHHHHHHHHTTCCEEEEEEEEE
T ss_pred             EEEEEEEEC-CCCCHHHHHHHHHHHcCCCchhhhcccc
Confidence            466777775 6899999999999999999999987653

>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=90.87  E-value=0.63  Score=28.94  Aligned_cols=42  Identities=7%  Similarity=-0.046  Sum_probs=33.3

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVI  172 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti  172 (179)
                      +.++.. +++|.|.++..+|.+.|+.+.+.++....+.-+.-|
T Consensus         6 isV~~e-NkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Ri   47 (70)
T d2f06a2           6 LSIFLE-NKSGRLTEVTEVLAKENINLSALCIAENADFGILRG   47 (70)
T ss_dssp             EEEEEC-SSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEE
T ss_pred             EEEEEe-CCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEE
Confidence            445555 579999999999999999999999987666544433

>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=88.55  E-value=0.32  Score=30.76  Aligned_cols=45  Identities=13%  Similarity=0.126  Sum_probs=29.3

Q ss_pred             EEEEEcCCCCchHHHHHHHHHhCCcEEEEEEEEE-eCCE--EEEEEEEE
Q 030331          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNT--IFHVIHAE  175 (179)
Q Consensus       130 I~i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~-~~~~--v~~ti~~k  175 (179)
                      |.+.|. +++|+|.+|..++-+++..|++.+..+ .+|.  +..+|..+
T Consensus         4 i~i~~~-Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~   51 (77)
T d1y7pa2           4 LRIIAE-NKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFE   51 (77)
T ss_dssp             EEEEEE-CCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEE
T ss_pred             EEEEEe-cCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEE
Confidence            455565 689999999999999999999998764 3332  34455444

>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=87.24  E-value=1.8  Score=26.59  Aligned_cols=36  Identities=19%  Similarity=0.043  Sum_probs=30.3

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEEEeCCEEEEEE
Q 030331          137 DDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVI  172 (179)
Q Consensus       137 ~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~v~~ti  172 (179)
                      +++|.|.++++.|.+.|+.|........++.-+..|
T Consensus         8 d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl   43 (71)
T d2f06a1           8 NVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVI   43 (71)
T ss_dssp             SSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEE
T ss_pred             CCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEE
Confidence            579999999999999999999998877777654433

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

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

Probab=84.23  E-value=1.7  Score=27.40  Aligned_cols=45  Identities=7%  Similarity=-0.043  Sum_probs=33.9

Q ss_pred             EEEcCCCCchHHHHHHHHHhCCcEEEEEEEEEeCCE-EEEEEEEEE
Q 030331          132 LTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNT-IFHVIHAEV  176 (179)
Q Consensus       132 i~c~~~~~~~l~~vl~~Le~~gL~Vv~a~vs~~~~~-v~~ti~~kv  176 (179)
                      ++.-.+++|.|.++|..|.++|+...+..+-+..+. --|.|.+.+
T Consensus         6 i~~~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~   51 (80)
T d2qmwa2           6 ITPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQA   51 (80)
T ss_dssp             EEESSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEE
T ss_pred             EEeCCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEE
Confidence            344446799999999999999999999998877654 234444444