Citrus Sinensis ID: 027547

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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-------180-------190-------200-------210-------220--
Protein Sequence
MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPELWEF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEEccEEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEEcccccccHHHHHHHHHHHHHccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEEEcccEEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEccccccccHHHHHHHHHHHHccccccccccccHHccEEEcccHccc
Coil and Loop (DISEMBL)
mgylgqsleakgsmkrkqcssssptkieRKTIEKNRRDQMKNLYSTLKsllpnqpskeelslpdqvDEAINYIKMLETKLKECKKRKEslqgrershacisdgtearlmtssspkapeieiheMGSNLEVILtsgvddqfIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFvsgcasegemqlpelwdfeinpelwef
Flexible Loop (DISEMBL)
mgylgqsleakgsmkrkqcssssptkierktieknRRDQMKNLYSTLKsllpnqpskeelslpdqVDEAINYIKMLETKLKECKkrkeslqgrershacisdgtearlmtsssPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASegemqlpelwdfeinpelwef
Low Complexity Region (SEG)
MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPELWEF
Disordered region (IsUnstruct)
********************************************************************AINYIKML***********************************************MGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPEL***
Disordered Region (DISOPRED)
**********************************NRRDQMKNLYSTLKSLLPNQP****LSLPDQVDEAINYIKMLE*******************************************IHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPELWEF
Disordered Region (DISEMBL)
MGYLGQSL*******************ERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKEC**************ACISDGTE********PKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPELWEF
Disordered Region (DISPRO)
***************************ERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQ*********************SPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPELWEF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQxxxxxxxxxxxxxxxxxxxxxxxxxxxxERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPELWDFEINPELWEF
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	222	2.2.26 [Sep-21-2011]
Q9FLI1	174	Transcription factor bHLH	no	no	0.752	0.959	0.297	3e-13
Q9STJ6	221	Transcription factor bHLH	no	no	0.648	0.651	0.269	8e-09
Q9STJ7	163	Transcription factor bHLH	no	no	0.630	0.858	0.292	2e-08
Q9M1K1	253	Transcription factor ORG2	no	no	0.756	0.664	0.230	3e-06
Q9LQ08	259	Transcription factor bHLH	no	no	0.297	0.254	0.333	7e-05
Q9LN95	257	Transcription factor bHLH	no	no	0.297	0.256	0.363	7e-05
Q9FYE6	240	Transcription factor bHLH	no	no	0.306	0.283	0.352	0.0003
Q9ZPY8	566	Transcription factor ABA-	no	no	0.549	0.215	0.258	0.0003

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

 Score = 75.1 bits (183), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 88/168 (52%), Gaps = 1/168 (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 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERL 192
           V+++L + G  +LN+  S+V + + + I AE+ D       A++ +RL
Sbjct: 123 VLQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMIDLAELEKRL 170

Arabidopsis thaliana (taxid: 3702)

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

 Score = 60.5 bits (145), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 41/152 (26%), 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 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEI 176
           V+  + + G E++++  + V + + H I  E+
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 = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/157 (29%), Positives = 80/157 (50%), Gaps = 17/157 (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 FYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRD 178
           F  V+++L + G  +L    S V + + H + AE+ D
Sbjct: 110 FSSVLQVLREHGLYVLGYICSSVNDRLIHTLQAEVND 146

Arabidopsis thaliana (taxid: 3702)

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

 Score = 52.0 bits (123), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 42/182 (23%), Positives = 86/182 (47%), Gaps = 14/182 (7%)

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-VVGNTIFHVIHAEIRD-SMFGFGAAKISERLKGFVS 197
           F    V+  + +DG  +++   S   G  +F+ +H ++ +   +     ++SER+     
Sbjct: 187 FSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQVENMDDYKINCEELSERMLYLYE 246

Query: 198 GC 199
            C
Sbjct: 247 KC 248

Arabidopsis thaliana (taxid: 3702)

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

 Score = 47.8 bits (112), Expect = 7e-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 = 47.8 bits (112), Expect = 7e-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 = 45.4 bits (106), 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 = 45.1 bits (105), Expect = 3e-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	222
356544962	211	PREDICTED: transcription factor bHLH36-l	0.900	0.947	0.561	1e-58
225446384	206	PREDICTED: transcription factor bHLH118-	0.873	0.941	0.550	3e-54
302143302	215	unnamed protein product [Vitis vinifera]	0.873	0.902	0.550	3e-54
356515176	224	PREDICTED: transcription factor bHLH36-l	0.891	0.883	0.539	2e-53
356543837	222	PREDICTED: transcription factor bHLH36-l	0.846	0.846	0.536	6e-52
224121740	218	predicted protein [Populus trichocarpa]	0.900	0.917	0.550	1e-51
255553725	246	DNA binding protein, putative [Ricinus c	0.977	0.882	0.511	1e-50
224127063	236	predicted protein [Populus trichocarpa]	0.905	0.851	0.514	4e-50
357474369	208	Transcription factor bHLH36 [Medicago tr	0.882	0.942	0.523	1e-49
224127065	216	predicted protein [Populus trichocarpa]	0.864	0.888	0.517	3e-49

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

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 114/203 (56%), Positives = 152/203 (74%), Gaps = 3/203 (1%)

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 IFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA 200
           IFYE+I+ILH++  E+ +   S+ G+++ HV+HAEI  S   FGA K+SERLK FV+G  
Sbjct: 130 IFYEIIQILHEENIEVRSVNSSLAGDSVLHVVHAEIPQSFLQFGATKVSERLKRFVNGSC 189

Query: 201 SEGEMQLPELWDFEI-NPELWEF 222
           S+ E Q PELWDFEI   ++W F
Sbjct: 190 SDVETQ-PELWDFEIGTDDMWGF 211

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (552), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 109/198 (55%), Positives = 144/198 (72%), Gaps = 4/198 (2%)

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 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGE 204
           +I ILH++ AE+L+A FSVVGN+ FHV+ A++ DS F FG   I +RL  FV G  SE E
Sbjct: 130 IIGILHEESAEVLSASFSVVGNSAFHVLIAQVGDSTFSFGTKWICDRLNKFVHGSTSEEE 189

Query: 205 MQLPELWDFEINPELWEF 222
           +Q PELWDFE +PE W F
Sbjct: 190 LQ-PELWDFEFHPETWAF 206

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (552), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 109/198 (55%), Positives = 144/198 (72%), Gaps = 4/198 (2%)

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 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGE 204
           +I ILH++ AE+L+A FSVVGN+ FHV+ A++ DS F FG   I +RL  FV G  SE E
Sbjct: 139 IIGILHEESAEVLSASFSVVGNSAFHVLIAQVGDSTFSFGTKWICDRLNKFVHGSTSEEE 198

Query: 205 MQLPELWDFEINPELWEF 222
           +Q PELWDFE +PE W F
Sbjct: 199 LQ-PELWDFEFHPETWAF 215

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 =  214 bits (546), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 109/202 (53%), Positives = 150/202 (74%), Gaps = 4/202 (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 FIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC 199
           FIF E+IR+LH++  ++ +A  S+ G+++ HV+HAEI  S+  FGA K+S+RLK FV+G 
Sbjct: 130 FIFSEIIRMLHEENIDVRSANSSLAGDSMLHVVHAEIPQSLLQFGATKVSQRLKRFVNGS 189

Query: 200 ASEGEMQLPELWDFEI-NPELW 220
            S+ E Q PELWDFEI   ++W
Sbjct: 190 CSDVETQ-PELWDFEIGTDDMW 210

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 =  209 bits (532), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 103/192 (53%), Positives = 143/192 (74%), Gaps = 4/192 (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 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGE 204
           +IRILH++  E++NA  S+VG+ + HV+H E+  S++ FGA K+SE+LK F++G  S+ E
Sbjct: 129 IIRILHEENVEVINANSSMVGDLVIHVVHGEVEPSIYQFGATKVSEKLKWFMNGSFSDVE 188

Query: 205 MQLPELWDFEIN 216
           M+   +W+F+I+
Sbjct: 189 MEPELMWNFKID 200

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  209 bits (531), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 114/207 (55%), Positives = 156/207 (75%), Gaps = 7/207 (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 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISE 190
           +LTSG D+QF+FYE+IRILH++G E+++A F V+G++IF V+HA++++S  GFGAAK++E
Sbjct: 122 VLTSGPDNQFLFYEIIRILHEEGVEVVSANFQVLGDSIFQVLHAQMKESDNGFGAAKVTE 181

Query: 191 RLKGFVSGCASEGEMQLPELWDFEINP 217
           RL  F++G  SE E+ L ELWDFEI+P
Sbjct: 182 RLNMFINGSTSEIELDL-ELWDFEIHP 207

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553725|ref|XP_002517903.1| DNA binding protein, putative [Ricinus communis] gi|223542885|gb|EEF44421.1| DNA binding protein, putative [Ricinus communis]

 Score =  205 bits (521), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 114/223 (51%), Positives = 159/223 (71%), Gaps = 6/223 (2%)

Query: 1   MGYLGQSLEAKGSMKRKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEEL 60
           +G L +       M      S+S TK ERK IEKNRR+QMK L+S L SL P + +KE  
Sbjct: 29  LGTLMKMNHPSSRMAMAPSGSTSSTKTERKVIEKNRRNQMKTLFSNLNSLFPRRNAKEAP 88

Query: 61  SLPDQVDEAINYIKMLETKLKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIE 120
            LPDQ+DEAIN+IK LE KLK+ K +KESL  R+R  +  SD  E    ++S+ +AP+++
Sbjct: 89  PLPDQIDEAINHIKSLEEKLKKLKVKKESLSARKRPFSECSDSYE----SASASRAPQLQ 144

Query: 121 IHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSM 180
           I EMGS LE++L SG+D+QF+FYE+IRILHQ+G +I +A +SV GN+I +++HAEIR+S 
Sbjct: 145 IKEMGSALEIVLISGLDNQFMFYEIIRILHQEGVDIASASYSVAGNSIVYIVHAEIRESN 204

Query: 181 FGFGAAKISERLKGFVSGCASEGEMQLPELWDF-EINPELWEF 222
           F FGAAK+++RL  FV+  +SE E++ PELWDF ++ P+ W F
Sbjct: 205 FSFGAAKVTDRLNRFVNELSSEIEVE-PELWDFNDLQPDTWAF 246

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127063|ref|XP_002329378.1| predicted protein [Populus trichocarpa] gi|222870428|gb|EEF07559.1| predicted protein [Populus trichocarpa]

 Score =  203 bits (516), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 108/210 (51%), Positives = 158/210 (75%), Gaps = 9/210 (4%)

Query: 16  RKQCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKM 75
           R   S+ S TK ERK +E+NRR+QMK+LYS+L SLLPNQ  KE   LPDQ+D AINYIK 
Sbjct: 33  RSGRSNISSTKTERKVVERNRRNQMKSLYSSLNSLLPNQNFKEAQPLPDQIDRAINYIKS 92

Query: 76  LETKLKECKKRKESL-QGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTS 134
           LE KL++ +++KESL + R+RS+ C  D      ++S++ K+P+++IHE+GS LE++LTS
Sbjct: 93  LEEKLEKAREKKESLARSRKRSYTCTFDP-----ISSAASKSPQLKIHEIGSALEIVLTS 147

Query: 135 GVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG 194
           G+ +QF+FYE+I ILH++G E+++A F  +G++ FH++HA+++ S  GFGAA+++ERL  
Sbjct: 148 GLGNQFLFYEIISILHEEGVEVVSANFQALGDSFFHIVHAQMKGSADGFGAARVTERLNR 207

Query: 195 FVSGCASEGEMQLPELWDFEI-NPEL-WEF 222
           F+SG  SE E+   ELWDF + +PE  WEF
Sbjct: 208 FISGSTSEIELD-SELWDFAVHHPETNWEF 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357474369|ref|XP_003607469.1| Transcription factor bHLH36 [Medicago truncatula] gi|355508524|gb|AES89666.1| Transcription factor bHLH36 [Medicago truncatula]

 Score =  202 bits (513), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 110/210 (52%), Positives = 143/210 (68%), Gaps = 14/210 (6%)

Query: 18  QCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKE-ELSLPDQVDEAINYIKML 76
           Q SSS+ TK+ER+ +EKNRR+QMK LYS L SLLPN   KE  L+LPDQVDEAINYIK L
Sbjct: 8   QPSSSNTTKVERRLVEKNRRNQMKILYSKLNSLLPNYNPKELPLALPDQVDEAINYIKSL 67

Query: 77  ETKLKECKKRKESLQGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGV 136
           E  ++   ++KE L               +R      PK+P  EIHE+GS+L++ILT G+
Sbjct: 68  EANVQMAMEKKERLLA--------GKNKRSREYCLDLPKSPCFEIHEIGSSLQIILTCGL 119

Query: 137 DDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAEIRDSMFGFGAAKISERLKGF 195
           D+QFIFYE+IR+LH++  +I +   S VG N++ HV+HAEI  S   FGA K+SERLK F
Sbjct: 120 DNQFIFYEIIRVLHEENVDIRSVNSSKVGDNSLLHVVHAEIPPSCVQFGATKVSERLKSF 179

Query: 196 VSGCASEGEMQLPELWDFEINPE---LWEF 222
           V G +S+ E+Q PELWDFEI P+   +W F
Sbjct: 180 VYGSSSDVEIQ-PELWDFEIGPDDHNMWGF 208

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127065|ref|XP_002329379.1| predicted protein [Populus trichocarpa] gi|222870429|gb|EEF07560.1| predicted protein [Populus trichocarpa]

 Score =  200 bits (509), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 104/201 (51%), Positives = 154/201 (76%), Gaps = 9/201 (4%)

Query: 25  TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECK 84
           TK ERK +E+NRR+QMK+LYS+L SLLPNQ  KE   LPDQ+D AINYIK LE KL++ +
Sbjct: 22  TKTERKVVERNRRNQMKSLYSSLNSLLPNQNFKEAQPLPDQIDRAINYIKSLEEKLEKAR 81

Query: 85  KRKESL-QGRERSHACISDGTEARLMTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFIFY 143
           ++KESL + R+RS+ C  D      ++S++ K+P+++IHE+GS LE++LTSG+ +QF+FY
Sbjct: 82  EKKESLARSRKRSYTCTFDP-----ISSAASKSPQLKIHEIGSALEIVLTSGLGNQFLFY 136

Query: 144 EVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEG 203
           E+I ILH++G E+++A F  +G++ FH++HA+++ S  GFGAA+++ERL  F+SG  SE 
Sbjct: 137 EIISILHEEGVEVVSANFQALGDSFFHIVHAQMKGSADGFGAARVTERLNRFISGSTSEI 196

Query: 204 EMQLPELWDFEI-NPEL-WEF 222
           E+   ELWDF + +P+  WEF
Sbjct: 197 ELD-SELWDFAVHHPKTNWEF 216

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	222
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.824	0.963	0.382	5.4e-31
TAIR|locus:2165311	174	AT5G51780 "AT5G51780" [Arabido	0.752	0.959	0.297	1.3e-15
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.788	0.705	0.256	1.5e-12
TAIR|locus:4515102513	174	AT1G10586 [Arabidopsis thalian	0.734	0.936	0.247	2.8e-11
TAIR|locus:2138019	163	AT4G25400 "AT4G25400" [Arabido	0.630	0.858	0.292	5.8e-11
TAIR|locus:505006117	181	AT1G10585 [Arabidopsis thalian	0.738	0.906	0.245	3.2e-10
TAIR|locus:2080600	253	bHLH38 "basic helix-loop-helix	0.756	0.664	0.230	1.3e-08
TAIR|locus:2146663	240	BHLH101 "AT5G04150" [Arabidops	0.752	0.695	0.232	3.2e-07
TAIR|locus:2080615	258	bHLH39 "basic helix-loop-helix	0.765	0.658	0.228	1.4e-06
TAIR|locus:2040287	242	BHLH100 "basic helix-loop-heli	0.765	0.702	0.223	2.6e-06

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

 Score = 341 (125.1 bits), Expect = 5.4e-31, P = 5.4e-31
 Identities = 72/188 (38%), Positives = 119/188 (63%)

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-GAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKIS 189
              L + ++ +F+F E+IR+L ++ GAEI +A +S+V + +FH +H ++ +  +G   ++I 
Sbjct:   121 FLVTSLEHKFMFCEIIRVLTEELGAEITHAGYSIVDDAVFHTLHCKVEEHDYG-ARSQIP 179

Query:   190 ERLKGFVS 197
             ERL+  V+
Sbjct:   180 ERLEKIVN 187

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 50/168 (29%), Positives = 88/168 (52%)

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 VIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERL 192
             V+++L + G  +LN+  S+V + + + I AE+ D       A++ +RL
Sbjct:   123 VLQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMIDLAELEKRL 170

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 = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 46/179 (25%), Positives = 88/179 (49%)

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-VGNTIFHVIHAEIRDSMFGFGAAKISERLKGFV 196
              +   + I++L  +G   +++  S   GN  F+ IH +  +           ERL+  V
Sbjct:   184 VLPLSKCIKVLENEGLHFISSSTSSGFGNRTFYSIHLQRSEGTINEECPAFCERLEKVV 242

GO:0005634 "nucleus" evidence=IC

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

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 44/178 (24%), Positives = 95/178 (53%)

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-YEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS 197
             +  ++++ +  ++GA++++A    + +  F+ I A+      G   ++I ERL+  +S
Sbjct:   117 VMLHKLVSVFEEEGAQVMSANLQNLNDRTFYTIIAQAIICRIGIDPSRIEERLRDIIS 174

GO:0005634 "nucleus" evidence=ISM

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

 Score = 152 (58.6 bits), Expect = 5.8e-11, P = 5.8e-11
 Identities = 46/157 (29%), Positives = 80/157 (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 FYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRD 178
             F  V+++L + G  +L    S V + + H + AE+ D
Sbjct:   110 FSSVLQVLREHGLYVLGYICSSVNDRLIHTLQAEVND 146

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:505006117 AT1G10585 [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 44/179 (24%), Positives = 96/179 (53%)

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 FIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSG 198
              + +E++ I  ++GA++++A    + +   + I A+   S  G   ++I ER++  + G
Sbjct:   117 VMLHELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQAIISRIGIDPSRIEERVRKIIYG 175

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0006865 "amino acid transport" evidence=RCA

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

 Score = 145 (56.1 bits), Expect = 1.3e-08, P = 1.3e-08
 Identities = 42/182 (23%), Positives = 86/182 (47%)

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-VVGNTIFHVIHAEIRD-SMFGFGAAKISERLKGFVS 197
             F    V+  + +DG  +++   S   G  +F+ +H ++ +   +     ++SER+     
Sbjct:   187 FSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQVENMDDYKINCEELSERMLYLYE 246

Query:   198 GC 199
              C
Sbjct:   247 KC 248

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

 Score = 134 (52.2 bits), Expect = 3.2e-07, P = 3.2e-07
 Identities = 41/176 (23%), Positives = 84/176 (47%)

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-IFHVIHAEIRDSMFGFGAAKISERLKGFVSG 198
             +++  L ++G  +++   SV     IF+ +H ++R    G    ++ E + G + G
Sbjct:   185 DMLLRLEENGLNVISVSSSVSSTARIFYTLHLQMR----GDCKVRLEELINGMLLG 236

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 = 130 (50.8 bits), Expect = 1.4e-06, P = 1.4e-06
 Identities = 42/184 (22%), Positives = 83/184 (45%)

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-VVGNTIFHVIHAEIRD-SMFGFGAAKISERLKGFVS 197
             F    V+  L +D   +++   S   G  +F+ +H ++     +     ++S+R+     
Sbjct:   192 FSISNVLSGLEEDRFVLVDMSSSRSQGERLFYTLHLQVEKIENYKLNCEELSQRMLYLYE 251

Query:   198 GCAS 201
              C +
Sbjct:   252 ECGN 255

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:2040287 BHLH100 "basic helix-loop-helix protein 100" [Arabidopsis thaliana (taxid:3702)]

 Score = 127 (49.8 bits), Expect = 2.6e-06, P = 2.6e-06
 Identities = 40/179 (22%), Positives = 87/179 (48%)

Query:    26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKK 85
             K+     E+ RR ++  ++S+L+S LP     ++LS+   V +A+ YI  L+ ++K+  K
Sbjct:    63 KLNHNASERERRKKINTMFSSLRSCLPPTNQTKKLSVSATVSQALKYIPELQEQVKKLMK 122

Query:    86 RKESLQGR---ERSHACISDGTEARL-MTSSSPKAPEIEIHEMGSNLEVILTSGVDDQFI 141
             +KE L  +   +R        +++   +TS +       + E  + + V ++S   ++  
Sbjct:   123 KKEELSFQISGQRDLVYTDQNSKSEEGVTSYASTVSSTRLSE--TEVMVQISSLQTEKCS 180

Query:   142 FYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC 199
             F  V+  + +DG  ++ A  S   G  +F+ +H +I++      + ++ +RL      C
Sbjct:   181 FGNVLSGVEEDGLVLVGASSSRSHGERLFYSMHLQIKNGQVN--SEELGDRLLYLYEKC 237

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:0009414 "response to water deprivation" evidence=IEP

GO:0055072 "iron ion homeostasis" evidence=IGI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	222
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-09
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	1e-07
smart00353	53	smart00353, HLH, helix loop helix domain	4e-06

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

 Score = 51.7 bits (125), Expect = 2e-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 = 46.8 bits (112), Expect = 1e-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 = 42.6 bits (101), Expect = 4e-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	222
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.42
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.41
smart00353	53	HLH helix loop helix domain.	99.34
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.86
KOG1318	411	consensus Helix loop helix transcription factor EB	98.68
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.58
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.55
KOG0561	373	consensus bHLH transcription factor [Transcription	98.46
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.37
PLN03217	93	transcription factor ATBS1; Provisional	98.37
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.19
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	98.13
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	98.02
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.99
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.93
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	97.92
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.86
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.67
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.66
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.55
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.5
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	97.14
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.97
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	96.93
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	96.9
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	96.82
PRK05007	884	PII uridylyl-transferase; Provisional	96.74
PRK03381	774	PII uridylyl-transferase; Provisional	96.68
PRK00194	90	hypothetical protein; Validated	96.67
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	96.59
PRK00275	895	glnD PII uridylyl-transferase; Provisional	96.59
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.58
KOG3898	254	consensus Transcription factor NeuroD and related	96.47
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.47
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	96.45
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	96.45
PRK05092	931	PII uridylyl-transferase; Provisional	96.41
PRK04374	869	PII uridylyl-transferase; Provisional	96.39
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	96.36
PRK03059	856	PII uridylyl-transferase; Provisional	96.31
PRK01759	854	glnD PII uridylyl-transferase; Provisional	96.19
PRK03381	774	PII uridylyl-transferase; Provisional	96.04
PRK05007	884	PII uridylyl-transferase; Provisional	95.77
PRK01759	854	glnD PII uridylyl-transferase; Provisional	95.72
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	95.68
KOG4395	285	consensus Transcription factor Atonal, contains HT	95.59
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	95.58
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	95.57
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	95.52
KOG3910	632	consensus Helix loop helix transcription factor [T	95.4
PRK04374	869	PII uridylyl-transferase; Provisional	95.26
PRK05092	931	PII uridylyl-transferase; Provisional	95.12
PRK03059	856	PII uridylyl-transferase; Provisional	94.98
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	94.84
PRK00275	895	glnD PII uridylyl-transferase; Provisional	94.79
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	94.65
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	94.57
PRK04435	147	hypothetical protein; Provisional	94.49
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	94.22
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	93.93
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	93.87
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	93.73
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	93.58
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	92.95
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	92.92
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	92.91
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	92.73
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	92.69
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	92.63
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	92.39
PRK08577	136	hypothetical protein; Provisional	92.21
COG3830	90	ACT domain-containing protein [Signal transduction	92.2
cd02116	60	ACT ACT domains are commonly involved in specifica	92.06
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	91.78
cd04885	68	ACT_ThrD-I Tandem C-terminal ACT domains of threon	91.46
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	91.37
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	91.3
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	90.15
PLN02705	681	beta-amylase	89.96
PF13710	63	ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.	89.85
COG4492	150	PheB ACT domain-containing protein [General functi	89.64
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	89.61
PRK07334	403	threonine dehydratase; Provisional	89.3
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	88.94
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	88.64
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	88.18
PRK11152	76	ilvM acetolactate synthase 2 regulatory subunit; P	88.02
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	87.99
PRK00227	693	glnD PII uridylyl-transferase; Provisional	87.69
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	87.48
PRK11589	190	gcvR glycine cleavage system transcriptional repre	86.81
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	86.8
TIGR00119	157	acolac_sm acetolactate synthase, small subunit. ac	86.67
PRK11895	161	ilvH acetolactate synthase 3 regulatory subunit; R	85.61
PRK06737	76	acetolactate synthase 1 regulatory subunit; Valida	84.29
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	84.04
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	82.75
CHL00100	174	ilvH acetohydroxyacid synthase small subunit	82.6
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	81.68
PRK13562	84	acetolactate synthase 1 regulatory subunit; Provis	80.79
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	80.25

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

Probab=99.42  E-value=5.3e-13  Score=90.68  Aligned_cols=53  Identities=32%  Similarity=0.572  Sum_probs=48.3

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCCCCChhHHHHHHHHHHHHHH
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQ--PSKEELSLPDQVDEAINYIKMLE   77 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~--~~~~k~si~~iL~~ai~YIk~Lq   77 (222)
                      +|..|+..||+||..||+.|..|+.+||..  ....|.+.++||..||+||++||
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            478999999999999999999999999996  35567888889999999999997

; 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=99.41  E-value=7.8e-13  Score=90.60  Aligned_cols=57  Identities=30%  Similarity=0.577  Sum_probs=50.6

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL   80 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v   80 (222)
                      .++..|+..||+||.+||..|..|+++||......|.+.+.||..|++||+.|+..+
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            478899999999999999999999999999965555666667999999999999876

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=99.34  E-value=3.5e-12  Score=85.57  Aligned_cols=52  Identities=35%  Similarity=0.622  Sum_probs=45.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 027547           30 KTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (222)
Q Consensus        30 ~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~   81 (222)
                      +..||+||.+||.+|..|+++||......|.+.+.||..|++||++|+.+++
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            4689999999999999999999976544556666679999999999999875

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

Probab=98.86  E-value=1.2e-08  Score=88.53  Aligned_cols=73  Identities=25%  Similarity=0.373  Sum_probs=59.6

Q ss_pred             CCCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           20 SSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        20 ~~~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      ++..++|..||..||+||.+|+++|..|+.+||......+-....||+.|..||+.|+.+.....+..++|..
T Consensus        54 ~~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~  126 (232)
T KOG2483|consen   54 SSAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSR  126 (232)
T ss_pred             CCCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            4667899999999999999999999999999999875433325667999999999999877776665555443

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

Probab=98.68  E-value=4.3e-08  Score=90.99  Aligned_cols=60  Identities=18%  Similarity=0.361  Sum_probs=50.4

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCC-CCCCChhHHHHHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPS-KEELSLPDQVDEAINYIKMLETKLKEC   83 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~-~~k~si~~iL~~ai~YIk~Lq~~v~~L   83 (222)
                      -+|-.||++||+||..||+....|..|||.... ..|..+..||..+++||++||+..++.
T Consensus       232 ~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~  292 (411)
T KOG1318|consen  232 RKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRA  292 (411)
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHH
Confidence            366789999999999999999999999998743 335556666999999999999877643

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.58  E-value=1.4e-07  Score=78.94  Aligned_cols=66  Identities=26%  Similarity=0.466  Sum_probs=58.1

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCC----CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027547           26 KIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKE----ELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (222)
Q Consensus        26 ~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~----k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~   91 (222)
                      |..|.-.||+||+-||.-|+.|..|||.....+    |.|.+-||..+|+||..|+.++.+-+.+...|.
T Consensus        63 r~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~  132 (229)
T KOG1319|consen   63 RRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR  132 (229)
T ss_pred             HHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999887665    889899999999999999988877776655544

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

Probab=98.55  E-value=3.5e-08  Score=86.73  Aligned_cols=63  Identities=22%  Similarity=0.407  Sum_probs=53.9

Q ss_pred             CCCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC-----CCCChhHHHHHHHHHHHHHHHHHHH
Q 027547           20 SSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK-----EELSLPDQVDEAINYIKMLETKLKE   82 (222)
Q Consensus        20 ~~~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~-----~k~si~~iL~~ai~YIk~Lq~~v~~   82 (222)
                      ...-.+|..|-..||+||.+||.+++.|+.|||...++     .|.-+++||.-|++|+++|+.....
T Consensus        27 ~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   27 KTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            34456888999999999999999999999999988766     4777888899999999999876544

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.46  E-value=1.3e-07  Score=84.22  Aligned_cols=63  Identities=22%  Similarity=0.353  Sum_probs=52.3

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRK   87 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~   87 (222)
                      -+|.--|--||+|-+-||.-|..||+|||.... .|.|++.||..+.+||.+|+..--+|-.+.
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~eG-EKLSKAAILQQTa~yI~~Le~~Kt~ll~qn  121 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKEG-EKLSKAAILQQTADYIHQLEGHKTELLPQN  121 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCcccc-hhhHHHHHHHHHHHHHHHHHhccccccccc
Confidence            355667888999999999999999999998764 578888889999999999987665554433

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

Probab=98.37  E-value=6.4e-07  Score=77.48  Aligned_cols=65  Identities=25%  Similarity=0.454  Sum_probs=58.1

Q ss_pred             CCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCC-CCCCChhHHHHHHHHHHHHHHHHHHHHHH
Q 027547           21 SSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPS-KEELSLPDQVDEAINYIKMLETKLKECKK   85 (222)
Q Consensus        21 ~~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~-~~k~si~~iL~~ai~YIk~Lq~~v~~L~~   85 (222)
                      .....+..+|..||+|-+.+|..|..||.+||.... ..|.|+.++|..||.||..|++-++.-+.
T Consensus       105 ~~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  105 QTSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             chhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            345678889999999999999999999999999987 88999999999999999999987766554

>PLN03217 transcription factor ATBS1; Provisional

Probab=98.37  E-value=1e-06  Score=64.87  Aligned_cols=57  Identities=25%  Similarity=0.456  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHhcCCCCCC---CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 027547           37 RDQMKNLYSTLKSLLPNQPS---KEELSLPDQVDEAINYIKMLETKLKECKKRKESLQGR   93 (222)
Q Consensus        37 R~~mn~~~~~LrsLlP~~~~---~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~~   93 (222)
                      -++|+++.+.|+.|+|....   .+|+|.+.+|.+++.||+.|+++|.+|.++..+|...
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            47899999999999998643   4799999999999999999999999999999888753

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

Probab=98.19  E-value=2.5e-05  Score=56.25  Aligned_cols=66  Identities=17%  Similarity=0.137  Sum_probs=53.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      |.|.+ .++||+|.+|.++|.++||+|..|.+++.|+++..+|.+.-.++. .++-....+.|++.+.
T Consensus         4 iev~a-~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~-kl~d~~~~~~l~~~L~   69 (72)
T cd04895           4 VKVDS-ARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGN-KLTDDSLIAYIEKSLG   69 (72)
T ss_pred             EEEEE-CCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCC-CCCCHHHHHHHHHHhc
Confidence            45555 589999999999999999999999999999999999999866554 4444455566666554

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

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

Probab=98.13  E-value=3.8e-05  Score=55.75  Aligned_cols=66  Identities=12%  Similarity=0.218  Sum_probs=54.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccC----HHHHHHHHHHHHh
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFG----AAKISERLKGFVS  197 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~----~~~l~~aL~~~I~  197 (222)
                      |.|.| +++||+|.+|..+|-++|++|.+|.+++.++++.-+|.+.-.++. .+.    .+.|.++|.+++.
T Consensus         4 veV~~-~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~-kl~~~~~~~~l~~~L~~al~   73 (75)
T cd04897           4 VTVQC-RDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGR-TLSTEGERQRVIKCLEAAIE   73 (75)
T ss_pred             EEEEe-CCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCC-ccCCHHHHHHHHHHHHHHHh
Confidence            55556 599999999999999999999999999999999999999877765 333    3466677776665

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

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

Probab=98.02  E-value=0.00011  Score=52.17  Aligned_cols=67  Identities=19%  Similarity=0.226  Sum_probs=50.0

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe-CCEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      +|.|.| .++||+|+++..+|..+|++|++|.+.+. ++.++.+|.+.-.++. .....+..++|++.|.
T Consensus         3 ~i~v~~-~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~~~~-~~~~~~~~~~l~~~L~   70 (73)
T cd04900           3 EVFIYT-PDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDPDGE-PIGERERLARIREALE   70 (73)
T ss_pred             EEEEEe-cCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECCCCC-CCChHHHHHHHHHHHH
Confidence            566666 58999999999999999999999999877 6899999998744433 3333444445555443

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.

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

Probab=97.99  E-value=7.7e-06  Score=81.71  Aligned_cols=59  Identities=24%  Similarity=0.483  Sum_probs=49.7

Q ss_pred             CCCCCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCC----CCCCCChhHHHHHHHHHHHHHHHH
Q 027547           18 QCSSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQP----SKEELSLPDQVDEAINYIKMLETK   79 (222)
Q Consensus        18 ~~~~~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~----~~~k~si~~iL~~ai~YIk~Lq~~   79 (222)
                      +.+.....|..|+.+||+||++||..+..|.+|||...    |+||..|   |..||.+|+.+++.
T Consensus        13 ~d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tV---Lr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   13 SDSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTV---LRMAVDHLRLIKEQ   75 (803)
T ss_pred             ccchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHH---HHHHHHHHHHHhhh
Confidence            33444456899999999999999999999999999875    5566655   99999999999884

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

Probab=97.93  E-value=9.9e-05  Score=53.57  Aligned_cols=66  Identities=20%  Similarity=0.307  Sum_probs=52.2

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE--EeCCEEEEEEEEEeccCcccc-C---HHHHHHHHHHHHhc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFS--VVGNTIFHVIHAEIRDSMFGF-G---AAKISERLKGFVSG  198 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s--~~~~~~~~ti~~kv~~~~~~~-~---~~~l~~aL~~~I~~  198 (222)
                      +.|.| .++||+|++|.++|..+|++|.+|.++  +.|+++.-+|.+ -.++. .+ +   ...|+++|.+++.+
T Consensus         3 lev~a-~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~~g~-kl~d~~~~~~L~~~L~~~l~~   74 (75)
T cd04896           3 LQIRC-VDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QSDGK-KIMDPKKQAALCARLREEMVC   74 (75)
T ss_pred             EEEEe-CCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eCCCC-ccCCHHHHHHHHHHHHHHhcC
Confidence            45556 589999999999999999999999999  999999999988 33333 23 2   45677777777653

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

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

Probab=97.92  E-value=0.00017  Score=51.40  Aligned_cols=64  Identities=13%  Similarity=0.098  Sum_probs=54.4

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE-eCCEEEEEEEEEeccCccccCHHHHHHHHHHHH
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAEIRDSMFGFGAAKISERLKGFV  196 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~-~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I  196 (222)
                      +|.|.+ +++|++|.++..+|..+||+|+.|.+.+ .++.++.+|.+.-.+   +-+...+.++|++++
T Consensus         3 eI~V~~-~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~---~~~~~~~~~~~~~~~   67 (68)
T cd04928           3 EITFAA-GDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWK---RGETAALGHALQKEI   67 (68)
T ss_pred             EEEEEE-CCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCC---ccchHHHHHHHHHhh
Confidence            566666 5899999999999999999999999885 578899999988655   348889999998876

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.

>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=97.86  E-value=0.0002  Score=51.59  Aligned_cols=67  Identities=12%  Similarity=0.110  Sum_probs=49.7

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE-eCCEEEEEEEEEeccCccccC---HHHHHHHHHHHHh
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAEIRDSMFGFG---AAKISERLKGFVS  197 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~-~~~~~~~ti~~kv~~~~~~~~---~~~l~~aL~~~I~  197 (222)
                      .+.|.| .++||+|.++..+|..+|++|++|.+++ .++.++.+|.+.-.++. ..+   ...+.++|.+++.
T Consensus         2 ~~ei~~-~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~~~-~~~~~~~~~l~~~L~~~L~   72 (76)
T cd04927           2 LLKLFC-SDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDAREL-LHTKKRREETYDYLRAVLG   72 (76)
T ss_pred             EEEEEE-CCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCCCC-CCCHHHHHHHHHHHHHHHc
Confidence            356666 5899999999999999999999999996 89999999998643322 112   2345555555554

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.

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

Probab=97.67  E-value=0.00017  Score=63.14  Aligned_cols=70  Identities=23%  Similarity=0.340  Sum_probs=56.4

Q ss_pred             CCCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027547           20 SSSSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESL   90 (222)
Q Consensus        20 ~~~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l   90 (222)
                      +.+..+|+.--+.||+|=+++|+.|.+|+.-.-.. +..+..+.+||..||.||..||.-++++.+....+
T Consensus       113 s~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~N-PNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  113 STSVDRRKAATMRERRRLKKVNEAFETLKRRTSSN-PNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-ccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            45567899999999999999999999998755322 23456677789999999999999999988765544

>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=97.66  E-value=0.00079  Score=47.76  Aligned_cols=66  Identities=17%  Similarity=0.248  Sum_probs=50.7

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .|.|.+ .+++|+|.+|..+|.++|++|++|.+.+.++..+.+|++.-.++. ..+. +..++|++.|.
T Consensus         3 ri~V~~-~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~~~~~-~~~~-~~~~~l~~~l~   68 (72)
T cd04926           3 RLELRT-EDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTDANGN-PVDP-KTIEAVRQEIG   68 (72)
T ss_pred             EEEEEE-CCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEECCCCC-cCCH-HHHHHHHHHhc
Confidence            456655 589999999999999999999999999888888888888644433 3333 45566777665

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.

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

Probab=97.55  E-value=0.0015  Score=46.64  Aligned_cols=65  Identities=20%  Similarity=0.242  Sum_probs=49.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEecc-Ccccc-C---HHHHHHHHHHHH
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRD-SMFGF-G---AAKISERLKGFV  196 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~-~~~~~-~---~~~l~~aL~~~I  196 (222)
                      |.|.+ .++||+|.+|..+|..+|++|+.|.+++.++.++.+|.+.-.+ +. .. +   .+.|.++|.+++
T Consensus         3 ~~v~~-~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~-~~~~~~~~~~i~~~L~~~l   72 (74)
T cd04925           3 IELTG-TDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGA-PIDDPIRLASIEDRLDNVL   72 (74)
T ss_pred             EEEEE-CCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCC-CCCCHHHHHHHHHHHHHHh
Confidence            44545 5899999999999999999999999999999999999886433 22 22 2   345555555554

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

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

Probab=97.50  E-value=0.002  Score=44.50  Aligned_cols=50  Identities=26%  Similarity=0.321  Sum_probs=43.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSM  180 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~  180 (222)
                      +.|.+ .+++|+|.+|+.+|.++++.|.++.+.+.++.++.+|++...++.
T Consensus         3 l~v~~-~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~   52 (70)
T cd04899           3 LELTA-LDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQ   52 (70)
T ss_pred             EEEEE-cCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCC
Confidence            44545 589999999999999999999999999888888899998876655

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.

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

Probab=97.14  E-value=0.0056  Score=43.79  Aligned_cols=68  Identities=16%  Similarity=0.263  Sum_probs=54.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      +-|++.+ +++||++..|..+|.++|.++..++.++.++.+...+.+.+..    .+.++++.+|.++-...-
T Consensus         3 ~vItv~G-~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~----~~~~~l~~~L~~l~~~~~   70 (76)
T PF13740_consen    3 LVITVVG-PDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPE----DSLERLESALEELAEELG   70 (76)
T ss_dssp             EEEEEEE-E--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESH----HHHHHHHHHHHHHHHHTT
T ss_pred             EEEEEEe-cCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCc----ccHHHHHHHHHHHHHHCC
Confidence            4566655 5899999999999999999999999999999988888888763    367888888888766543

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

Probab=96.97  E-value=0.017  Score=39.31  Aligned_cols=65  Identities=20%  Similarity=0.259  Sum_probs=48.2

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      |.|.| .+++|+|.+++.+|.++++.|.++.+.+.++.....|++.-.++. .. ..+-.+.|++.+.
T Consensus         3 l~i~~-~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~~~-~~-~~~~~~~l~~~l~   67 (70)
T cd04873           3 VEVYA-PDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSDGR-PL-DPERIARLEEALE   67 (70)
T ss_pred             EEEEe-CCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCCCC-cC-CHHHHHHHHHHHH
Confidence            55555 588999999999999999999999999887777778887765544 22 3344445555553

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

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

Probab=96.93  E-value=0.0086  Score=40.36  Aligned_cols=62  Identities=23%  Similarity=0.164  Sum_probs=44.7

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      |.+.| .++||.|.+|.++|-++|+.|.++......+...+.+.+...+   ......+.++|+++
T Consensus         3 v~v~~-~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~   64 (66)
T PF01842_consen    3 VRVIV-PDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIVVD---EEDLEKLLEELEAL   64 (66)
T ss_dssp             EEEEE-ETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEEE---GHGHHHHHHHHHHH
T ss_pred             EEEEc-CCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEECC---CCCHHHHHHHHHcc
Confidence            55556 4899999999999999999999999998876212222222222   24677888888775

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 ....

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=96.90  E-value=0.00056  Score=69.17  Aligned_cols=67  Identities=27%  Similarity=0.385  Sum_probs=56.1

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~   91 (222)
                      ..+|..||..||+=|--||++...|+.+||....+  ..++..|..||+||++|+..-+.++.....+.
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aK--l~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAK--LNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhh--hhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            47899999999999999999999999999987532  23344499999999999988888887666555

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

Probab=96.82  E-value=0.019  Score=41.15  Aligned_cols=69  Identities=19%  Similarity=0.250  Sum_probs=56.4

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccccc
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASE  202 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~  202 (222)
                      -+++.| +++||+..+|-+.|-++|.+|+.++....++.+++.+...+..    .+.+.+.++|..+-..+..+
T Consensus         3 iltv~g-~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~~----~~~~~l~~~l~~~~~~~~l~   71 (77)
T cd04893           3 VISALG-TDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSW----DAIAKLEAALPGLARRLDLT   71 (77)
T ss_pred             EEEEEe-CCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEecc----ccHHHHHHHHHHHHHHcCCE
Confidence            456666 5899999999999999999999999999999888877777652    46788999888876654433

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

>PRK05007 PII uridylyl-transferase; Provisional

Probab=96.74  E-value=0.01  Score=60.88  Aligned_cols=79  Identities=14%  Similarity=0.234  Sum_probs=58.3

Q ss_pred             CeeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccC---HHHHHHH
Q 027547          117 PEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFG---AAKISER  191 (222)
Q Consensus       117 p~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~---~~~l~~a  191 (222)
                      |.|.+....+  .-.|.|.+ .++||+|++|.++|.++|++|.+|.|+|.++++..+|.+.-.++. .++   .+.|+++
T Consensus       796 ~~V~~d~~~s~~~TvlEV~a-~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~~g~-~l~~~~~~~l~~~  873 (884)
T PRK05007        796 TEVSFLPTHTDRRSYMELIA-LDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATADRR-ALNEELQQELRQR  873 (884)
T ss_pred             CEEEEccCCCCCeEEEEEEe-CCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcCCCC-cCCHHHHHHHHHH
Confidence            4555554333  23455555 589999999999999999999999999999999999998755544 344   3456666


Q ss_pred             HHHHHh
Q 027547          192 LKGFVS  197 (222)
Q Consensus       192 L~~~I~  197 (222)
                      |..++.
T Consensus       874 L~~~l~  879 (884)
T PRK05007        874 LTEALN  879 (884)
T ss_pred             HHHHHh
Confidence            666654

>PRK03381 PII uridylyl-transferase; Provisional

Probab=96.68  E-value=0.021  Score=57.71  Aligned_cols=80  Identities=15%  Similarity=0.110  Sum_probs=63.1

Q ss_pred             CeeEEEee-CCeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          117 PEIEIHEM-GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       117 p~VeV~~~-g~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      |.|.+... ....+|.|+| +++||+|.+|..+|..+|++|++|++.+.++.++.+|.+.-..+. ....+.++++|.++
T Consensus       588 ~~v~~~~~~~~~~~V~V~~-~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~~~~-~~~~~~l~~~L~~~  665 (774)
T PRK03381        588 VHVEIAPADPHMVEVTVVA-PDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPRFGS-PPDAALLRQDLRRA  665 (774)
T ss_pred             CEEEEeeCCCCeEEEEEEe-cCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCC-cchHHHHHHHHHHH
Confidence            44444322 3557788766 589999999999999999999999999988999999888754443 34457888999888


Q ss_pred             Hhc
Q 027547          196 VSG  198 (222)
Q Consensus       196 I~~  198 (222)
                      +.+
T Consensus       666 L~~  668 (774)
T PRK03381        666 LDG  668 (774)
T ss_pred             HcC
Confidence            877

>PRK00194 hypothetical protein; Validated

Probab=96.67  E-value=0.013  Score=42.89  Aligned_cols=76  Identities=16%  Similarity=0.163  Sum_probs=59.0

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccccccccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQ  206 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~  206 (222)
                      +.|++.| .++||++.+|.+.|-++|++|...+..+.++.++..+.+.+...  ..+.+.+.+.|.++-........++
T Consensus         4 ~~ltv~g-~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~~~--~~~~~~l~~~l~~l~~~~~~~~~~~   79 (90)
T PRK00194          4 AIITVIG-KDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDISES--KKDFAELKEELEELGKELGVKIRIQ   79 (90)
T ss_pred             EEEEEEc-CCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEecCC--CCCHHHHHHHHHHHHHHcCCEEEEE
Confidence            4466666 58999999999999999999999998888887777777776531  2467889998888776655555444

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

Probab=96.59  E-value=0.041  Score=39.07  Aligned_cols=67  Identities=16%  Similarity=0.117  Sum_probs=51.9

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC------CEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG------NTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~------~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      |.+.| .+++|++.+|-+.|.++|++|...+..+.+      +.++..+.+.+..   ..+...+.++|..+-....
T Consensus         2 l~v~g-~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p~---~~~~~~l~~~l~~l~~~~~   74 (81)
T cd04869           2 VEVVG-NDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPA---GTDLDALREELEELCDDLN   74 (81)
T ss_pred             EEEEe-CCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecCC---CCCHHHHHHHHHHHHHHhc
Confidence            45656 589999999999999999999999998876      4555555555542   4678899999888776544

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

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=96.59  E-value=0.022  Score=58.47  Aligned_cols=80  Identities=13%  Similarity=0.177  Sum_probs=59.5

Q ss_pred             CeeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCH----HHHHH
Q 027547          117 PEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGA----AKISE  190 (222)
Q Consensus       117 p~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~----~~l~~  190 (222)
                      |.|.+....+  ...|.|.+ .++||+|.+|..+|..+|++|++|.+++.|+++..+|.+.-.++. .++.    +.|++
T Consensus       802 ~~V~i~~~~~~~~T~i~V~a-~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~-~l~~~~~~~~l~~  879 (895)
T PRK00275        802 TQVTISNDAQRPVTVLEIIA-PDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQ-PLSDPQLCSRLQD  879 (895)
T ss_pred             CEEEEEECCCCCeEEEEEEE-CCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCC-CCCCHHHHHHHHH
Confidence            4555554332  34566555 689999999999999999999999999999999999999865544 2322    45677


Q ss_pred             HHHHHHhc
Q 027547          191 RLKGFVSG  198 (222)
Q Consensus       191 aL~~~I~~  198 (222)
                      +|.+++.+
T Consensus       880 ~L~~~L~~  887 (895)
T PRK00275        880 AICEQLDA  887 (895)
T ss_pred             HHHHHHhc
Confidence            77777643

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.58  E-value=0.0017  Score=53.04  Aligned_cols=56  Identities=23%  Similarity=0.463  Sum_probs=48.4

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL   80 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v   80 (222)
                      .++..||..||+|-+.+|+.|..||..+|..+. ||.|+...|.-|.-||.-|-+-.
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPs-dklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPS-DKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCc-cccccccchhhcccCCchhhhcc
Confidence            477889999999999999999999999998764 67788777999999998876543

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

Probab=96.47  E-value=0.0024  Score=56.37  Aligned_cols=57  Identities=19%  Similarity=0.348  Sum_probs=50.1

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETK   79 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~   79 (222)
                      ..+|..-|..||+|-..+|+.|+.||.++|......|.++..+|.-|-+||..|++-
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            356677889999999999999999999999877777888889999999999998753

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

Probab=96.47  E-value=0.036  Score=39.27  Aligned_cols=67  Identities=16%  Similarity=0.136  Sum_probs=52.7

Q ss_pred             EcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccc
Q 027547          134 SGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEG  203 (222)
Q Consensus       134 ~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~  203 (222)
                      .+.++||+..++.++|-++|+++...+.++.++.+...+.+.+..   ..+.++++++|..+-......+
T Consensus         5 ~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p~---~~~~~~l~~~l~~l~~~l~l~i   71 (75)
T cd04870           5 TGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIPD---SADSEALLKDLLFKAHELGLQV   71 (75)
T ss_pred             EcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcCC---CCCHHHHHHHHHHHHHHcCceE
Confidence            346899999999999999999999999888888766666665543   3578899999888776544333

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.

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

Probab=96.45  E-value=0.037  Score=38.95  Aligned_cols=68  Identities=15%  Similarity=0.153  Sum_probs=49.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSG  198 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~  198 (222)
                      |.+.| .++||++.+|.+.|-++|+.+...+..+..+...+.+.+++.-.....+.+++.++|..+-..
T Consensus         2 i~v~g-~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~l~~~l~~l~~~   69 (74)
T cd04875           2 LTLSC-PDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFELEGFDLSREALEAAFAPVAAE   69 (74)
T ss_pred             EEEEc-CCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            45555 589999999999999999999999988643322344455554433125788999998887653

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.

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

Probab=96.45  E-value=0.02  Score=41.86  Aligned_cols=75  Identities=15%  Similarity=0.154  Sum_probs=58.9

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccccccccc
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQ  206 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~  206 (222)
                      .|.+.| +++||++.+|.+.|-++|++|..++..+.++.++..+.+.+..  ...+.+++.++|..+-........++
T Consensus         3 vl~i~g-~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~~--~~~~~~~L~~~l~~l~~~~~l~~~i~   77 (88)
T cd04872           3 VITVVG-KDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDISE--SNLDFAELQEELEELGKELGVKIRIQ   77 (88)
T ss_pred             EEEEEc-CCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeCC--CCCCHHHHHHHHHHHHHHcCCEEEEE
Confidence            356666 5899999999999999999999999888888777777776553  13578999999998877655444443

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.

>PRK05092 PII uridylyl-transferase; Provisional

Probab=96.41  E-value=0.044  Score=56.52  Aligned_cols=82  Identities=17%  Similarity=0.155  Sum_probs=61.8

Q ss_pred             CeeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccC---HHHHHHH
Q 027547          117 PEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFG---AAKISER  191 (222)
Q Consensus       117 p~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~---~~~l~~a  191 (222)
                      |.|.+....+  ...|.|.+ .++||+|.+|..+|.++|++|.+|.+++.++++..+|.+.-.++....+   .+.|+++
T Consensus       831 ~~V~~~~~~s~~~t~i~I~~-~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~~~~~l~~~  909 (931)
T PRK05092        831 PRVTIDNEASNRFTVIEVNG-RDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEARQAAIRRA  909 (931)
T ss_pred             CEEEEeeCCCCCeEEEEEEE-CCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHHHHHHHHHH
Confidence            4555554333  34566655 5899999999999999999999999999999999999997655441122   3568888


Q ss_pred             HHHHHhcc
Q 027547          192 LKGFVSGC  199 (222)
Q Consensus       192 L~~~I~~~  199 (222)
                      |.+++...
T Consensus       910 L~~~L~~~  917 (931)
T PRK05092        910 LLAALAEG  917 (931)
T ss_pred             HHHHhcCc
Confidence            88888654

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.39  E-value=0.035  Score=56.93  Aligned_cols=78  Identities=13%  Similarity=0.226  Sum_probs=57.3

Q ss_pred             CeeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCH---HHHHHH
Q 027547          117 PEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGA---AKISER  191 (222)
Q Consensus       117 p~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~---~~l~~a  191 (222)
                      |.|.+....+  ...|.|.+ .++||+|.+|..+|..+|++|++|.++|.++++..+|.+.-.++. ..+.   ..|+++
T Consensus       784 ~~V~~~~~~~~~~t~leI~a-~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~-~~~~~~~~~l~~~  861 (869)
T PRK04374        784 PRVEFSESAGGRRTRISLVA-PDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDR-PLSESARQALRDA  861 (869)
T ss_pred             CeEEEeecCCCCeEEEEEEe-CCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCC-cCChHHHHHHHHH
Confidence            4566554333  34566655 589999999999999999999999999999999999999755444 2322   455555


Q ss_pred             HHHHH
Q 027547          192 LKGFV  196 (222)
Q Consensus       192 L~~~I  196 (222)
                      |..++
T Consensus       862 L~~~l  866 (869)
T PRK04374        862 LCACL  866 (869)
T ss_pred             HHHHh
Confidence            55555

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

Probab=96.36  E-value=0.023  Score=40.55  Aligned_cols=49  Identities=12%  Similarity=0.249  Sum_probs=40.3

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE--eCCEEEEEEEEEecc
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV--VGNTIFHVIHAEIRD  178 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~--~~~~~~~ti~~kv~~  178 (222)
                      .+.|.+ .+++|+|.+|..++-+.++.|.++++..  .++.+...|.+++.+
T Consensus         8 ~l~i~~-~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d   58 (80)
T PF13291_consen    8 RLRIEA-EDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKD   58 (80)
T ss_dssp             EEEEEE-E--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESS
T ss_pred             EEEEEE-EcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECC
Confidence            445555 4889999999999999999999999998  467889999999875

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.31  E-value=0.031  Score=57.13  Aligned_cols=78  Identities=10%  Similarity=0.149  Sum_probs=53.7

Q ss_pred             eeEEEeeC--CeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          118 EIEIHEMG--SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       118 ~VeV~~~g--~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      .|.+....  ....|.|.+ .++||+|.+|..+|..+|++|++|.+++.|+++..+|.+.-.......-.+.|+++|.++
T Consensus       775 ~V~~~~~~~~~~T~i~V~a-~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~~~~~~~~~~~~l~~~L~~~  853 (856)
T PRK03059        775 RVDLRPDERGQYYILSVSA-NDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDGSGLSDNRLQIQLETELLDA  853 (856)
T ss_pred             eEEEEEcCCCCEEEEEEEe-CCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcCCCCCCHHHHHHHHHHHHHH
Confidence            45544332  235666656 589999999999999999999999999999999999998322111011133555555554


Q ss_pred             H
Q 027547          196 V  196 (222)
Q Consensus       196 I  196 (222)
                      +
T Consensus       854 L  854 (856)
T PRK03059        854 L  854 (856)
T ss_pred             h
Confidence            4

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=96.19  E-value=0.033  Score=56.97  Aligned_cols=78  Identities=15%  Similarity=0.207  Sum_probs=55.3

Q ss_pred             CeeEEEeeCCe--eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          117 PEIEIHEMGSN--LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       117 p~VeV~~~g~~--v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      |.|.+....+.  -.|.|.+ .++||+|.+|.++|.++|++|.+|.|+|.++++..+|.+.-.++. .++.++. +.|++
T Consensus       771 ~~V~~dn~~s~~~T~iev~a-~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g~-~l~~~~~-~~l~~  847 (854)
T PRK01759        771 TEVRFLNEEKQEQTEMELFA-LDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQGQ-ALDEEER-KALKS  847 (854)
T ss_pred             CEEEEccCCCCCeEEEEEEe-CCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCCC-cCChHHH-HHHHH
Confidence            45555443332  3455555 589999999999999999999999999999999999998755544 3333222 44444


Q ss_pred             HHh
Q 027547          195 FVS  197 (222)
Q Consensus       195 ~I~  197 (222)
                      .+.
T Consensus       848 ~L~  850 (854)
T PRK01759        848 RLL  850 (854)
T ss_pred             HHH
Confidence            443

>PRK03381 PII uridylyl-transferase; Provisional

Probab=96.04  E-value=0.071  Score=53.98  Aligned_cols=75  Identities=12%  Similarity=0.139  Sum_probs=55.6

Q ss_pred             eeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          118 EIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       118 ~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      .|.+....+  ...|.|.+ .++||+|.+|..+|..+|++|.+|.+++.++++..+|.+.-.++. .++ +. .+.|++.
T Consensus       696 ~v~~~~~~~~~~t~i~V~a-~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g~-~~~-~~-~~~l~~~  771 (774)
T PRK03381        696 RVLWLDGASPDATVLEVRA-ADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAGG-PLA-DA-RAAVEQA  771 (774)
T ss_pred             EEEEEECCCCCeEEEEEEe-CCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCCC-cCc-hH-HHHHHHH
Confidence            444443332  35566655 689999999999999999999999999999999999999755544 333 23 5666655


Q ss_pred             H
Q 027547          196 V  196 (222)
Q Consensus       196 I  196 (222)
                      +
T Consensus       772 L  772 (774)
T PRK03381        772 V  772 (774)
T ss_pred             h
Confidence            4

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.77  E-value=0.1  Score=53.59  Aligned_cols=82  Identities=13%  Similarity=0.179  Sum_probs=60.7

Q ss_pred             CCeeEEEee--CCeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe-CCEEEEEEEEEeccCccccCH---HHHH
Q 027547          116 APEIEIHEM--GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAEIRDSMFGFGA---AKIS  189 (222)
Q Consensus       116 ~p~VeV~~~--g~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-~~~~~~ti~~kv~~~~~~~~~---~~l~  189 (222)
                      .|.|.+...  .....|.|.| .+++|+|.+|..+|..+|++|+.|.+.+. ++.++-+|.+.-.++. ..+.   +.|.
T Consensus       688 ~p~V~i~~~~~~~~t~V~V~a-~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~-~~~~~~~~~I~  765 (884)
T PRK05007        688 KPLVLLSKQATRGGTEIFIWS-PDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGS-PLSQDRHQVIR  765 (884)
T ss_pred             CCeEEEEecCCCCeEEEEEEe-cCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCC-CCCHHHHHHHH
Confidence            455555543  3356777766 58999999999999999999999998866 5599888888766554 3333   3477


Q ss_pred             HHHHHHHhcc
Q 027547          190 ERLKGFVSGC  199 (222)
Q Consensus       190 ~aL~~~I~~~  199 (222)
                      ++|.+++...
T Consensus       766 ~~L~~aL~~~  775 (884)
T PRK05007        766 KALEQALTQS  775 (884)
T ss_pred             HHHHHHHcCC
Confidence            7777777654

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=95.72  E-value=0.11  Score=53.27  Aligned_cols=82  Identities=10%  Similarity=0.110  Sum_probs=61.0

Q ss_pred             CCeeEEEeeC--CeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE-eCCEEEEEEEEEeccCccccCHH---HHH
Q 027547          116 APEIEIHEMG--SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAEIRDSMFGFGAA---KIS  189 (222)
Q Consensus       116 ~p~VeV~~~g--~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~-~~~~~~~ti~~kv~~~~~~~~~~---~l~  189 (222)
                      .|.|.+....  ....|.|.+ .++||+|.+|..+|..+||+|++|.+.+ .++.++.+|.+.-.++. .++.+   .|.
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~-~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~-~~~~~~~~~l~  741 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYC-QDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGK-LLEFDRRRQLE  741 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEe-cCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCC-CCCHHHHHHHH
Confidence            4555554432  345777766 5899999999999999999999999876 79999999998765554 33432   566


Q ss_pred             HHHHHHHhcc
Q 027547          190 ERLKGFVSGC  199 (222)
Q Consensus       190 ~aL~~~I~~~  199 (222)
                      ++|.+++.+.
T Consensus       742 ~~L~~aL~~~  751 (854)
T PRK01759        742 QALTKALNTN  751 (854)
T ss_pred             HHHHHHHcCC
Confidence            7777777654

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

Probab=95.68  E-value=0.11  Score=34.96  Aligned_cols=56  Identities=14%  Similarity=0.163  Sum_probs=39.8

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe-----CCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV-----GNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-----~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .++||.|.+|+++|.+.|++|.+.+....     ++.....+++.+.+.   .....+.++|++
T Consensus         6 ~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~---~~l~~l~~~l~~   66 (73)
T cd04886           6 PDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGA---EHIEEIIAALRE   66 (73)
T ss_pred             CCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCH---HHHHHHHHHHHH
Confidence            58899999999999999999999987754     355666677666431   223455555443

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.

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

Probab=95.59  E-value=0.024  Score=49.90  Aligned_cols=58  Identities=21%  Similarity=0.363  Sum_probs=51.9

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~   81 (222)
                      -+|..-|..||+|-..+|..|+.||..+|......|.|.-+.|..|-.||--|-...+
T Consensus       173 ~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  173 HRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             hhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            3566788999999999999999999999999999999999999999999988876553

>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=95.58  E-value=0.12  Score=35.82  Aligned_cols=43  Identities=9%  Similarity=0.067  Sum_probs=36.9

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe-CCEEEEEEEEEecc
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAEIRD  178 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-~~~~~~ti~~kv~~  178 (222)
                      .+++|.|.+|+.+|.+.|..|.+++.... ++.....|.+++.+
T Consensus         7 ~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~   50 (74)
T cd04887           7 PNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPS   50 (74)
T ss_pred             CCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCC
Confidence            48899999999999999999999998876 46777778887765

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.

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=95.57  E-value=0.1  Score=53.20  Aligned_cols=82  Identities=13%  Similarity=0.092  Sum_probs=61.6

Q ss_pred             CCeeEEEe--eCCeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-EeCCEEEEEEEEEeccCccccC----HHHH
Q 027547          116 APEIEIHE--MGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEIRDSMFGFG----AAKI  188 (222)
Q Consensus       116 ~p~VeV~~--~g~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s-~~~~~~~~ti~~kv~~~~~~~~----~~~l  188 (222)
                      .|.|.+..  ......|.|.+ .++||+|.+|..+|..+|++|++|.++ +.++.++.+|.++-.++. ..+    .+.|
T Consensus       655 ~~~v~~~~~~~~~~t~i~V~~-~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~-~~~~~~~~~~i  732 (850)
T TIGR01693       655 GPLALIDGTRPSGGTEVFIYA-PDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGS-PPAAERVFQEL  732 (850)
T ss_pred             CCEEEEeccCCCCeEEEEEEe-CCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCC-CCCcHHHHHHH
Confidence            34555433  22345677766 589999999999999999999999999 779999999999876655 332    3357


Q ss_pred             HHHHHHHHhcc
Q 027547          189 SERLKGFVSGC  199 (222)
Q Consensus       189 ~~aL~~~I~~~  199 (222)
                      .++|.+++..-
T Consensus       733 ~~~L~~~L~~~  743 (850)
T TIGR01693       733 LQGLVDVLAGL  743 (850)
T ss_pred             HHHHHHHHcCC
Confidence            77887887664

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

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=95.52  E-value=0.1  Score=53.27  Aligned_cols=77  Identities=19%  Similarity=0.198  Sum_probs=55.4

Q ss_pred             CeeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          117 PEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       117 p~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      |.|.+....+  .-.|.|.+ .++||+|.+|.++|.++|++|.+|.+++.++++..+|.+....+. ..+. ...+.|++
T Consensus       767 ~~V~~d~~~s~~~t~~~v~~-~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~-~~~~-~~~~~l~~  843 (850)
T TIGR01693       767 PRVTILNTASRKATIMEVRA-LDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGL-KLTD-EEEQRLLE  843 (850)
T ss_pred             CeEEEccCCCCCeEEEEEEE-CCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCC-CCCH-HHHHHHHH
Confidence            4555554443  24555555 589999999999999999999999999999999988888765544 2332 33344444


Q ss_pred             HH
Q 027547          195 FV  196 (222)
Q Consensus       195 ~I  196 (222)
                      .+
T Consensus       844 ~L  845 (850)
T TIGR01693       844 VL  845 (850)
T ss_pred             HH
Confidence            44

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=95.40  E-value=0.017  Score=55.20  Aligned_cols=60  Identities=15%  Similarity=0.246  Sum_probs=47.8

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCC-CChhHHHHHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEE-LSLPDQVDEAINYIKMLETKLKE   82 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k-~si~~iL~~ai~YIk~Lq~~v~~   82 (222)
                      ..+|+.+|+.||-|-..||+.|..|..+.=...+.+| .++..||-.|+..|-.|+++|++
T Consensus       524 kERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  524 KERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             HHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            3578889999999999999999999887654433322 24556699999999999999976

>PRK04374 PII uridylyl-transferase; Provisional

Probab=95.26  E-value=0.14  Score=52.64  Aligned_cols=73  Identities=22%  Similarity=0.306  Sum_probs=56.8

Q ss_pred             CeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE-eCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcc
Q 027547          126 SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC  199 (222)
Q Consensus       126 ~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~-~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~  199 (222)
                      ...+|.|.| .+++|+|.++.-+|..+|++|+.|.+.+ .+|.++.+|.+.-.++........|.++|.+++.+-
T Consensus       689 ~~~~v~v~~-~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~~l~~~l~~~  762 (869)
T PRK04374        689 DALEVFVYS-PDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAAALRQVLAGD  762 (869)
T ss_pred             CeEEEEEEe-CCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHHHHHHHHcCC
Confidence            467888877 5899999999999999999999999986 688999999987544431122445777777777653

>PRK05092 PII uridylyl-transferase; Provisional

Probab=95.12  E-value=0.27  Score=50.77  Aligned_cols=82  Identities=15%  Similarity=0.145  Sum_probs=59.7

Q ss_pred             CCeeEEEee--CCeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE-eCCEEEEEEEEEeccCccccC---HHHHH
Q 027547          116 APEIEIHEM--GSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNTIFHVIHAEIRDSMFGFG---AAKIS  189 (222)
Q Consensus       116 ~p~VeV~~~--g~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~-~~~~~~~ti~~kv~~~~~~~~---~~~l~  189 (222)
                      .+.|.++..  .....|.|+| .+++|+|.+|..+|..+|++|+.|.+++ .++.++.+|.+.-.++....+   .+.|.
T Consensus       719 ~~~v~~~~~~~~~~t~v~I~~-~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~~~~l~  797 (931)
T PRK05092        719 PLATEVRPDPARGVTEVTVLA-ADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRRLARLA  797 (931)
T ss_pred             CcEEEEEecCCCCeEEEEEEe-CCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHHHHHHH
Confidence            355655543  2467888877 5899999999999999999999999886 688888888887655431112   44566


Q ss_pred             HHHHHHHhc
Q 027547          190 ERLKGFVSG  198 (222)
Q Consensus       190 ~aL~~~I~~  198 (222)
                      ++|.+++.+
T Consensus       798 ~~L~~~l~~  806 (931)
T PRK05092        798 KAIEDALSG  806 (931)
T ss_pred             HHHHHHHcC
Confidence            677666643

>PRK03059 PII uridylyl-transferase; Provisional

Probab=94.98  E-value=0.22  Score=51.07  Aligned_cols=71  Identities=13%  Similarity=0.145  Sum_probs=55.4

Q ss_pred             CeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-EeCCEEEEEEEEEeccCcccc---CHHHHHHHHHHHHhc
Q 027547          126 SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEIRDSMFGF---GAAKISERLKGFVSG  198 (222)
Q Consensus       126 ~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s-~~~~~~~~ti~~kv~~~~~~~---~~~~l~~aL~~~I~~  198 (222)
                      ...+|.|.| .++||+|.++.-+|..+||+|+.|.+. +.+|.++.+|.+.-.++. ..   -.+.|.++|.+++.+
T Consensus       677 ~~~~v~i~~-~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~~-~~~~~~~~~i~~~l~~~l~~  751 (856)
T PRK03059        677 EGLQVMVYT-PDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEED-VHYRDIINLVEHELAERLAE  751 (856)
T ss_pred             CeEEEEEEe-cCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCCC-CChHHHHHHHHHHHHHHHcC
Confidence            467888877 589999999999999999999999995 568899999998754433 11   244577777777755

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

Probab=94.84  E-value=0.18  Score=35.04  Aligned_cols=48  Identities=10%  Similarity=0.078  Sum_probs=36.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe-CCEEEEEEEEEecc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAEIRD  178 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-~~~~~~ti~~kv~~  178 (222)
                      +.+.+ .+++|.|.+|++.|.+++++|...+.+.. ++.....|.+.+.+
T Consensus         3 l~i~~-~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~   51 (76)
T cd04888           3 LSLLL-EHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTST   51 (76)
T ss_pred             EEEEe-cCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCc
Confidence            44444 47899999999999999999999987654 45566666666644

a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=94.79  E-value=0.24  Score=51.03  Aligned_cols=72  Identities=13%  Similarity=0.072  Sum_probs=55.2

Q ss_pred             CeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-EeCCEEEEEEEEEeccCcccc-C---HHHHHHHHHHHHhc
Q 027547          126 SNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEIRDSMFGF-G---AAKISERLKGFVSG  198 (222)
Q Consensus       126 ~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s-~~~~~~~~ti~~kv~~~~~~~-~---~~~l~~aL~~~I~~  198 (222)
                      ...+|.|.| .++||+|.++..+|..+|++|+.|.+. +.++.++-+|.+.-.++.... +   .+.|.++|.+++.+
T Consensus       703 ~~t~V~V~~-~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~~~~~~~~r~~~i~~~L~~~L~~  779 (895)
T PRK00275        703 GGTQIFIYA-PDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGEPIGDNPARIEQIREGLTEALRN  779 (895)
T ss_pred             CeEEEEEEe-CCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCCCccchHHHHHHHHHHHHHHHcC
Confidence            467888877 589999999999999999999999975 567889999998866655212 2   23466777777654

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

Probab=94.65  E-value=0.25  Score=34.76  Aligned_cols=66  Identities=17%  Similarity=0.124  Sum_probs=53.2

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      .|+|.| +++.|+-.++.+.+-+.||.|....+++.|..-+..+-+.-......+.=+.++++|..+
T Consensus         2 vitvnC-PDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv~~~~~~~~rW~lLK~RL~~~   67 (69)
T cd04894           2 VITINC-PDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVVPRPPSIKVRWDLLKNRLMSA   67 (69)
T ss_pred             EEEEeC-CCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEecCCCCCcccHHHHHHHHHhc
Confidence            367777 588999999999999999999999999999877777777655544456677888888654

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

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

Probab=94.57  E-value=0.41  Score=33.56  Aligned_cols=59  Identities=7%  Similarity=0.042  Sum_probs=40.7

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeCC-EEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGN-TIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~-~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .++||.|.+|++.|.++|+.+.+..+....+ ..-|.|.+.+...........+.+.|++
T Consensus         7 ~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~   66 (75)
T cd04880           7 KNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKR   66 (75)
T ss_pred             CCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999998886654 4556666666542111233444444444

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

>PRK04435 hypothetical protein; Provisional

Probab=94.49  E-value=0.27  Score=39.76  Aligned_cols=67  Identities=16%  Similarity=0.193  Sum_probs=47.8

Q ss_pred             eCCeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe-CCEEEEEEEEEeccCccccCHHHHHHHHH
Q 027547          124 MGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-GNTIFHVIHAEIRDSMFGFGAAKISERLK  193 (222)
Q Consensus       124 ~g~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-~~~~~~ti~~kv~~~~~~~~~~~l~~aL~  193 (222)
                      .|..+.+.+.+ .+++|.|.+|++.|.+.|++|...+.+.. ++.+..+|.+.+.+..  ...+++.++|+
T Consensus        66 ~~r~vtL~i~l-~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~~--~~L~~Li~~L~  133 (147)
T PRK04435         66 KGKIITLSLLL-EDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSME--GDIDELLEKLR  133 (147)
T ss_pred             CCcEEEEEEEE-ecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCChH--HHHHHHHHHHH
Confidence            34455666655 37899999999999999999999987653 6777778888775422  23445555444

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

Probab=94.22  E-value=0.25  Score=50.13  Aligned_cols=79  Identities=15%  Similarity=0.216  Sum_probs=58.1

Q ss_pred             CCeeEEEeeCC--eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHH
Q 027547          116 APEIEIHEMGS--NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLK  193 (222)
Q Consensus       116 ~p~VeV~~~g~--~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~  193 (222)
                      +|.|.+..+.+  .-.+.|.+ .++||+|..|-.+|.+++|++.+|.++++|.++.-+|.+....+. .+ ...+++.|.
T Consensus       778 ~p~v~i~~t~~~~~t~lEv~a-lDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~~-~l-~~~~~q~l~  854 (867)
T COG2844         778 PPRVTILPTASNDKTVLEVRA-LDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADGQ-AL-NAELRQSLL  854 (867)
T ss_pred             CCceeeccccCCCceEEEEEe-CCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEeccccc-cC-CHHHHHHHH
Confidence            35666654333  23455545 589999999999999999999999999999998888888766655 33 445555555


Q ss_pred             HHHh
Q 027547          194 GFVS  197 (222)
Q Consensus       194 ~~I~  197 (222)
                      +.+-
T Consensus       855 ~~ll  858 (867)
T COG2844         855 QRLL  858 (867)
T ss_pred             HHHH
Confidence            5443

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=93.93  E-value=0.52  Score=42.30  Aligned_cols=79  Identities=13%  Similarity=0.090  Sum_probs=60.5

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccccccC
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQL  207 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~~  207 (222)
                      +.|+|.| .++||+...|-+.|-++|++|...+..+....-+|++.+.+.... ..+.+.|+++|..+-...-..+.++-
T Consensus         8 ~vitv~G-~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~-~~~~~~L~~~L~~l~~~l~l~i~i~~   85 (286)
T PRK13011          8 FVLTLSC-PSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEE-GLDEDALRAGFAPIAARFGMQWELHD   85 (286)
T ss_pred             EEEEEEe-CCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCC-CCCHHHHHHHHHHHHHHhCcEEEEee
Confidence            4577777 589999999999999999999999998554444444666665433 46799999999998887766666664


Q ss_pred             C
Q 027547          208 P  208 (222)
Q Consensus       208 ~  208 (222)
                      |
T Consensus        86 ~   86 (286)
T PRK13011         86 P   86 (286)
T ss_pred             c
Confidence            4

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

Probab=93.87  E-value=0.28  Score=34.48  Aligned_cols=45  Identities=13%  Similarity=0.130  Sum_probs=34.4

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEecc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRD  178 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~  178 (222)
                      +.|.+. +++|+|.+|+.++.+.+..+.+.++... +.  ..+..++.+
T Consensus         3 l~I~~~-dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~--i~l~i~v~~   47 (74)
T cd04877           3 LEITCE-DRLGITQEVLDLLVEHNIDLRGIEIDPK-GR--IYLNFPTIE   47 (74)
T ss_pred             EEEEEE-ccchHHHHHHHHHHHCCCceEEEEEecC-Ce--EEEEeEecC
Confidence            555563 7899999999999999999999998765 44  334555543

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

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

Probab=93.73  E-value=0.74  Score=32.75  Aligned_cols=56  Identities=11%  Similarity=0.192  Sum_probs=41.3

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC-CEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .+++|.|.++++.|.++|+.+.+..+.... +...|.|.+.....   .+...+.++|..
T Consensus         9 ~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~---~~~~~~~~~l~~   65 (80)
T cd04905           9 PNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGH---IEDPNVAEALEE   65 (80)
T ss_pred             CCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECC---CCCHHHHHHHHH
Confidence            478999999999999999999999877653 45667777776642   234555555543

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

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

Probab=93.58  E-value=0.61  Score=30.04  Aligned_cols=43  Identities=14%  Similarity=0.251  Sum_probs=33.8

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC-CEEEEEEEEEecc
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAEIRD  178 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-~~~~~ti~~kv~~  178 (222)
                      .++++.+.++++.|.++++++.+......+ +...+.+..++.+
T Consensus         6 ~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~   49 (71)
T cd04876           6 IDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRD   49 (71)
T ss_pred             eccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECC
Confidence            478999999999999999999999887655 5555556665543

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

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=92.95  E-value=0.94  Score=40.60  Aligned_cols=76  Identities=16%  Similarity=0.170  Sum_probs=56.6

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE--eCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV--VGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEM  205 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~--~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~  205 (222)
                      +.|++.| .++||+...|-++|-++|++|...+.++  .++.+...+.+.+.. . ..+.++|.++|.++-...-..+.+
T Consensus         7 ~vitv~G-~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~-~-~~~~~~L~~~L~~l~~~l~l~i~l   83 (286)
T PRK06027          7 YVLTLSC-PDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDG-L-IFNLETLRADFAALAEEFEMDWRL   83 (286)
T ss_pred             EEEEEEC-CCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCC-C-CCCHHHHHHHHHHHHHHhCCEEEE
Confidence            4566666 5899999999999999999999999998  777544444444422 1 356889999998887776655544


Q ss_pred             c
Q 027547          206 Q  206 (222)
Q Consensus       206 ~  206 (222)
                      +
T Consensus        84 ~   84 (286)
T PRK06027         84 L   84 (286)
T ss_pred             c
Confidence            4

>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=92.92  E-value=0.55  Score=32.00  Aligned_cols=48  Identities=23%  Similarity=0.168  Sum_probs=36.2

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe-C-CEEEEEEEEEec
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-G-NTIFHVIHAEIR  177 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-~-~~~~~ti~~kv~  177 (222)
                      .+.|.+ .+++|.|.+++..|.+.++.+.+.+.... + +.....+...+.
T Consensus         2 yl~i~~-~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~~~   51 (79)
T cd04881           2 YLRLTV-KDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTHET   51 (79)
T ss_pred             EEEEEe-CCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEccC
Confidence            355655 37899999999999999999999987654 3 556566666544

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.

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

Probab=92.91  E-value=0.94  Score=30.21  Aligned_cols=41  Identities=10%  Similarity=0.037  Sum_probs=33.4

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEe
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEI  176 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv  176 (222)
                      .+++|.|.+++..|.++++.+.+.+....  ++...+.|.+.+
T Consensus         8 ~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~   50 (72)
T cd04878           8 ENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEG   50 (72)
T ss_pred             cCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEEC
Confidence            47899999999999999999999987764  455666666664

ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of

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

Probab=92.73  E-value=1.1  Score=31.11  Aligned_cols=41  Identities=15%  Similarity=0.032  Sum_probs=31.1

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe---CCEEEEEEEEEe
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV---GNTIFHVIHAEI  176 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~---~~~~~~ti~~kv  176 (222)
                      .++||.|.++++.|.++|+.|++......   .+.-...+++..
T Consensus         7 ~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~   50 (72)
T cd04884           7 EDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTP   50 (72)
T ss_pred             cCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEE
Confidence            58999999999999999999999987754   233334444444

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.

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=92.69  E-value=0.78  Score=41.08  Aligned_cols=68  Identities=10%  Similarity=0.251  Sum_probs=50.9

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHH-HHhccc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKG-FVSGCA  200 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~-~I~~~~  200 (222)
                      |++.| ++++|+...|-..|-++|.+|+.++....+  ++++..+.+.+..  ...+.++++++|.. +-....
T Consensus         3 itv~g-~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~~~~--~~~~~~~l~~~l~~~~~~~~~   73 (280)
T TIGR00655         3 LLVSC-PDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQLEG--FRLEESSLLAAFKSALAEKFE   73 (280)
T ss_pred             EEEEC-CCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEEeCC--CCCCHHHHHHHHHHHHHHHhC
Confidence            56666 589999999999999999999999988764  5555444444432  23678899999988 555443

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

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

Probab=92.63  E-value=0.89  Score=30.26  Aligned_cols=51  Identities=24%  Similarity=0.231  Sum_probs=36.1

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .++||.|.+++..|.++|+.|.+...+...  +...+.++++  .      .+++.+.|++
T Consensus         7 ~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve--~------~~~~~~~L~~   59 (65)
T cd04882           7 PDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE--D------IEKAIEVLQE   59 (65)
T ss_pred             CCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC--C------HHHHHHHHHH
Confidence            488999999999999999999888765443  4555544443  1      4455555554

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.

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

Probab=92.39  E-value=1.5  Score=29.36  Aligned_cols=43  Identities=7%  Similarity=0.133  Sum_probs=32.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC-CEEEEEEE
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIH  173 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-~~~~~ti~  173 (222)
                      +.+.+ .+++|.|.+++..|.++++.+.+.+....+ +.....+.
T Consensus         3 l~i~~-~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~   46 (72)
T cd04874           3 LSIIA-EDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYME   46 (72)
T ss_pred             EEEEe-CCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEE
Confidence            44545 488999999999999999999998877653 44443333

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.

>PRK08577 hypothetical protein; Provisional

Probab=92.21  E-value=1.8  Score=34.16  Aligned_cols=65  Identities=22%  Similarity=0.307  Sum_probs=45.8

Q ss_pred             eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          127 NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       127 ~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .+.+.+.+ .+++|.|.++++.|.+++..+.+.+..+.  ++.+...+.+.+.+..  ...+++.++|++
T Consensus        56 ~~~I~V~~-~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~~~--~~l~~l~~~L~~  122 (136)
T PRK08577         56 LVEIELVV-EDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSKSD--IDLEELEEELKK  122 (136)
T ss_pred             EEEEEEEE-cCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCCch--hhHHHHHHHHHc
Confidence            45666666 48899999999999999999999887765  3455556677776531  234555555543

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

Probab=92.20  E-value=0.13  Score=38.59  Aligned_cols=79  Identities=18%  Similarity=0.222  Sum_probs=63.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccccccCCC
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLPE  209 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~~~~  209 (222)
                      |+| .+.+|+|....|-.+|-++|+++++.+-+..++++...+.+....  ...+...+++.|......--..+-||.-+
T Consensus         6 ITV-~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV~~~~--~~~d~~~lr~~l~~~~~~lgv~V~vq~ed   82 (90)
T COG3830           6 ITV-IGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVDISK--EVVDFAALRDELAAEGKKLGVDVRVQRED   82 (90)
T ss_pred             EEE-EcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeEEcCCh--HhccHHHHHHHHHHHHHhcCcEEEEeeHH
Confidence            444 457899999999999999999999999998888776666665544  34789999999999998888777777444


Q ss_pred             CC
Q 027547          210 LW  211 (222)
Q Consensus       210 ~~  211 (222)
                      +.
T Consensus        83 ~f   84 (90)
T COG3830          83 IF   84 (90)
T ss_pred             HH
Confidence            43

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

Probab=92.06  E-value=1.2  Score=27.00  Aligned_cols=34  Identities=18%  Similarity=0.308  Sum_probs=28.1

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC
Q 027547          131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG  165 (222)
Q Consensus       131 ~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~  165 (222)
                      .+.+ .++++.+.+++..|...++.+..+.....+
T Consensus         2 ~i~~-~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           2 TVSG-PDRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             EEEe-cCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            3444 367899999999999999999999987654

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

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

Probab=91.78  E-value=2.4  Score=28.87  Aligned_cols=51  Identities=18%  Similarity=0.176  Sum_probs=36.6

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .++||.|.+|++.|.+.|+.|.+.-....++.  ..++....      +.+.+.+.|++
T Consensus         9 ~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~--~~~rl~~~------~~~~~~~~L~~   59 (66)
T cd04908           9 ENKPGRLAAVTEILSEAGINIRALSIADTSEF--GILRLIVS------DPDKAKEALKE   59 (66)
T ss_pred             cCCCChHHHHHHHHHHCCCCEEEEEEEecCCC--CEEEEEEC------CHHHHHHHHHH
Confidence            48899999999999999999999987766554  44444442      24455555543

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.

>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase)

Probab=91.46  E-value=1.3  Score=30.56  Aligned_cols=55  Identities=15%  Similarity=0.215  Sum_probs=38.6

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC-CEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      +++||.|.++++.|.+ |.+|...+....+ +.....+.+++.+.   ....++.++|.+
T Consensus         6 pdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~~~~v~v~ie~~~~---~~~~~i~~~L~~   61 (68)
T cd04885           6 PERPGALKKFLELLGP-PRNITEFHYRNQGGDEARVLVGIQVPDR---EDLAELKERLEA   61 (68)
T ss_pred             CCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCCceEEEEEEEeCCH---HHHHHHHHHHHH
Confidence            5799999999999999 9999999887543 33444455555542   245566666654

This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=91.37  E-value=2.9  Score=28.47  Aligned_cols=59  Identities=14%  Similarity=0.178  Sum_probs=41.2

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .+.+.. .++||.|.++++.|.++|+.+.+......  ++...+.|++...      +.+++.+.|++
T Consensus         3 ~~~v~~-~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~------~~~~~~~~L~~   63 (72)
T cd04883           3 QIEVRV-PDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTM------NPRPIIEDLRR   63 (72)
T ss_pred             EEEEEE-CCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecC------CHHHHHHHHHH
Confidence            344444 47899999999999999999998865533  3566666776542      24466666654

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.

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

Probab=91.30  E-value=1.9  Score=28.55  Aligned_cols=53  Identities=19%  Similarity=0.176  Sum_probs=39.0

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .+++|.+.+++..|.+.++.|.+..+....  +...+.+.+  .+ .   ....+.+.|++
T Consensus         7 ~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v--~~-~---~~~~l~~~l~~   61 (71)
T cd04879           7 KDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV--DS-P---VPEEVLEELKA   61 (71)
T ss_pred             cCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc--CC-C---CCHHHHHHHHc
Confidence            478999999999999999999999987654  566666655  22 1   34556665554

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

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=90.15  E-value=1.8  Score=38.99  Aligned_cols=73  Identities=10%  Similarity=0.067  Sum_probs=52.9

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE--EeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFS--VVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASE  202 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s--~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~  202 (222)
                      +-|+++| ++++|+...|-+.|-++|++|+.++..  +..+.++..+........ ..+.+.++++|..+-.....+
T Consensus        10 ~iitv~G-~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~~~~-~~~~~~l~~~l~~l~~~l~l~   84 (289)
T PRK13010         10 YVLTLAC-PSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQSAE-AASVDTFRQEFQPVAEKFDMQ   84 (289)
T ss_pred             EEEEEEC-CCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcCCCC-CCCHHHHHHHHHHHHHHhCCe
Confidence            3477777 589999999999999999999999986  333444444433322222 568899999999887765433

>PLN02705 beta-amylase

Probab=89.96  E-value=0.45  Score=46.87  Aligned_cols=28  Identities=21%  Similarity=0.286  Sum_probs=23.7

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhc
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSL   50 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsL   50 (222)
                      ...|...+..||+||.--...|.-||.+
T Consensus        82 ~~e~e~~~~rer~rrai~~ki~aglr~~  109 (681)
T PLN02705         82 EKEKERTKLRERHRRAITSRMLAGLRQY  109 (681)
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence            3567888899999999988889888875

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

Probab=89.85  E-value=0.82  Score=31.63  Aligned_cols=56  Identities=9%  Similarity=0.096  Sum_probs=39.9

Q ss_pred             CCCChHHHHHHHHHhCCceEEEEEEEE--eCCEEEEEEEEEeccCccccCHHHHHHHHHHHH
Q 027547          137 DDQFIFYEVIRILHQDGAEILNAKFSV--VGNTIFHVIHAEIRDSMFGFGAAKISERLKGFV  196 (222)
Q Consensus       137 ~~~~~L~~vl~~Le~lgL~V~~a~~s~--~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I  196 (222)
                      ++||.|.+|+..+..-|+.|-+.++..  .++..-++|.+...+    ...+.+..-|.+++
T Consensus         1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~~----~~i~~l~~Ql~Kli   58 (63)
T PF13710_consen    1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGDD----REIEQLVKQLEKLI   58 (63)
T ss_dssp             SSTTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES-C----CHHHHHHHHHHCST
T ss_pred             CCcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeCc----hhHHHHHHHHhccC
Confidence            468999999999999999999999997  455666666665322    34566666665544

>COG4492 PheB ACT domain-containing protein [General function prediction only]

Probab=89.64  E-value=2.1  Score=34.55  Aligned_cols=58  Identities=14%  Similarity=0.190  Sum_probs=48.6

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEE-EeCCEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s-~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      .++-|.|+++|+++-+.++.|++.+-+ ..++++-.+|.......  ..+++.+.++|+++
T Consensus        80 edr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtlsi~~ssm--~~~V~~ii~kl~k~  138 (150)
T COG4492          80 EDRVGILSDVLDVIAREEINVLTIHQTIPLQGRANVTLSIDTSSM--EKDVDKIIEKLRKV  138 (150)
T ss_pred             hhhhhhHHHHHHHHHHhCCcEEEEecccccCceeeEEEEEEchhh--hhhHHHHHHHHhcc
Confidence            378899999999999999999999977 67999888888877643  46788888888764

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

Probab=89.61  E-value=3.2  Score=28.21  Aligned_cols=34  Identities=24%  Similarity=0.308  Sum_probs=27.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV  164 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~  164 (222)
                      +.+.+ .++||.|.++++.|.++|+.+.+......
T Consensus         4 ~~v~~-~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           4 LYVDV-PDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEc-CCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            44444 58899999999999999999998876654

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

>PRK07334 threonine dehydratase; Provisional

Probab=89.30  E-value=2.3  Score=39.63  Aligned_cols=63  Identities=14%  Similarity=0.168  Sum_probs=46.4

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe-----CCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV-----GNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~-----~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      +.+.|.+ .+++|+|.+|+.+|.+.++.|.++++...     ++.....|..++.+..   .-..|..+|++
T Consensus       327 v~l~I~~-~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~---~L~~vi~~Lr~  394 (403)
T PRK07334        327 ARLRVDI-RDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAA---HLQEVIAALRA  394 (403)
T ss_pred             EEEEEEe-CCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHH---HHHHHHHHHHH
Confidence            5566655 48999999999999999999999998764     5677777777776522   33455555554

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

Probab=88.94  E-value=3.6  Score=27.21  Aligned_cols=53  Identities=19%  Similarity=0.218  Sum_probs=36.5

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .+++|.|.+++..|.++++.+.+......  ++.....|.  +.+.    ....+.++|++
T Consensus         7 ~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~--v~~~----~~~~~i~~l~~   61 (71)
T cd04903           7 KDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIE--VDQP----IDEEVIEEIKK   61 (71)
T ss_pred             CCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEE--eCCC----CCHHHHHHHHc
Confidence            48899999999999999999999887652  355544443  3331    34455555543

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.

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

Probab=88.64  E-value=2.8  Score=27.42  Aligned_cols=40  Identities=15%  Similarity=0.042  Sum_probs=33.1

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC-CEEEEEEEEE
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAE  175 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-~~~~~ti~~k  175 (222)
                      .++||.|.+++..|-+.|+.|.+......+ +..+..|...
T Consensus         6 ~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~   46 (56)
T cd04889           6 ENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFS   46 (56)
T ss_pred             CCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEEC
Confidence            478999999999999999999888877654 6677666654

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

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

Probab=88.18  E-value=0.46  Score=32.24  Aligned_cols=54  Identities=15%  Similarity=0.172  Sum_probs=38.7

Q ss_pred             cCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          135 GVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       135 ~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      ..+++|+|.+++..|.+.++.+...+....++..+..+...+.      ...++.++|++
T Consensus         6 ~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~~~------~l~~li~~l~~   59 (69)
T cd04901           6 HKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDIDSE------VSEELLEALRA   59 (69)
T ss_pred             ecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcCCC------CCHHHHHHHHc
Confidence            3588999999999999999999887665555666666655443      34455555553

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

>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional

Probab=88.02  E-value=3.5  Score=29.83  Aligned_cols=57  Identities=12%  Similarity=0.156  Sum_probs=42.5

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .++||.|.+++..+..-|+.|.+.++...  ++..-.+|.+.  +   ....+.+..-|.+++.
T Consensus        11 ~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~--~---~~~i~ql~kQL~KL~d   69 (76)
T PRK11152         11 RFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA--S---ERPIDLLSSQLNKLVD   69 (76)
T ss_pred             ECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC--C---CchHHHHHHHHhcCcC
Confidence            47899999999999999999999999874  44455555552  2   2456777776766554

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

Probab=87.99  E-value=2.2  Score=28.99  Aligned_cols=53  Identities=19%  Similarity=0.222  Sum_probs=39.2

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEE--eCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSV--VGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~--~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .+++|.+.++.+.|.++|+.+.+.....  .++..++.|.++.   .   .+..+.++|++
T Consensus         7 ~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~---~---~~~~~~~~l~~   61 (73)
T cd04902           7 TDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDE---P---VPDEVLEELRA   61 (73)
T ss_pred             CCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCC---C---CCHHHHHHHHc
Confidence            5889999999999999999998887665  3567777776643   1   23456666554

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

>PRK00227 glnD PII uridylyl-transferase; Provisional

Probab=87.69  E-value=3.7  Score=41.34  Aligned_cols=72  Identities=13%  Similarity=0.058  Sum_probs=59.8

Q ss_pred             eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          127 NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       127 ~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      +-.|+|....+++|.|.++..+|--+++.|.+|++.+ ++.....|.+.-.-+. ..++..+.+.++.++...-
T Consensus       546 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~a~~~~-~~~~~~~~~v~~~~~~-~~~~~~~~~~~~~~~~~~~  617 (693)
T PRK00227        546 DGFFTVIWHGDYPRELVRVLALIAAKGWNILSARMVA-NGPWSAEFDVRANGPQ-DFDPQEFLQAYKSGVYSEL  617 (693)
T ss_pred             CCeEEEEecCCcccHHHHHHHHHHhcCceeeEeEEec-CCceEEEEEEecCCCC-CCChHHHHHHHHHhhcCCC
Confidence            3567776645889999999999999999999999999 8887777777765555 6789999999998887553

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

Probab=87.48  E-value=5.1  Score=28.20  Aligned_cols=55  Identities=2%  Similarity=0.041  Sum_probs=39.8

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeCC-EEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGN-TIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~-~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      .++||.|.++|..+...|+.+.+..+-...+ .--|.|.+.+..     ....+.++|.++
T Consensus         8 ~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~-----~~~~~~~~l~~L   63 (74)
T cd04904           8 KEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEV-----DRGDLDQLISSL   63 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEc-----ChHHHHHHHHHH
Confidence            4689999999999999999999999987654 344666666553     223455555444

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

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=86.81  E-value=4.9  Score=34.01  Aligned_cols=77  Identities=12%  Similarity=0.123  Sum_probs=58.7

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC----CEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG----NTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEG  203 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~----~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~  203 (222)
                      +.|.+ .+.++||++.+|-+.|-++|++|.+.+..+.+    +.-+|.+++++.-+. ..+.+.++++|..+-...-..+
T Consensus        96 ~~v~v-~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~lP~-~~~~~~L~~~l~~l~~eL~vd~  173 (190)
T PRK11589         96 VWVQV-EVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPA-SQDAANIEQAFKALCTELNAQG  173 (190)
T ss_pred             EEEEE-EECCCCCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEEcCC-CCCHHHHHHHHHHHHHHhCceE
Confidence            44555 34689999999999999999999999887664    456777777776655 5678899999988877665555


Q ss_pred             ccc
Q 027547          204 EMQ  206 (222)
Q Consensus       204 ~~~  206 (222)
                      .+.
T Consensus       174 ~l~  176 (190)
T PRK11589        174 SIN  176 (190)
T ss_pred             EEE
Confidence            443

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

Probab=86.80  E-value=5.9  Score=29.44  Aligned_cols=43  Identities=5%  Similarity=0.013  Sum_probs=34.0

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeCC-EEEEEEEEEecc
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGN-TIFHVIHAEIRD  178 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~-~~~~ti~~kv~~  178 (222)
                      .+++|.|.++|..|...|+.+.+..+-..-+ .--|.|.+.+..
T Consensus        22 ~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg   65 (90)
T cd04931          22 KEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDK   65 (90)
T ss_pred             CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEc
Confidence            4689999999999999999999999987543 344666666543

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.

>TIGR00119 acolac_sm acetolactate synthase, small subunit

Probab=86.67  E-value=3.3  Score=34.02  Aligned_cols=58  Identities=12%  Similarity=0.084  Sum_probs=44.2

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .++||.|.+|...|...|+.+.+..+...+  +....+|++...    ....+.+..-|.+++.
T Consensus         9 en~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~d----~~~i~qi~kQl~Kli~   68 (157)
T TIGR00119         9 ENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVGD----DKVLEQITKQLNKLVD   68 (157)
T ss_pred             cCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEECC----HHHHHHHHHHHhcCcc
Confidence            488999999999999999999999988665  456677777541    2346666777766665

acetohydroxyacid synthase is a synonym.

>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed

Probab=85.61  E-value=4.3  Score=33.52  Aligned_cols=58  Identities=10%  Similarity=0.109  Sum_probs=43.7

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .++||.|.+|...|...|+.|.+..+...+  +....+|++...+    ...+.+..-|.+++.
T Consensus        10 eN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~----~~i~qi~kQl~KLid   69 (161)
T PRK11895         10 ENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDE----QVIEQITKQLNKLID   69 (161)
T ss_pred             cCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCH----HHHHHHHHHHhcccc
Confidence            488999999999999999999999988654  5566677665422    346666666666655

>PRK06737 acetolactate synthase 1 regulatory subunit; Validated

Probab=84.29  E-value=4.4  Score=29.34  Aligned_cols=62  Identities=15%  Similarity=0.140  Sum_probs=41.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHH
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFV  196 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I  196 (222)
                      +.+.. .++||.|.++..++..-|+.|-+.++....  +..-.+|.+...+    ...+.+..-|.+++
T Consensus         5 isi~v-~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~~~sriti~~~~~~----~~i~qi~kQL~KLi   68 (76)
T PRK06737          5 FSLVI-HNDPSVLLRISGIFARRGYYISSLNLNERDTSGVSEMKLTAVCTE----NEATLLVSQLKKLI   68 (76)
T ss_pred             EEEEE-ecCCCHHHHHHHHHhccCcceEEEEecccCCCCeeEEEEEEECCH----HHHHHHHHHHhCCc
Confidence            34444 478999999999999999999999988544  4556666664222    23445555554443

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

Probab=84.04  E-value=6.6  Score=40.26  Aligned_cols=77  Identities=14%  Similarity=0.135  Sum_probs=57.0

Q ss_pred             EEeeCCeeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-EeCCEEEEEEEEEeccCccccCHH---HHHHHHHHHH
Q 027547          121 IHEMGSNLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFS-VVGNTIFHVIHAEIRDSMFGFGAA---KISERLKGFV  196 (222)
Q Consensus       121 V~~~g~~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s-~~~~~~~~ti~~kv~~~~~~~~~~---~l~~aL~~~I  196 (222)
                      ++....+.+|.|.| +++|.+|..+..++...|++|+.|++. +.+|.++-||.+...++. .++.+   .+...|.+++
T Consensus       678 ~r~~~~~teV~V~a-~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~~~g~-~~~~dr~~~~~~~l~~~l  755 (867)
T COG2844         678 VRPHSGGTEVFVYA-PDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLEPDGF-PVEEDRRAALRGELIEAL  755 (867)
T ss_pred             ecccCCceEEEEEc-CCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEecCCCC-ccchhHHHHHHHHHHHHH
Confidence            44444678899988 589999999999999999999999987 468889999887755544 33433   3344555555


Q ss_pred             hcc
Q 027547          197 SGC  199 (222)
Q Consensus       197 ~~~  199 (222)
                      .+.
T Consensus       756 ~s~  758 (867)
T COG2844         756 LSG  758 (867)
T ss_pred             hcC
Confidence            544

>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=82.75  E-value=13  Score=26.37  Aligned_cols=55  Identities=5%  Similarity=0.085  Sum_probs=40.0

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeC-CEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVG-NTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      .+++|.|.++|..++..|+.+.+..+-... ..--|.|.+.+...     .+.++++|.++
T Consensus         8 ~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e~~-----~~~i~~~l~~l   63 (74)
T cd04929           8 KNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCECD-----QRRLDELVQLL   63 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcC-----HHHHHHHHHHH
Confidence            477999999999999999999999998653 33446666665432     23566666544

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.

>CHL00100 ilvH acetohydroxyacid synthase small subunit

Probab=82.60  E-value=7.6  Score=32.49  Aligned_cols=66  Identities=8%  Similarity=0.042  Sum_probs=47.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      +.+.. .++||.|.+|...|-..|++|.+.++...  .+..-.+|.+.  ...  ...+.|.+.|.+++.-..
T Consensus         5 isvlv-~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~~sr~TIvv~--~~~--~~ieqL~kQL~KLidVl~   72 (174)
T CHL00100          5 LSVLV-EDESGVLTRIAGLFARRGFNIESLAVGPAEQKGISRITMVVP--GDD--RTIEQLTKQLYKLVNILK   72 (174)
T ss_pred             EEEEE-eCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCCccEEEEEEE--CCH--HHHHHHHHHHHHHhHhhE
Confidence            34433 48999999999999999999999999863  34444455543  322  227888888988887654

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=81.68  E-value=2.2  Score=35.15  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHH
Q 027547           30 KTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLE   77 (222)
Q Consensus        30 ~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq   77 (222)
                      -..||.|.+++++.|.-|++|+|..+...|.-+ ..|.-+..||..|.
T Consensus        27 ~~~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~-ktlr~~~~~~~~~d   73 (173)
T KOG4447|consen   27 QRKERGRKRRLSDASTLLGKLEPGSPADGKRGK-KTLRIGTDSIQSLD   73 (173)
T ss_pred             hHHHHhHHhhhhhhhhhccccCCCCCCcccccc-cccccCCCchhhHH
Confidence            345999999999999999999998764333222 22566666666553

>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional

Probab=80.79  E-value=6.5  Score=29.13  Aligned_cols=64  Identities=13%  Similarity=0.083  Sum_probs=44.0

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      +.+.. .++||.|.++...|-..|+.|.+.+++...  +..-.+|.+.+.+   ....+.+..-|.+.+.
T Consensus         5 isvlV-eN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d---~~~ieqI~kQL~Klid   70 (84)
T PRK13562          5 LKLQV-ADQVSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQD---DTSLHILIKKLKQQIN   70 (84)
T ss_pred             EEEEE-ECCCCHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCC---HHHHHHHHHHHhCCcc
Confidence            34444 378999999999999999999999988654  4566667665322   1234566666665554

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=80.25  E-value=1.6  Score=42.61  Aligned_cols=39  Identities=28%  Similarity=0.526  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCC----CCCCCCChhHHHHHHHHHHH
Q 027547           33 EKNRRDQMKNLYSTLKSLLPNQ----PSKEELSLPDQVDEAINYIK   74 (222)
Q Consensus        33 ER~RR~~mn~~~~~LrsLlP~~----~~~~k~si~~iL~~ai~YIk   74 (222)
                      -++-|+++|.-++.|.+|||..    +|.||.|+   |.-++.|++
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSV---LRLSVSyLr   75 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSV---LRLSVSYLR   75 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhh---hhhhHHHHH
Confidence            4556899999999999999976    46789998   999999974

---

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	222
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	7e-08
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	4e-07
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-06
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	2e-06
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-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 = 47.7 bits (114), Expect = 7e-08
 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 = 45.6 bits (108), Expect = 4e-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 = 43.9 bits (104), Expect = 2e-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 = 43.5 bits (103), Expect = 2e-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 = 40.8 bits (96), Expect = 2e-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	222
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.66
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.62
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.62
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.6
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.6
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.54
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.53
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.47
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.47
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.46
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.42
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.37
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.32
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.05
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.75
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.67
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.57
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.31
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	97.5
1u8s_A	192	Glycine cleavage system transcriptional repressor,	95.95
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	95.7
1u8s_A	192	Glycine cleavage system transcriptional repressor,	95.64
2nyi_A	195	Unknown protein; protein structure initiative, PSI	95.35
2nyi_A	195	Unknown protein; protein structure initiative, PSI	95.3
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	92.58
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	90.57
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	89.9
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	89.81
2f1f_A	164	Acetolactate synthase isozyme III small subunit; f	89.3
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	88.29
2fgc_A	193	Acetolactate synthase, small subunit; regulatory s	87.67
2pc6_A	165	Probable acetolactate synthase isozyme III (small;	87.41
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	86.87
3nrb_A	287	Formyltetrahydrofolate deformylase; N-terminal ACT	85.32
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	84.31

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

Probab=99.66  E-value=4e-16  Score=113.54  Aligned_cols=68  Identities=25%  Similarity=0.331  Sum_probs=62.8

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      +|..||..||+||..||++|..|+++||......|.|...||..|++||++|+++.+.|..+++.|..
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            37899999999999999999999999999887888899999999999999999999999998877654

>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=99.62  E-value=5.1e-16  Score=114.87  Aligned_cols=70  Identities=16%  Similarity=0.307  Sum_probs=61.8

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027547           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQ   91 (222)
Q Consensus        22 ~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~   91 (222)
                      +..+|..||..||+||..||+.|..|+++||......|.|++.||..||+||+.|+++.+.+..+++.|.
T Consensus         3 d~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~   72 (88)
T 1nkp_A            3 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4467899999999999999999999999999987667888888899999999999999988877665544

>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=99.62  E-value=5.7e-16  Score=113.14  Aligned_cols=67  Identities=24%  Similarity=0.370  Sum_probs=59.0

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      .+|..|+.+||+||.+||+.|..|++|||...  .|.++++||.+||+||+.|+.+++.|+.+.+.|..
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 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999862  34455666999999999999999999999887765

>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=99.60  E-value=1.7e-15  Score=110.00  Aligned_cols=70  Identities=21%  Similarity=0.448  Sum_probs=62.8

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        22 ~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      ...+|..|+..||+||..||+.|..|+++||.... .|.|+++||..||+||+.|++++++|+.+++.|..
T Consensus         9 ~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~-~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~   78 (80)
T 1hlo_A            9 DADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQG-EKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTT-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             hHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34688999999999999999999999999998653 46888888999999999999999999999987753

>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=99.60  E-value=3e-15  Score=109.34  Aligned_cols=67  Identities=22%  Similarity=0.456  Sum_probs=59.7

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      +|..||..||+||..||+.|..|+++||... ..|.|+++||..||+||+.|+++++.|+.+++.|..
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            6889999999999999999999999999864 356788888999999999999999999988877654

>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=99.54  E-value=1.4e-15  Score=105.82  Aligned_cols=56  Identities=25%  Similarity=0.344  Sum_probs=49.5

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCC----CCCCChhHHHHHHHHHHHHHHHHH
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPS----KEELSLPDQVDEAINYIKMLETKL   80 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~----~~k~si~~iL~~ai~YIk~Lq~~v   80 (222)
                      +|.+|+.+||+||.+||..|..|++|||...+    ..|.|+++||+.||+||++||+++
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    347777888999999999999765

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

Probab=99.53  E-value=2.2e-15  Score=108.56  Aligned_cols=62  Identities=15%  Similarity=0.275  Sum_probs=50.6

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC-ChhHHHHHHHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEEL-SLPDQVDEAINYIKMLETKLKECK   84 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~-si~~iL~~ai~YIk~Lq~~v~~L~   84 (222)
                      ..+|..||..||+||..||+.|..||.+||...+.+|. |+.+||..||+||+.||+++++++
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999965455666 788889999999999999998765

>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=99.47  E-value=1.2e-14  Score=101.42  Aligned_cols=58  Identities=21%  Similarity=0.392  Sum_probs=48.8

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC---CCCChhHHHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK---EELSLPDQVDEAINYIKMLETKL   80 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~---~k~si~~iL~~ai~YIk~Lq~~v   80 (222)
                      ..++..|+.+||+||.+||+.|..|++|||.....   .|.++++||..||+||++||++.
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999987632   24455555999999999999764

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

Probab=99.47  E-value=8.5e-14  Score=108.14  Aligned_cols=65  Identities=18%  Similarity=0.323  Sum_probs=52.1

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCC-CCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSK-EELSLPDQVDEAINYIKMLETKLKECKKRK   87 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~-~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~   87 (222)
                      ..++..|+.+||+||.+||+.|..|++|||...+. .|.++++||..||+||+.||++++.|+...
T Consensus        25 ~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           25 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999988653 477888889999999999999999998753

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

Probab=99.46  E-value=1.1e-13  Score=95.27  Aligned_cols=58  Identities=22%  Similarity=0.357  Sum_probs=54.1

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~   81 (222)
                      ++|..||..||+|+..||+.|+.||.+||......|.|+.+||..||+||..|++.++
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            4688999999999999999999999999998888899999999999999999998753

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

Probab=99.42  E-value=2.8e-13  Score=96.22  Aligned_cols=61  Identities=21%  Similarity=0.397  Sum_probs=51.1

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 027547           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECK   84 (222)
Q Consensus        22 ~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~   84 (222)
                      +..+|.+|+.+||+||.+||+.|..|++|||...  .|.++++||..||+||+.||+.+.=|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~--~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNA--RKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCC--SCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCC--CCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            4568999999999999999999999999999643  244445559999999999999886554

>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=99.37  E-value=4.7e-13  Score=94.37  Aligned_cols=58  Identities=22%  Similarity=0.366  Sum_probs=52.6

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHH
Q 027547           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKL   80 (222)
Q Consensus        22 ~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v   80 (222)
                      ...+|..||..||+|+..||+.|..||.+||..+ ..|.|+.+||..||+||..|++.+
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~-~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCT-TSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3468889999999999999999999999999765 569999999999999999999765

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

Probab=99.32  E-value=3.8e-13  Score=96.07  Aligned_cols=56  Identities=27%  Similarity=0.371  Sum_probs=46.0

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCCChhHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQP-SKEELSLPDQVDEAINYIKMLET   78 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~-~~~k~si~~iL~~ai~YIk~Lq~   78 (222)
                      ..++..|+.+||+||++||+.|..|++|||... ...|.++++||..||+||+.|+.
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            457899999999999999999999999999752 12344445559999999999873

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

Probab=99.05  E-value=4.3e-11  Score=83.80  Aligned_cols=50  Identities=28%  Similarity=0.420  Sum_probs=46.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHH
Q 027547           29 RKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLET   78 (222)
Q Consensus        29 h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~   78 (222)
                      -+..||+|+..||+.|+.||.+||..+...|.|+.+||..||+||..||.
T Consensus        18 a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           18 AAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            35679999999999999999999999888899999999999999999984

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

Probab=98.75  E-value=4.7e-09  Score=94.26  Aligned_cols=55  Identities=25%  Similarity=0.512  Sum_probs=39.4

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCC-CCCCCCCCChhHHHHHHHHHHHHHHHH
Q 027547           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLP-NQPSKEELSLPDQVDEAINYIKMLETK   79 (222)
Q Consensus        22 ~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP-~~~~~~k~si~~iL~~ai~YIk~Lq~~   79 (222)
                      ...+|..|+.+||+||++||..|..|++||| ...+.||++|   |..||.||+.|+..
T Consensus         9 ~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~i---l~~~~~~~~~~~~~   64 (361)
T 4f3l_A            9 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTV---LQKSIDFLRKHKET   64 (361)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHH---HHHHHHHHHHHHHH
T ss_pred             cchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHH---HHHHHHHHHHHHhh
Confidence            4567899999999999999999999999999 3345666666   99999999999864

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

Probab=98.67  E-value=4.2e-08  Score=73.23  Aligned_cols=52  Identities=27%  Similarity=0.393  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHH
Q 027547           31 TIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKE   82 (222)
Q Consensus        31 ~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~   82 (222)
                      ..||.|-..||+.|..||.+||......|.|+.++|.-||+||..|++-+++
T Consensus        31 ~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           31 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            3468899999999999999999988888999999999999999999987643

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

Probab=98.57  E-value=3e-08  Score=90.02  Aligned_cols=54  Identities=28%  Similarity=0.445  Sum_probs=47.5

Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHHHhcCC----CCCCCCCCChhHHHHHHHHHHHHHHHH
Q 027547           23 SPTKIERKTIEKNRRDQMKNLYSTLKSLLP----NQPSKEELSLPDQVDEAINYIKMLETK   79 (222)
Q Consensus        23 ~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP----~~~~~~k~si~~iL~~ai~YIk~Lq~~   79 (222)
                      ..+|.+|+.+||+||.+||..|..|++|||    ...+.||++|   |..||.||+.|+..
T Consensus        11 ~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~i---l~~~~~~l~~~~~~   68 (387)
T 4f3l_B           11 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTV---LRMAVQHMKTLRGA   68 (387)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHH---HHHHHHHHHHHHCC
T ss_pred             hhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHH---HHHHHHHHHHhhcc
Confidence            457899999999999999999999999999    4566777777   99999999999843

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

Probab=98.31  E-value=2.2e-06  Score=62.18  Aligned_cols=52  Identities=15%  Similarity=0.318  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHhcCCCC-CCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027547           37 RDQMKNLYSTLKSLLPNQ-PSKEELSLPDQVDEAINYIKMLETKLKECKKRKE   88 (222)
Q Consensus        37 R~~mn~~~~~LrsLlP~~-~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~   88 (222)
                      |..||+.+..|..|||.. .+..|.++..||..|++||+.||+..+.+.+...
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            778999999999999985 3556888999999999999999998887776543

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

Probab=97.50  E-value=0.0014  Score=46.65  Aligned_cols=81  Identities=10%  Similarity=0.073  Sum_probs=64.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccccccC
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQL  207 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~~  207 (222)
                      +.+.|.| .++||++.+|..+|-+.|..|.+++....++.+...+.+.+.+   ....+.|.++|.++-...-....++-
T Consensus         6 ~~l~v~~-~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~~---~~~l~~l~~~L~~~~~~~~~~~~~~~   81 (91)
T 1zpv_A            6 AIITVVG-KDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE---KQDFTYLRNEFEAFGQTLNVKINIQS   81 (91)
T ss_dssp             EEEEEEE-SCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS---CCCHHHHHHHHHHHHHHHTEEEEEEE
T ss_pred             EEEEEEE-CCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeCC---CCCHHHHHHHHHHHHHHcCCEEEEee
Confidence            4566666 5899999999999999999999999998888777777777665   24789999999988776666666654


Q ss_pred             CCCCC
Q 027547          208 PELWD  212 (222)
Q Consensus       208 ~~~~~  212 (222)
                      -++|+
T Consensus        82 ~~if~   86 (91)
T 1zpv_A           82 AAIFE   86 (91)
T ss_dssp             GGGTC
T ss_pred             HHHHH
Confidence            45554

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

Probab=95.95  E-value=0.059  Score=43.51  Aligned_cols=66  Identities=17%  Similarity=0.261  Sum_probs=53.0

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSG  198 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~  198 (222)
                      +.|.|.| +++||++..|..+|.++|++|+.++..+..+.++..+.+....    ...+.|.++|.++...
T Consensus         7 ~~itv~~-~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~~~----~~~~~l~~~L~~~~~~   72 (192)
T 1u8s_A            7 LVITAVG-TDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP----SNITRVETTLPLLGQQ   72 (192)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH----HHHHHHHHHHHHHHHH
T ss_pred             EEEEEEc-CCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEecCC----CCHHHHHHHHHHHHHh
Confidence            5577777 5899999999999999999999999998888877777775432    3567788888777653

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

Probab=95.70  E-value=0.038  Score=38.33  Aligned_cols=49  Identities=4%  Similarity=0.043  Sum_probs=37.8

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEec
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIR  177 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~  177 (222)
                      ..+.|.+ .++||.|.+|..+|.+.|+.|.+++....++.+...|.+.+.
T Consensus         6 ~~l~v~~-~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~~~   54 (88)
T 2ko1_A            6 AGIRIVG-EDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIFVK   54 (88)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEEES
T ss_pred             EEEEEEE-ECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEEEC
Confidence            3455555 489999999999999999999999998776644455555554

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

Probab=95.64  E-value=0.066  Score=43.21  Aligned_cols=75  Identities=15%  Similarity=0.232  Sum_probs=56.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--------CEEEEEEEEEeccCccccCHHHHHHHHHHHHhcc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--------NTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC  199 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--------~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~  199 (222)
                      ..|.|.| .+++|++.+|.+.|-++|++|..+...+.+        +.++..+.+.+.  . ..+.+.|+++|..+....
T Consensus        94 ~~l~v~~-~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~~~~~~~~~~~F~~~~~~~~~--~-~~~~~~l~~~l~~~~~~~  169 (192)
T 1u8s_A           94 VEVYVES-DDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVD--S-GCNLMQLQEEFDALCTAL  169 (192)
T ss_dssp             EEEEEEE-SCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEEC--T-TSCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEe-CCCccHHHHHHHHHHHcCCcHHHhhhhcccCCccCCCCCEEEEEEEEeCC--C-CCCHHHHHHHHHHHHHHh
Confidence            4566666 589999999999999999999999988765        234444444332  2 468899999999888877


Q ss_pred             ccccccc
Q 027547          200 ASEGEMQ  206 (222)
Q Consensus       200 ~~~~~~~  206 (222)
                      -..+.++
T Consensus       170 ~~~~~~~  176 (192)
T 1u8s_A          170 DVQGSLN  176 (192)
T ss_dssp             TCEEEEE
T ss_pred             CceEEEE
Confidence            6555554

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

Probab=95.35  E-value=0.079  Score=43.16  Aligned_cols=71  Identities=13%  Similarity=0.106  Sum_probs=53.0

Q ss_pred             eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC------CEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          127 NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG------NTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       127 ~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~------~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      ...|.|.| .++||++..|-..|-++|+.|..++..+.+      ++++..+...+..   ..+ +.|+++|..+....-
T Consensus        93 ~~iltv~g-~DrpGiva~Vt~~La~~g~nI~~~~~~t~~~~~~~~~~F~m~~~~~~~~---~~~-~~l~~~l~~~a~~l~  167 (195)
T 2nyi_A           93 EYELYVEG-PDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRMGSRVAFPF---PLY-QEVVTALSRVEEEFG  167 (195)
T ss_dssp             EEEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEEECSSTTCEEEEEEEEEEEEG---GGH-HHHHHHHHHHHHHHT
T ss_pred             EEEEEEEe-CCCcCHHHHHHHHHHHcCCCEEEceeeecccccCCCCeEEEEEEEEcCC---Ccc-HHHHHHHHHHHHHcC
Confidence            35677777 489999999999999999999999999876      4455455544432   345 888888888777654


Q ss_pred             cc
Q 027547          201 SE  202 (222)
Q Consensus       201 ~~  202 (222)
                      ..
T Consensus       168 ~d  169 (195)
T 2nyi_A          168 VD  169 (195)
T ss_dssp             CE
T ss_pred             eE
Confidence            33

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

Probab=95.30  E-value=0.1  Score=42.48  Aligned_cols=49  Identities=12%  Similarity=0.196  Sum_probs=41.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEec
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIR  177 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~  177 (222)
                      +.|.|.| +++||++..|..+|.++|+.|+.++..+..+.++..+.+...
T Consensus         6 ~~ltv~~-~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~~~   54 (195)
T 2nyi_A            6 FVVSVAG-SDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVSLN   54 (195)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES
T ss_pred             EEEEEEe-CCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEEec
Confidence            5677777 589999999999999999999999999888877666666543

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

Probab=92.58  E-value=0.53  Score=41.99  Aligned_cols=76  Identities=12%  Similarity=0.178  Sum_probs=58.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccccccccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQ  206 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~  206 (222)
                      +.|++.| .++||+...|...|-++|.+|+.++....+++++..+.+.+...  ..+.+.|.++|..+-...-....+.
T Consensus        13 ~~lt~~g-~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~   88 (415)
T 3p96_A           13 VLITVTG-VDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCPAD--VADGPALRHDVEAAIRKVGLDVSIE   88 (415)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEECHH--HHTSHHHHHHHHHHHHHTTCEEEEE
T ss_pred             EEEEEEc-CCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEecCC--cCCHHHHHHHHHHHHHHcCeEEEEE
Confidence            5577777 48999999999999999999999999999998777777766442  1355788888887766554443333

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

Probab=90.57  E-value=2.3  Score=37.27  Aligned_cols=69  Identities=13%  Similarity=0.092  Sum_probs=52.4

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC  199 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~  199 (222)
                      .-+++.| .+++|+...|-..|-++|..|+.++....  .++++..+.+.....  ..+.+.|.++|..+-..+
T Consensus        23 ~iLtv~c-~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~FfMr~~~~~~~~--~~~~~~L~~~l~~la~~l   93 (302)
T 3o1l_A           23 FRLVIAC-PDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHEIRADTL--PFDLDGFREAFTPIAEEF   93 (302)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEEEEEEEEGGGS--SSCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEEEEEEEecCCC--CCCHHHHHHHHHHHHHHh
Confidence            4577777 48999999999999999999999998875  566555454443322  367889999998776644

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

Probab=89.90  E-value=1.9  Score=37.47  Aligned_cols=70  Identities=16%  Similarity=0.131  Sum_probs=53.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      +.+++.| .+++|+...|-..|-++|..|+.++..+.  .+.++..+.+.+...  ..+.+.|+++|..+-..+-
T Consensus         7 ~iLtv~g-~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~~--~~~~~~L~~~f~~la~~~~   78 (288)
T 3obi_A            7 YVLTLSC-PDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVVFNAAAK--VIPLASLRTGFGVIAAKFT   78 (288)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEESSC--CCCHHHHHHHHHHHHHHTT
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEEEEcCCC--CCCHHHHHHHHHHHHHHcC
Confidence            4577777 48999999999999999999999998643  456665555555432  3678999999987766543

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

Probab=89.81  E-value=2.2  Score=36.93  Aligned_cols=69  Identities=12%  Similarity=-0.013  Sum_probs=52.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHhccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCA  200 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~  200 (222)
                      +.+++.| ++++|+...|-..|-++|..|+.++..+.  .+.++..+.+....   ..+.+.++++|..+-..+-
T Consensus         9 ~vLtv~c-~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~---~~~~~~L~~~f~~la~~l~   79 (286)
T 3n0v_A            9 WILTADC-PSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPD---DFDEAGFRAGLAERSEAFG   79 (286)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEECCS---SCCHHHHHHHHHHHHGGGT
T ss_pred             EEEEEEe-CCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeEEEEEEecCC---CCCHHHHHHHHHHHHHHcC
Confidence            4577777 48999999999999999999999998853  45555545444332   4678899999987766443

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

Probab=89.30  E-value=0.72  Score=36.94  Aligned_cols=64  Identities=16%  Similarity=0.118  Sum_probs=45.7

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .+.|.. .++||.|.+|...|.+.|++|.+.++....  +....+|.+. .+   ....+.+...|.+++.
T Consensus         5 ~IsV~v-~NrpGvLarIt~lfs~rg~NI~Sl~v~~t~d~~~sriti~V~-~d---~~~leqI~kqL~Kl~d   70 (164)
T 2f1f_A            5 ILSVLL-ENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTV-GD---EKVLEQIEKQLHKLVD   70 (164)
T ss_dssp             EEEEEE-ECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEEEE-SC---HHHHHHHHHHHHHSTT
T ss_pred             EEEEEE-eCCCcHHHHHHHHHHHCCCCeeeceeeecCCCCEEEEEEEEe-cc---HHHHHHHHHHHcCCCC
Confidence            355555 389999999999999999999999988554  5566666665 22   1345666666666544

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

Probab=88.29  E-value=1.2  Score=34.16  Aligned_cols=35  Identities=11%  Similarity=0.176  Sum_probs=31.1

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV  164 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~  164 (222)
                      .+.|.|. +++|+|.+|+++|-+.++++..+++...
T Consensus         2 ~~~v~~~-dr~g~l~~i~~~l~~~~~ni~~~~~~~~   36 (190)
T 2jhe_A            2 RLEVFCE-DRLGLTRELLDLLVLRGIDLRGIEIDPI   36 (190)
T ss_dssp             EEEEEEC-SCTTHHHHHHHHHHHTTCCEEEEEEETT
T ss_pred             EEEEEEe-cCCcHHHHHHHHHHHcCCCeEEEEEecC
Confidence            4667774 8999999999999999999999999766

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

Probab=87.67  E-value=1.2  Score=36.66  Aligned_cols=65  Identities=14%  Similarity=0.061  Sum_probs=47.1

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHHhc
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFVSG  198 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~  198 (222)
                      .+.|.. .++||.|.+|...|...|++|.+.++....  +....+|.+...+    ...+.|...|.+++.-
T Consensus        31 ~LsVlV-eN~pGvLaRItglfsrRG~NI~SLtV~~ted~gisRitIvV~g~e----~~ieqL~kQL~KLidV   97 (193)
T 2fgc_A           31 LVSMLV-HNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVKGDD----KTIEQIEKQAYKLVEV   97 (193)
T ss_dssp             EEEEEE-ECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEEECT----THHHHHHHHHTTSTTE
T ss_pred             EEEEEE-CCCChHHHHHHHHHHHCCceEEEEEeeccCCCCEEEEEEEEECCH----HHHHHHHHHhcCcCce
Confidence            345544 389999999999999999999999987543  5566777775332    3467777777765543

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

Probab=87.41  E-value=0.71  Score=37.05  Aligned_cols=64  Identities=9%  Similarity=0.050  Sum_probs=46.1

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .+.|... ++||.|.+|...|.+.|++|.+.++....  +....+|.+.-.    ....+.+...|.+++.
T Consensus         6 ~IsV~ve-NrpGvL~rI~~lfs~rg~NI~Sl~v~~t~d~g~sritivV~~d----~~~leql~kQL~Kl~d   71 (165)
T 2pc6_A            6 IISLLME-NEAGALSRVAGLFSARGYNIESLSVAPTEDPTLSRMTLVTNGP----DEIVEQITKQLNKLIE   71 (165)
T ss_dssp             EEEEEEE-CSTTHHHHHHHHHHHHTCCCCEEEEEECSSTTEEEEEEEEEEC----HHHHHHHHHHHHHSTT
T ss_pred             EEEEEEe-CCCcHHHHHHHHHHHCCCcEEEEEEEecCCCCEEEEEEEEecc----HHHHHHHHHHhcCCCC
Confidence            4555553 89999999999999999999999987543  566677777522    1345666666666554

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

Probab=86.87  E-value=3.6  Score=35.72  Aligned_cols=71  Identities=7%  Similarity=0.007  Sum_probs=50.7

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC  199 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~  199 (222)
                      ..+++.| .+++|+...|-..|-++|..|+.++..+.  .++++..+.+...-.....+.+.+.++|..+-..+
T Consensus        11 ~vLtv~c-~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~~~~~~~~~~~L~~~f~~la~~~   83 (292)
T 3lou_A           11 FVLTLSC-PSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFFVRCVFHATDDADALRVDALRREFEPIAERF   83 (292)
T ss_dssp             EEEEEEE-ESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEECC----CCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEc-CCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceEEEEEEEccCcccCCCHHHHHHHHHHHHHhc
Confidence            4577777 48999999999999999999999998853  45555544444430011367889999988766544

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

Probab=85.32  E-value=4.5  Score=35.01  Aligned_cols=67  Identities=22%  Similarity=0.252  Sum_probs=46.7

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGC  199 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~  199 (222)
                      +-+++.| .+++|+...|-..|-++|..|+.++..+.  .+.++..+.+...  .  .+.+.+.++|..+-..+
T Consensus         8 ~vLtv~c-~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~~--~--~~~~~L~~~f~~la~~~   76 (287)
T 3nrb_A            8 YVLSLAC-QDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIP--V--AGVNDFNSAFGKVVEKY   76 (287)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEECC--C-----CHHHHHHHHHHGGG
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHCCCCEEeeeeeecCCCCeEEEEEEEEcC--C--CCHHHHHHHHHHHHHHc
Confidence            4577777 48999999999999999999999998743  4555544444332  2  34458888887765544

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

Probab=84.31  E-value=2.6  Score=35.51  Aligned_cols=61  Identities=21%  Similarity=0.297  Sum_probs=40.9

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC-----CEEEEEEEEEeccCccccCHHHHHHHHHHH
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG-----NTIFHVIHAEIRDSMFGFGAAKISERLKGF  195 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~-----~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~  195 (222)
                      +.+.|.+ .+++|+|.+|+.+|-+.+..|.+.+.....     +.+..+  .++.+   . ..+++-++|+++
T Consensus         5 VtL~I~a-~DRpGLLsDIt~vLAe~kiNIltIn~~~~~kG~~ng~A~I~--IEV~d---~-~Le~LL~kLrkI   70 (223)
T 1y7p_A            5 RGLRIIA-ENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIY--FEIEG---G-DFEKILERVKTF   70 (223)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEE--EEECS---S-CHHHHHHHHHTC
T ss_pred             EEEEEEE-cCCCCHHHHHHHHHHHcCCCceEEEEEccccCCcCCEEEEE--EEECC---C-CHHHHHHHHhCC
Confidence            3455555 489999999999999999999999998764     444333  66664   2 667777776643

---

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	222
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-11
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	3e-10
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	3e-09
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	3e-07
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	4e-07
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	4e-07
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	4e-06
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	3e-05

>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 = 56.8 bits (137), Expect = 1e-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 = 52.6 bits (126), Expect = 3e-10
 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 = 49.5 bits (118), Expect = 3e-09
 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

>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 = 44.1 bits (104), Expect = 3e-07
 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

>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 = 44.5 bits (105), Expect = 4e-07
 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

>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 = 44.2 bits (104), Expect = 4e-07
 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 = 40.9 bits (96), Expect = 4e-06
 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 = 38.6 bits (90), Expect = 3e-05
 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	222
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.62
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.52
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.52
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.38
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.28
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	97.52
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.79
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	96.39
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	94.59
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	94.52
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	94.4
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	90.94
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	90.5
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	85.74
d1ygya3	78	Phosphoglycerate dehydrogenase, regulatory (C-term	84.65
d1phza1	97	Phenylalanine hydroxylase N-terminal domain {Rat (	82.44
d2f1fa1	76	Acetolactate synthase small subunit, IlvH {Escheri	82.03

>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=99.65  E-value=2.3e-16  Score=112.44  Aligned_cols=68  Identities=25%  Similarity=0.331  Sum_probs=62.4

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      +|..||..||+||.+||++|..|+++||......|.|.++||..||+||+.|+.+++.|..+++.|..
T Consensus         1 ~R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~   68 (79)
T d1nlwa_           1 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (79)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999999999877778899999999999999999999999988877653

>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=99.62  E-value=6.6e-16  Score=112.19  Aligned_cols=69  Identities=16%  Similarity=0.308  Sum_probs=63.0

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      .+|..||..||+||+.||+.|..|+++||+.....|.|+++||..||+||+.|+++++.|..+++.+..
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            468899999999999999999999999998877778899999999999999999999999988776654

>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=99.56  E-value=3.6e-15  Score=106.52  Aligned_cols=67  Identities=24%  Similarity=0.370  Sum_probs=59.0

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      .+|..|+.+||+||.+||+.|..|++|||...  .|.+.++||..||+||+.|+++++.|..+.+.|..
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            57889999999999999999999999999754  34566777999999999999999999998877654

>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=99.55  E-value=6.5e-15  Score=105.70  Aligned_cols=67  Identities=22%  Similarity=0.456  Sum_probs=59.0

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      +|..|+..||+||.+||+.|..|+++||..+ ..|.|+++||..||+||+.|+++++.|..+.+.+..
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            6889999999999999999999999999654 346788888999999999999999999988776543

>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=99.52  E-value=2.8e-15  Score=104.09  Aligned_cols=59  Identities=22%  Similarity=0.375  Sum_probs=52.3

Q ss_pred             CCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 027547           22 SSPTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPSKEELSLPDQVDEAINYIKMLETKLK   81 (222)
Q Consensus        22 ~~~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~~~k~si~~iL~~ai~YIk~Lq~~v~   81 (222)
                      ...+|..||..||+||..||+.|..|++|||..+. +|.|.++||..||+||+.||+.++
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            34678899999999999999999999999998764 477888889999999999998764

>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=99.52  E-value=3.2e-15  Score=102.23  Aligned_cols=56  Identities=25%  Similarity=0.361  Sum_probs=47.9

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCCCCChhHHHHHHHHHHHHHHHHH
Q 027547           25 TKIERKTIEKNRRDQMKNLYSTLKSLLPNQ----PSKEELSLPDQVDEAINYIKMLETKL   80 (222)
Q Consensus        25 ~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~----~~~~k~si~~iL~~ai~YIk~Lq~~v   80 (222)
                      +|..|+.+||+||.+||+.|..|++|||..    ....|.++++||..||+||++||+++
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    23346666677999999999999865

>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=99.38  E-value=7.8e-14  Score=95.76  Aligned_cols=56  Identities=23%  Similarity=0.434  Sum_probs=47.4

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCC---CCCCChhHHHHHHHHHHHHHHHH
Q 027547           24 PTKIERKTIEKNRRDQMKNLYSTLKSLLPNQPS---KEELSLPDQVDEAINYIKMLETK   79 (222)
Q Consensus        24 ~~~~~h~~~ER~RR~~mn~~~~~LrsLlP~~~~---~~k~si~~iL~~ai~YIk~Lq~~   79 (222)
                      .+|..|+.+||+||..||+.|..|++|||....   ..|.++++||..|++||+.||++
T Consensus         4 ~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999997642   23555556699999999999865

>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=99.28  E-value=1.2e-12  Score=88.58  Aligned_cols=53  Identities=21%  Similarity=0.305  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHhcCCCCC-CCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027547           37 RDQMKNLYSTLKSLLPNQP-SKEELSLPDQVDEAINYIKMLETKLKECKKRKESLQG   92 (222)
Q Consensus        37 R~~mn~~~~~LrsLlP~~~-~~~k~si~~iL~~ai~YIk~Lq~~v~~L~~~~~~l~~   92 (222)
                      |.+||+.|..||++||+.. +.+|+++   |.+||+||+.||++++.|+++...|..
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            5689999999999999864 5567777   999999999999999999999887764

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

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

Probab=97.52  E-value=0.0005  Score=47.28  Aligned_cols=78  Identities=10%  Similarity=0.054  Sum_probs=63.4

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccccccccCC
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASEGEMQLP  208 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~~~~~~~  208 (222)
                      -|++.| +++||++..|...|-++|..|..++..+.++.++..+.+.+..   ..+.+.+.++|..+-...-..+.++-.
T Consensus         4 vitv~g-~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~~~---~~~~~~l~~~l~~la~~l~l~i~i~~~   79 (83)
T d1zpva1           4 IITVVG-KDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE---KQDFTYLRNEFEAFGQTLNVKINIQSA   79 (83)
T ss_dssp             EEEEEE-SCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS---CCCHHHHHHHHHHHHHHHTEEEEEEEG
T ss_pred             EEEEEc-CCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEEec---CCCHHHHHHHHHHHHHHcCcEEEEEEH
Confidence            366666 5999999999999999999999999999999877777777654   357899999999887777666666644


Q ss_pred             CC
Q 027547          209 EL  210 (222)
Q Consensus       209 ~~  210 (222)
                      |+
T Consensus        80 di   81 (83)
T d1zpva1          80 AI   81 (83)
T ss_dssp             GG
T ss_pred             HH
Confidence            44

>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=96.79  E-value=0.0067  Score=41.71  Aligned_cols=69  Identities=16%  Similarity=0.232  Sum_probs=56.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHHHHhcccc
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCAS  201 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~  201 (222)
                      +-|++.| +++||++.+|...|-+.|.+|..++....++.+.+.+.+.+..    .+.++++..|.++-...-.
T Consensus         6 ~vitv~G-~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~~----~~~~~l~~~L~~l~~~l~l   74 (86)
T d1u8sa1           6 LVITAVG-TDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP----SNITRVETTLPLLGQQHDL   74 (86)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH----HHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEEEe-CCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcCc----ccHHHHHHHHHHHHHHhCC
Confidence            4566666 5999999999999999999999999999999988888777653    3577888888877665443

>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=96.39  E-value=0.02  Score=39.68  Aligned_cols=69  Identities=13%  Similarity=0.188  Sum_probs=51.3

Q ss_pred             eeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCC--------EEEEEEEEEeccCccccCHHHHHHHHHHHHhc
Q 027547          127 NLEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGN--------TIFHVIHAEIRDSMFGFGAAKISERLKGFVSG  198 (222)
Q Consensus       127 ~v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~--------~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~  198 (222)
                      .++|.|.| .++||++.+|-..|-++|+.|...+..+..+        .++..+.+.+.  . ..+.+.++++|..+-..
T Consensus         6 tv~v~v~g-~DrpGIV~~it~~la~~~~nI~~l~t~~~~a~~~~~~~~~f~~~~~~~~p--~-~~~~~~l~~~l~~l~~~   81 (93)
T d1u8sa2           6 TVEVYVES-DDKLGLTEKFTQFFAQRQIGMASLSAQTISKDKLHSEQNQFHIAISARVD--S-GCNLMQLQEEFDALCTA   81 (93)
T ss_dssp             EEEEEEEE-SCCTTHHHHHHHHHHHTTCCEEEEEEEEEC--------CEEEEEEEEEEC--T-TSCHHHHHHHHHHHHHH
T ss_pred             EEEEEEEE-CCCCCHHHHHHHHHHHcCCCchhhhcccccccCCcccCccEEEEEEEEcC--c-cccHHHHHHHHHHHHHH
Confidence            56788877 4899999999999999999999998765321        23344444443  3 56888999999887664


Q ss_pred             c
Q 027547          199 C  199 (222)
Q Consensus       199 ~  199 (222)
                      .
T Consensus        82 l   82 (93)
T d1u8sa2          82 L   82 (93)
T ss_dssp             H
T ss_pred             c
Confidence            4

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

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

Probab=94.59  E-value=0.16  Score=33.42  Aligned_cols=51  Identities=22%  Similarity=0.074  Sum_probs=40.5

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      .++||.|.++++.|.+.|+.|.........++.+..|.+  .      +++...+.|++
T Consensus         7 ~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~v--d------d~~~a~~~L~~   57 (71)
T d2f06a1           7 PNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRP--S------NMDKCIEVLKE   57 (71)
T ss_dssp             ESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEE--S------CHHHHHHHHHH
T ss_pred             cCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEE--C------CHHHHHHHHHH
Confidence            488999999999999999999999988888877655554  2      45666666654

>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=94.52  E-value=0.2  Score=32.94  Aligned_cols=57  Identities=11%  Similarity=-0.002  Sum_probs=43.5

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          129 EVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       129 ~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      ++.|... ++||.|.++...|.+.|+.+.+.+++...+..+.-|.+        .+++...+.|++
T Consensus         5 QisV~~e-NkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Riiv--------~~~e~a~~~L~~   61 (70)
T d2f06a2           5 QLSIFLE-NKSGRLTEVTEVLAKENINLSALCIAENADFGILRGIV--------SDPDKAYKALKD   61 (70)
T ss_dssp             EEEEEEC-SSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEEE--------SCHHHHHHHHHH
T ss_pred             EEEEEEe-CCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEEEE--------CChHHHHHHHHH
Confidence            3566664 89999999999999999999999999888776665532        246666666654

>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=94.40  E-value=0.016  Score=39.11  Aligned_cols=60  Identities=20%  Similarity=0.175  Sum_probs=38.4

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEE-eCCE--EEEEEEEEeccCccccCHHHHHHHHHH
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSV-VGNT--IFHVIHAEIRDSMFGFGAAKISERLKG  194 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~-~~~~--~~~ti~~kv~~~~~~~~~~~l~~aL~~  194 (222)
                      +.|.|. +++|+|.+|..++-+++..|.+++... .++.  ...+|..+..+    .+-+.+.++|++
T Consensus         4 i~i~~~-Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~~~----~~l~~ll~kL~~   66 (77)
T d1y7pa2           4 LRIIAE-NKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEG----GDFEKILERVKT   66 (77)
T ss_dssp             EEEEEE-CCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEECS----SCHHHHHHHHHT
T ss_pred             EEEEEe-cCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEcCc----ccHHHHHHHHHc
Confidence            455564 899999999999999999999999775 3444  34445554432    246666666654

>d1sc6a3 d.58.18.1 (A:327-410) Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
domain: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
species: Escherichia coli [TaxId: 562]

Probab=90.94  E-value=0.63  Score=31.09  Aligned_cols=48  Identities=13%  Similarity=0.176  Sum_probs=36.9

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCEEEEEEEEEe
Q 027547          128 LEVILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNTIFHVIHAEI  176 (222)
Q Consensus       128 v~V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~~~~ti~~kv  176 (222)
                      ..+.+.- .++||+|.+|...|-+.|+.|.+......++.....+..++
T Consensus        12 ~rl~i~~-~d~PGvla~I~~~l~~~~iNI~~~~~~~~~~~~~a~~~i~~   59 (84)
T d1sc6a3          12 RRLMHIH-ENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEA   59 (84)
T ss_dssp             EEEEEEE-ESCTTHHHHHHHHHHHTTCEEEEEEEEECSSEEEEEEEEEC
T ss_pred             eEEEEEe-CCcCCHHHHHHHHHHHcCCCHHHhccccCCCCcEEEEEEEC
Confidence            3444433 58999999999999999999999988887776555555543

>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=90.50  E-value=1.1  Score=29.83  Aligned_cols=64  Identities=6%  Similarity=-0.056  Sum_probs=45.5

Q ss_pred             EEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeCCE-EEEEEEEEeccCccccCHHHHHHHHHHHHhcc
Q 027547          132 LTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVGNT-IFHVIHAEIRDSMFGFGAAKISERLKGFVSGC  199 (222)
Q Consensus       132 v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~~-~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~  199 (222)
                      |+.-.++||.|.++|..+.++|+...+..+-...+. --|.|.+.+.. .  .+ +.++++|.++-..+
T Consensus         6 i~~~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~~g-~--~~-~~~~~~l~~L~~~~   70 (80)
T d2qmwa2           6 ITPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQADS-A--IT-TDIKKVIAILETLD   70 (80)
T ss_dssp             EEESSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEESC-C--SC-HHHHHHHHHHHHTT
T ss_pred             EEeCCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEec-C--Cc-HHHHHHHHHHHHhc
Confidence            333357899999999999999999999999876554 34666666643 2  23 35777776665443

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

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

Probab=85.74  E-value=1.1  Score=29.89  Aligned_cols=62  Identities=15%  Similarity=0.099  Sum_probs=44.9

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHH
Q 027547          130 VILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFV  196 (222)
Q Consensus       130 V~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I  196 (222)
                      +.+... ++||.|.++...|..-|+.+.+.++....  +..-.+|.+...+    ...+.+..-|.+++
T Consensus         6 isvlv~-n~pGvL~Ri~~lF~rRg~NI~SL~v~~te~~~iSR~tivv~g~~----~~i~qi~kQl~Kli   69 (78)
T d2fgca2           6 VSMLVH-NKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVKGDD----KTIEQIEKQAYKLV   69 (78)
T ss_dssp             EEEEEE-CCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEEECT----THHHHHHHHHTTST
T ss_pred             EEEEEe-CCCcHHHHHHHHHhhCCcceEEEEEeecCCCCeEEEEEEEEcCH----HHHHHHHHHHhCCc
Confidence            455553 78999999999999999999999988654  5666778877544    23555555555444

>d1ygya3 d.58.18.1 (A:452-529) Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
domain: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.65  E-value=3.4  Score=26.90  Aligned_cols=56  Identities=16%  Similarity=0.125  Sum_probs=42.5

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEe--CCEEEEEEEEEeccCccccCHHHHHHHHHHHHh
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVV--GNTIFHVIHAEIRDSMFGFGAAKISERLKGFVS  197 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~--~~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~  197 (222)
                      .++||++.+|-.+|-+.|+.|.+...+..  ++.++..|.+  ..    ...+++.++|+++-.
T Consensus        11 ~D~PGvi~~I~~~l~~~~iNI~~m~~~~~~~g~~a~~vi~v--D~----~~~~~vl~~I~~~~~   68 (78)
T d1ygya3          11 VDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRL--DQ----DVPDDVRTAIAAAVD   68 (78)
T ss_dssp             SCCTTHHHHHHHHHHHTTCCEEEEEEEECSSSSCEEEEEEE--SS----CCCHHHHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHhcCcChhhheeeecCCCCeEEEEEEc--CC----CccHHHHHHHHcCCC
Confidence            58999999999999999999999988754  4555555554  22    246778888877654

>d1phza1 d.58.18.3 (A:19-115) Phenylalanine hydroxylase N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phenylalanine metabolism regulatory domain
domain: Phenylalanine hydroxylase N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=82.44  E-value=1.1  Score=30.86  Aligned_cols=63  Identities=5%  Similarity=0.029  Sum_probs=46.7

Q ss_pred             CCCCChHHHHHHHHHhCCceEEEEEEEEeCC-EEEEEEEEEeccCccccCHHHHHHHHHHHHhccccc
Q 027547          136 VDDQFIFYEVIRILHQDGAEILNAKFSVVGN-TIFHVIHAEIRDSMFGFGAAKISERLKGFVSGCASE  202 (222)
Q Consensus       136 ~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~~-~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I~~~~~~  202 (222)
                      .+++|.|.++|..|.++|+......+-...+ .--|.|.+.+.. .   .-+.+..+|..+-..++..
T Consensus        24 ~~~pGaL~~vL~~f~~~~INLt~IeSRP~~~~~~~Y~F~id~eg-~---~~~~i~~~l~~L~~~~~~~   87 (97)
T d1phza1          24 KEEVGALAKVLRLFEENDINLTHIESRPSRLNKDEYEFFTYLDK-R---TKPVLGSIIKSLRNDIGAT   87 (97)
T ss_dssp             ECCTTHHHHHHHHHHTTTCCTTSEEEEECSSCTTEEEEEECBCG-G---GHHHHHHHHHHHHHTTCCC
T ss_pred             CCCCCHHHHHHHHHHHCCCCEEEEEeeccCCCCceEEEEEEccc-C---ChHHHHHHHHHHHHhhCcE
Confidence            4789999999999999999999999986544 345666666642 1   2356888887776666544

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

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

Probab=82.03  E-value=1.5  Score=29.06  Aligned_cols=61  Identities=15%  Similarity=0.099  Sum_probs=41.4

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEEeC--CEEEEEEEEEeccCccccCHHHHHHHHHHHH
Q 027547          131 ILTSGVDDQFIFYEVIRILHQDGAEILNAKFSVVG--NTIFHVIHAEIRDSMFGFGAAKISERLKGFV  196 (222)
Q Consensus       131 ~v~~~~~~~~~L~~vl~~Le~lgL~V~~a~~s~~~--~~~~~ti~~kv~~~~~~~~~~~l~~aL~~~I  196 (222)
                      .+.. .++||.|.++...|-.-|+.+.+.++....  +....+|.+...+    ...+.+..-|.+++
T Consensus         5 sv~v-~N~~GVL~RisglF~rRg~NI~Sl~v~~te~~~iSR~tivv~~~~----~~i~qi~kQL~Kli   67 (76)
T d2f1fa1           5 SVLL-ENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDE----KVLEQIEKQLHKLV   67 (76)
T ss_dssp             EEEE-ECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEEEESCH----HHHHHHHHHHHHST
T ss_pred             EEEE-ECCCcHHHHHHHHHHhcCcceEEEEEcccCCCCeeEEEEEEECCH----HHHHHHHHHHhCCC
Confidence            3444 378999999999999998888888887554  4555666654332    23555555555544