Citrus Sinensis ID: 036406

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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-------230-------240-
Protein Sequence
MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM
Secondary Structure (PSIPRED)
cccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEEEEcccEEEEEEEEcccccccHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccEEHHHHHHHHHHHHHHHHHHHHHHcccHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEEEEEccccEEEEEEcccccccccHHHHHHHHHHcccEEEEEEEEEEcccEEEEEEEEEccccccccHHHHHcc
Coil and Loop (DISEMBL)
mfplhsgdeLFIKVSsnshqqdkipqdlisghaseassiitndmgkshrgqsfsmetdkipsdnynsnnsnynnnkklmHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRLsnlsisasqietsdqndtspinrFVVHQSLVGIEIAYScgyleqelpLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNnvvpkfdadatiwm
Flexible Loop (DISEMBL)
MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMEtdkipsdnynsnnsnynnnkklMHRDVERQRRQEMATLYASLRALLPLEFIKGkrsisdqmnegVNYVKYLEKKIKELGVKRDELKrlsnlsisasqietsdqndtspiNRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIqaelnnvvpkfdadatiwm
Low Complexity Region (SEG)
MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDnynsnnsnynnnKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM
Disordered region (IsUnstruct)
*******************************************************************************************ATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVK***************************INRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATI**
Disordered Region (DISOPRED)
*******D*****************************************************************************QRRQEMATLYASLRALLP*********ISDQMNEGVNYVKY*********************************************QSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM
Disordered Region (DISEMBL)
MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISAS*********TSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM
Disordered Region (DISPRO)
*FPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSI**********************************NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRL******************SPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYxxxxxxxxxxxxxxxxxxxxxSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM
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	241	2.2.26 [Sep-21-2011]
Q9FLI1	174	Transcription factor bHLH	yes	no	0.659	0.913	0.540	1e-38
Q9STJ7	163	Transcription factor bHLH	no	no	0.605	0.895	0.480	2e-31
Q9STJ6	221	Transcription factor bHLH	no	no	0.651	0.710	0.439	2e-30
Q9FLI0	204	Transcription factor bHLH	no	no	0.668	0.789	0.434	4e-29
Q9LQ08	259	Transcription factor bHLH	no	no	0.734	0.683	0.367	4e-26
Q9LN95	257	Transcription factor bHLH	no	no	0.609	0.571	0.404	3e-23
Q9M1K1	253	Transcription factor ORG2	no	no	0.618	0.588	0.273	5e-06
Q9FYE6	240	Transcription factor bHLH	no	no	0.290	0.291	0.422	8e-05

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

 Score =  160 bits (404), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 87/161 (54%), Positives = 115/161 (71%), Gaps = 2/161 (1%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           +K+MHR+ ERQRRQEMA+LYASLR+LLPL FIKGKRS SDQ+NE VNY+KYL++KIKEL 
Sbjct: 2   EKMMHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKELS 61

Query: 136 VKRDELKRLSNLSI--SASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLS 193
           V+RD+L  LS  S+  S++     D    S  N  VV Q LVG+EI  S      +   S
Sbjct: 62  VRRDDLMVLSRGSLLGSSNGDFKEDVEMISGKNHVVVRQCLVGVEIMLSSRCCGGQPRFS 121

Query: 194 KVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFD 234
            VL+VL + GLC++N +S+ VD+RL++TIQAE+N++    D
Sbjct: 122 SVLQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMID 162

Arabidopsis thaliana (taxid: 3702)

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

 Score =  135 bits (341), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 74/154 (48%), Positives = 108/154 (70%), Gaps = 8/154 (5%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           +KL+H+++E++RRQEMA+LYASLR+LLPLEFI+GKRS SDQ+   VNY+ YL++ IK++ 
Sbjct: 2   EKLVHKEIEKRRRQEMASLYASLRSLLPLEFIQGKRSTSDQVKGAVNYIDYLQRNIKDIN 61

Query: 136 VKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKV 195
            KRD+L  LS  S  +S     + N+ S  N  V+   LVGIEI  S      + P S V
Sbjct: 62  SKRDDLVLLSGRSFRSSN--EQEWNEIS--NHVVIRPCLVGIEIVLSI----LQTPFSSV 113

Query: 196 LEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV 229
           L+VL + GL V+  + + V++RL+HT+QAE+N++
Sbjct: 114 LQVLREHGLYVLGYICSSVNDRLIHTLQAEVNDL 147

Arabidopsis thaliana (taxid: 3702)

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

 Score =  132 bits (332), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 73/166 (43%), Positives = 106/166 (63%), Gaps = 9/166 (5%)

Query: 80  HRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRD 139
           HRD+ERQRRQEMATL+A+LR  LPL++IKGKR++SD +N  VN++K  E +IKEL  +RD
Sbjct: 47  HRDIERQRRQEMATLFATLRTHLPLKYIKGKRAVSDHVNGAVNFIKDTEARIKELSARRD 106

Query: 140 ELKRLSNLSISASQ---IETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQE-LPLSKV 195
           EL R +     ++       SD   + P    +V   + G+E+  S      E LPLSKV
Sbjct: 107 ELSRETGQGYKSNPDPGKTGSDVGKSEPAT-VMVQPHVSGLEVVVSSNSSGPEALPLSKV 165

Query: 196 LEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM 241
           LE + ++GL V++  +TRV++RL+HTIQ E+N+    F     +W+
Sbjct: 166 LETIQEKGLEVMSSFTTRVNDRLMHTIQVEVNS----FGCIDLLWL 207

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLI0|BH120_ARATH Transcription factor bHLH120 OS=Arabidopsis thaliana GN=BHLH120 PE=2 SV=2

 Score =  128 bits (321), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 73/168 (43%), Positives = 108/168 (64%), Gaps = 7/168 (4%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           KKL+HR++ERQRRQEMA L+ASLR+ LPL++IKGKR++SD +N  V+++K  + +IK+L 
Sbjct: 27  KKLLHRNIERQRRQEMAILFASLRSQLPLKYIKGKRAMSDHVNGAVSFIKDTQTRIKDLS 86

Query: 136 VKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYS--CGYLEQELPLS 193
            +RDELKR      S +   +   +  S     +V   + G E+  S     LE   PLS
Sbjct: 87  ARRDELKREIGDPTSLTGSGSGSGSSRSEPASVMVQPCVSGFEVVVSSLASGLE-AWPLS 145

Query: 194 KVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFDADATIWM 241
           +VLEVL  +GL V++ ++ RV+ERL++TIQ E+N+    FD     W+
Sbjct: 146 RVLEVLHGQGLEVISSLTARVNERLMYTIQVEVNS----FDCFDLAWL 189

Arabidopsis thaliana (taxid: 3702)

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

 Score =  118 bits (296), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 79/215 (36%), Positives = 120/215 (55%), Gaps = 38/215 (17%)

Query: 40  ITNDMGKSHRGQSFSMETDKIPSDNYNSNNSNYNNN----KKLMHRDVERQRRQEMATLY 95
           ITN +G S++ +S    T       Y +N +N N++    KK+ HRD+ERQRRQE+++L+
Sbjct: 41  ITNKIGGSNKKRSLCDIT-------YGANEANKNDDDRESKKMKHRDIERQRRQEVSSLF 93

Query: 96  ASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR-LSNLSISASQI 154
             LR LLP ++I+GKRS SD + + VNY+K L+ KIKEL  KR+ +K+ +S  + + S I
Sbjct: 94  KRLRTLLPFQYIQGKRSTSDHIVQAVNYIKDLQIKIKELNEKRNRVKKVISATTTTHSAI 153

Query: 155 E--------------------TSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSK 194
           E                      D++ T      VV   LVG+EI  SC     +  LS 
Sbjct: 154 EECTSSLSSSAASTLSSSCSCVGDKHIT-----VVVTPCLVGVEIIISCCLGRNKSCLSS 208

Query: 195 VLEVLLDEG-LCVVNCVSTRVDERLLHTIQAELNN 228
           VL++L  E    VV+C+S R  +R +HTI +++ +
Sbjct: 209 VLQMLAQEQRFSVVSCLSARRQQRFMHTIVSQVED 243

Arabidopsis thaliana (taxid: 3702)

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

 Score =  108 bits (270), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 66/163 (40%), Positives = 97/163 (59%), Gaps = 16/163 (9%)

Query: 75  NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKEL 134
           NK+  H+++ERQRRQE  +L+  LR LLP ++IKGKRS +D + E VNY+K L+KKIKE+
Sbjct: 74  NKRAKHKELERQRRQENTSLFKILRYLLPSQYIKGKRSSADHVLEAVNYIKDLQKKIKEV 133

Query: 135 GVKRDELKR----------LSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCG 184
             KRD +KR           S  S+++S        + +     VV   L+G+EI  SC 
Sbjct: 134 SEKRDRIKRSITHPSSRGEFSIRSLASSTCSCVGDTNIA----VVVRPCLIGLEIVVSCC 189

Query: 185 YLEQELPLSKVLEVLLDE-GLCVVNCVSTRVDERLLHTIQAEL 226
               E  LS VL++L  E    +V+C+STR+ +  +HTI +E+
Sbjct: 190 N-RHESCLSSVLQLLAQEQCFNIVSCISTRLHQGFIHTIASEV 231

Arabidopsis thaliana (taxid: 3702)

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

 Score = 51.6 bits (122), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/161 (27%), Positives = 84/161 (52%), Gaps = 12/161 (7%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           KKL H   ER RR+++ TL++SLR+ LP      K SI + +++ + Y+  L++++K L 
Sbjct: 72  KKLNHNASERDRRKKINTLFSSLRSCLPASDQSKKLSIPETVSKSLKYIPELQQQVKRLI 131

Query: 136 VKRDE-LKRLSNLSISASQIETSDQNDTSPINRFV--VHQSLVG---IEIAYSCGYLEQE 189
            K++E L R+S         E  D+     +  ++  V  + +G   + +  S   +   
Sbjct: 132 QKKEEILVRVS----GQRDFELYDKQQPKAVASYLSTVSATRLGDNEVMVQVSSSKI-HN 186

Query: 190 LPLSKVLEVLLDEGLCVVNCVSTRVD-ERLLHTIQAELNNV 229
             +S VL  + ++G  +V+  S+R   ERL +T+  ++ N+
Sbjct: 187 FSISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQVENM 227

Arabidopsis thaliana (taxid: 3702)

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

 Score = 47.8 bits (112), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           KKL H   ER RR+++  LY+SLRALLPL   K K SI   +   V Y+   +++++ L 
Sbjct: 66  KKLNHNASERDRRRKLNALYSSLRALLPLSDQKRKLSIPMTVARVVKYIPEQKQELQRLS 125

Query: 136 VKRDE-LKRLS 145
            +++E LKR+S
Sbjct: 126 RRKEELLKRIS 136

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	241
224122516	240	predicted protein [Populus trichocarpa]	0.912	0.916	0.545	1e-59
224134607	246	predicted protein [Populus trichocarpa]	0.904	0.886	0.549	4e-59
356530925	248	PREDICTED: transcription factor bHLH118-	0.904	0.879	0.478	3e-45
356559901	246	PREDICTED: transcription factor bHLH126-	0.896	0.878	0.465	6e-45
225455627	247	PREDICTED: transcription factor bHLH120	0.879	0.858	0.471	5e-44
363808366	247	uncharacterized protein LOC100775836 [Gl	0.896	0.874	0.476	1e-43
217075046	247	unknown [Medicago truncatula] gi|3885191	0.883	0.862	0.440	5e-43
356535931	248	PREDICTED: transcription factor bHLH118-	0.917	0.891	0.458	7e-43
357444221	448	Transcription factor bHLH36 [Medicago tr	0.887	0.477	0.434	7e-42
255539631	196	DNA binding protein, putative [Ricinus c	0.684	0.841	0.534	7e-38

>gi|224122516|ref|XP_002318856.1| predicted protein [Populus trichocarpa] gi|222859529|gb|EEE97076.1| predicted protein [Populus trichocarpa]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 125/229 (54%), Positives = 159/229 (69%), Gaps = 9/229 (3%)

Query: 1   MFPLHSGDELFIKVSSNSHQQDKIPQDLI-SGHASEASSIITNDMGKSHRGQSFSMETDK 59
           MFPLH GDEL   +SS+ HQQ  IPQDLI + +A+   S  TN M    R    SM+   
Sbjct: 1   MFPLHQGDELCFNISSDPHQQHNIPQDLILARYAALQGSDTTNKMENDRRRFLISMD--- 57

Query: 60  IPSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNE 119
             S++  + + + NNNKK+MHR++ERQRRQEM TLYASLRALLPLEFIKGKRSISD MNE
Sbjct: 58  --SNHEVARDHSKNNNKKMMHRNIERQRRQEMTTLYASLRALLPLEFIKGKRSISDHMNE 115

Query: 120 GVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEI 179
            VNY+KYL+KKIKEL  KRD LK+  NLS  +    +   N  SPI+   +     GIE+
Sbjct: 116 SVNYIKYLQKKIKELSAKRDGLKKSPNLSFDSP---SGSSNKYSPISPVTLQPYPGGIEV 172

Query: 180 AYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
            +   +  Q+ PLS+VL+VLL+EG+ VVNCVST+V+ERL HT+Q E+N+
Sbjct: 173 VFDSDFRGQDSPLSRVLQVLLEEGISVVNCVSTKVNERLFHTVQTEVND 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134607|ref|XP_002321864.1| predicted protein [Populus trichocarpa] gi|222868860|gb|EEF05991.1| predicted protein [Populus trichocarpa]

 Score =  233 bits (595), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 127/231 (54%), Positives = 162/231 (70%), Gaps = 13/231 (5%)

Query: 1   MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHAS---EASSIITNDMGKSHRGQSFSMET 57
           MFPLH G EL  K+SS+ HQQD IP DLI  H       S+ ITN+M K  R    SM+ 
Sbjct: 1   MFPLHQGGELCFKISSSPHQQDNIP-DLILAHQYAEIHGSTDITNNMEKGRRRNIISMDN 59

Query: 58  DKIPSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQM 117
           ++   DN N      N+ KK+MHRD+ERQRRQEM TLYASLRALLPLEFIKGKRSISD M
Sbjct: 60  NEAARDNNN------NSKKKMMHRDIERQRRQEMTTLYASLRALLPLEFIKGKRSISDHM 113

Query: 118 NEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGI 177
           NE VNY+KYL+KKIKE   KRDELK+LS+ S  AS    S+++ +S +    +     GI
Sbjct: 114 NEAVNYIKYLQKKIKETSAKRDELKKLSDFSSVASPSGCSNKSSSSSV---ALQPYPGGI 170

Query: 178 EIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
           EI +    + ++LPLS+VL+VLL+EG+ V+NCVST+V+ERL H++Q E+N+
Sbjct: 171 EITFDSDLMGRDLPLSRVLQVLLEEGISVINCVSTKVNERLFHSVQTEVND 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530925|ref|XP_003534029.1| PREDICTED: transcription factor bHLH118-like [Glycine max]

 Score =  187 bits (475), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 112/234 (47%), Positives = 157/234 (67%), Gaps = 16/234 (6%)

Query: 1   MFPLHSGDELFIKVSSNSHQ--QDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETD 58
           MFPL  G+EL I+ S++ H   Q K+ QDLI     + +S+  ND  +     S S  T 
Sbjct: 1   MFPLQRGNELVIQFSNSPHHHLQHKMSQDLI---LDDYASLDVNDSNQKFSTSSISQPTK 57

Query: 59  KIPSDNYNSNNSNYNN--NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQ 116
           K+     N  N +Y+N   KK++H+++ERQRRQEMAT YASLR+LLPLEFIKGKRSISD 
Sbjct: 58  KLFY-GANKKNHDYSNEHKKKMIHKEIERQRRQEMATFYASLRSLLPLEFIKGKRSISDH 116

Query: 117 MNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQ--SL 174
           MNE VNY+K+++K IKELG KRDELK+LSN S   + +E + +   +  N F VH+   +
Sbjct: 117 MNEAVNYIKHMQKHIKELGAKRDELKKLSNHS---NNMENNHEGLHTSCN-FTVHEKNGI 172

Query: 175 VGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
           +GIEI  +  + E++  +SK+L+ L +EGL VV+  ST V+ RLLH++Q E+N+
Sbjct: 173 MGIEI--TSVFREEKPKISKLLQFLTEEGLEVVSFFSTEVNGRLLHSVQCEVNH 224

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559901|ref|XP_003548234.1| PREDICTED: transcription factor bHLH126-like [Glycine max]

 Score =  186 bits (472), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 109/234 (46%), Positives = 155/234 (66%), Gaps = 18/234 (7%)

Query: 1   MFPLHSGDELFIKVS-SNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDK 59
           M PL  G+EL I+ S S  HQQ KI +DLI     + +S+  ND  +     S S  T K
Sbjct: 1   MLPLQRGNELVIQFSNSPHHQQHKISEDLI---LDDYASLNVNDSNQKFITSSSSQPTKK 57

Query: 60  IPSDNYNSNNSNYNNN---KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQ 116
           +    Y +N  N+++N   KK++H ++ER+RRQEMAT YASLR+LLPLEFIKGKRSISD 
Sbjct: 58  LF---YGANKKNHDSNEHKKKMIHMEIERKRRQEMATFYASLRSLLPLEFIKGKRSISDH 114

Query: 117 MNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQS--L 174
           MNE  NY+K+++  IKELG KRDE+K+LSN     + +E +     +  N F +H++  +
Sbjct: 115 MNEAANYIKHMQNNIKELGAKRDEMKKLSN---HCNNMENNHAGLHTSCN-FTIHENNGI 170

Query: 175 VGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
           +GIEI  + G+ E++  +SK+L+ L +EG  VV+C ST V+ RLLH++Q E+NN
Sbjct: 171 MGIEI--TSGFREEKPKISKLLQFLTEEGFEVVSCFSTEVNGRLLHSVQCEVNN 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455627|ref|XP_002271141.1| PREDICTED: transcription factor bHLH120 [Vitis vinifera] gi|296084088|emb|CBI24476.3| unnamed protein product [Vitis vinifera]

 Score =  183 bits (465), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 109/231 (47%), Positives = 149/231 (64%), Gaps = 19/231 (8%)

Query: 1   MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKI 60
           MFPLH G+EL  ++     +Q  I QD+I  HAS  +S ++N  GKS   + F+ +    
Sbjct: 1   MFPLHQGNELLFRIPYTPSKQYIIQQDMILDHASLEASNLSNHKGKSPNRKLFAQD---- 56

Query: 61  PSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEG 120
             +N   +N      KK++HRDVERQRRQ+MATLY SLR+LLPLE+IKGKR+IS+ MN  
Sbjct: 57  --NNDEISNDGKKKKKKIVHRDVERQRRQDMATLYTSLRSLLPLEYIKGKRAISEHMNGA 114

Query: 121 VNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFV-VHQSLVGIEI 179
           VNY+K+L+KKIKELG KR+ELK L+N S   S               FV V     G+EI
Sbjct: 115 VNYIKHLQKKIKELGEKRNELKSLANSSSRNSS------------GNFVTVCPCWGGVEI 162

Query: 180 AYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVV 230
             S G  ++ +PLS+ LE LL+EGL V++C+ST+V+ RLLHTI  E++++ 
Sbjct: 163 VVSSGGEKEGMPLSRALETLLEEGLSVISCISTKVNGRLLHTIHCEVSDIT 213

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363808366|ref|NP_001242511.1| uncharacterized protein LOC100775836 [Glycine max] gi|255641055|gb|ACU20807.1| unknown [Glycine max]

 Score =  182 bits (461), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 112/235 (47%), Positives = 154/235 (65%), Gaps = 19/235 (8%)

Query: 1   MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQS----FSME 56
           MFPL  G+EL I+ S+  H Q KI QDLI        S +     K  R       F  E
Sbjct: 1   MFPLQRGNELVIQFSNGHHPQHKISQDLILDDQDIDQSPLVGYSDKKLRTSRPKKLFYHE 60

Query: 57  TDKIPSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQ 116
            D   +      NSN    KK++HR++E+QRRQEMATL+ASLR+LLPL+FIKGKRSISDQ
Sbjct: 61  ADTCHA------NSNQEYTKKMVHREIEKQRRQEMATLHASLRSLLPLDFIKGKRSISDQ 114

Query: 117 MNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQ---S 173
           MNE V+Y+ +L+K IKEL  KRD+LK+  ++  S+ +   + ++ +S    F VHQ    
Sbjct: 115 MNEAVSYINHLQKNIKELSDKRDKLKKRPSIINSSPEDHENYKHASSG---FTVHQNSGG 171

Query: 174 LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
            VGIEI+   G+ E+E+PLSK+LE++ +EGL VVNC+ST+V+ RLLH++Q E++N
Sbjct: 172 AVGIEIS---GFSEEEVPLSKLLELVFEEGLEVVNCLSTKVNGRLLHSLQCEVDN 223

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217075046|gb|ACJ85883.1| unknown [Medicago truncatula] gi|388519135|gb|AFK47629.1| unknown [Medicago truncatula]

 Score =  180 bits (456), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 108/245 (44%), Positives = 156/245 (63%), Gaps = 32/245 (13%)

Query: 1   MFPLHSGDELFIKVSS--NSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETD 58
           MFPL   +EL   +S+  N HQ  KIP+DLI     +  S++ +   K        M+T+
Sbjct: 1   MFPLQRCNELAKPLSNSLNHHQHHKIPEDLI---LDDCDSLVIDFSLKK-------MDTN 50

Query: 59  KIPSD-------NYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKR 111
           + P+        N+ SN ++  + KK++HR++E+QRRQEMATL+ SLR+LLPL FIKGKR
Sbjct: 51  RPPNKLFYIDRANHGSNRNSIEDKKKMVHREIEKQRRQEMATLHTSLRSLLPLHFIKGKR 110

Query: 112 SISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLSI-SASQIETSDQNDTSPINRFVV 170
           S+SDQMNE VNY+ +L+K +KEL  KRDELK+LSN S+ + S +  S          F +
Sbjct: 111 SLSDQMNEAVNYINHLKKNMKELSYKRDELKKLSNPSLKNKSHVSCS----------FTI 160

Query: 171 HQS--LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
           H++   VGIEI+   G++E+  PLSK LE L+  GL VV+C S +V+ +LLH++Q E++ 
Sbjct: 161 HKNNRTVGIEISTKTGFIEEGAPLSKFLEQLMRYGLDVVSCFSIQVNGKLLHSVQCEVHI 220

Query: 229 VVPKF 233
           V   F
Sbjct: 221 VYIFF 225

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535931|ref|XP_003536495.1| PREDICTED: transcription factor bHLH118-like [Glycine max]

 Score =  179 bits (455), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 106/231 (45%), Positives = 148/231 (64%), Gaps = 10/231 (4%)

Query: 1   MFPLHSGDELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKI 60
           MFPL  G+EL I  S+  + Q KI QDLI    +   S       K  R           
Sbjct: 1   MFPLQRGNELVIHFSNGLYPQHKISQDLIRDDQNIDQSPHVGYSDKKWRTSRPKKLFYHE 60

Query: 61  PSDNYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEG 120
            +   ++N+SN    KK++HR++ERQRRQEMATL+ASLR+LLPL FIKGKRSISDQMNE 
Sbjct: 61  AAATSHANSSNQEYAKKMVHREIERQRRQEMATLHASLRSLLPLRFIKGKRSISDQMNEA 120

Query: 121 VNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQ---SLVGI 177
           VNY+ +L+K IKEL  KRD+LK+  +++ +    E      +     F +HQ     VGI
Sbjct: 121 VNYINHLQKNIKELSDKRDKLKKKPSINSTPEGHENCKHVSSG----FTIHQNSGGAVGI 176

Query: 178 EIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN 228
           EI+   G+ E+E+PLSK+L+++L+E L VV+C+ST+V+ RLLH++Q E++N
Sbjct: 177 EIS---GFSEEEVPLSKLLKLVLEERLEVVSCLSTKVNGRLLHSLQCEVDN 224

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357444221|ref|XP_003592388.1| Transcription factor bHLH36 [Medicago truncatula] gi|355481436|gb|AES62639.1| Transcription factor bHLH36 [Medicago truncatula]

 Score =  176 bits (446), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 106/244 (43%), Positives = 154/244 (63%), Gaps = 30/244 (12%)

Query: 1   MFPLHSGDELFIKVSS--NSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETD 58
           MFPL   +EL   +S+  N HQ  KI +DLI     +  S++ +   K        M+T+
Sbjct: 62  MFPLQRCNELAKPLSNSLNHHQHHKISEDLI---LDDCDSLVIDFSLKK-------MDTN 111

Query: 59  KIPSD-------NYNSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKR 111
           + P+        N+ SN ++  + KK++HR++E+QRRQEMATL+ SLR+LLPL FIKGKR
Sbjct: 112 RPPNKLFYIDRANHGSNRNSIEDKKKMVHREIEKQRRQEMATLHTSLRSLLPLHFIKGKR 171

Query: 112 SISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVH 171
           S+SDQMNE VNY+ +L+K +KEL  KRDELK+LSN S+         +N +     F +H
Sbjct: 172 SLSDQMNEAVNYINHLKKNMKELSYKRDELKKLSNPSL---------KNKSHVSCSFTIH 222

Query: 172 QS--LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV 229
           ++   VGIEI+   G++E+  PLSK LE L+  GL VV+C S +V+ +LLH++Q E++ V
Sbjct: 223 KNNRTVGIEISTKTGFIEEGAPLSKFLEQLMRYGLDVVSCFSIQVNGKLLHSVQCEVHIV 282

Query: 230 VPKF 233
              F
Sbjct: 283 YIFF 286

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539631|ref|XP_002510880.1| DNA binding protein, putative [Ricinus communis] gi|223549995|gb|EEF51482.1| DNA binding protein, putative [Ricinus communis]

 Score =  162 bits (411), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 93/174 (53%), Positives = 120/174 (68%), Gaps = 9/174 (5%)

Query: 62  SDNYNSNNSNYN-------NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSIS 114
           +DN N N+   N       + KK+MHRD+ERQRRQEMATL+ASLR+LLPLE+IKGKRSIS
Sbjct: 3   ADNNNKNDHGINTPSLITNDKKKMMHRDIERQRRQEMATLHASLRSLLPLEYIKGKRSIS 62

Query: 115 DQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSL 174
           D MNE VNY+K+L K+I+EL  KRDELK+  N+    S        D SP +  ++   L
Sbjct: 63  DHMNEAVNYIKHLRKRIEELDTKRDELKQQMNIRDIPSGSSGGSSGDCSPSSGVLIRPCL 122

Query: 175 VGIEIAYSCGYLE--QELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAEL 226
            GIEI++S    E  Q   LS+VL+VLL+  + VVNCVST V++R+LHTIQ E+
Sbjct: 123 GGIEISFSSNLREKGQGFTLSRVLQVLLEAEISVVNCVSTNVNKRVLHTIQTEV 176

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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	241
TAIR|locus:2165311	174	AT5G51780 "AT5G51780" [Arabido	0.659	0.913	0.540	3e-37
TAIR|locus:2138019	163	AT4G25400 "AT4G25400" [Arabido	0.605	0.895	0.480	1.3e-31
TAIR|locus:504956298	259	AT1G62975 "AT1G62975" [Arabido	0.709	0.660	0.363	3.1e-19
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.900	0.875	0.239	3.8e-11
TAIR|locus:2040287	242	BHLH100 "basic helix-loop-heli	0.630	0.628	0.284	3.9e-09
TAIR|locus:2146663	240	BHLH101 "AT5G04150" [Arabidops	0.755	0.758	0.281	1.3e-08
TAIR|locus:2080600	253	bHLH38 "basic helix-loop-helix	0.622	0.592	0.268	3.2e-08
TAIR|locus:2080615	258	bHLH39 "basic helix-loop-helix	0.626	0.585	0.270	1.6e-06
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.593	0.752	0.240	2e-06

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

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 87/161 (54%), Positives = 115/161 (71%)

Query:    76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
             +K+MHR+ ERQRRQEMA+LYASLR+LLPL FIKGKRS SDQ+NE VNY+KYL++KIKEL 
Sbjct:     2 EKMMHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKELS 61

Query:   136 VKRDELKRLSNLSI--SASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLS 193
             V+RD+L  LS  S+  S++     D    S  N  VV Q LVG+EI  S      +   S
Sbjct:    62 VRRDDLMVLSRGSLLGSSNGDFKEDVEMISGKNHVVVRQCLVGVEIMLSSRCCGGQPRFS 121

Query:   194 KVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPKFD 234
              VL+VL + GLC++N +S+ VD+RL++TIQAE+N++    D
Sbjct:   122 SVLQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMID 162

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

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 74/154 (48%), Positives = 109/154 (70%)

Query:    76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
             +KL+H+++E++RRQEMA+LYASLR+LLPLEFI+GKRS SDQ+   VNY+ YL++ IK++ 
Sbjct:     2 EKLVHKEIEKRRRQEMASLYASLRSLLPLEFIQGKRSTSDQVKGAVNYIDYLQRNIKDIN 61

Query:   136 VKRDELKRLSNLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKV 195
              KRD+L  LS  S  +S  +  + N+ S  N  V+   LVGIEI  S      + P S V
Sbjct:    62 SKRDDLVLLSGRSFRSSNEQ--EWNEIS--NHVVIRPCLVGIEIVLSI----LQTPFSSV 113

Query:   196 LEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV 229
             L+VL + GL V+  + + V++RL+HT+QAE+N++
Sbjct:   114 LQVLREHGLYVLGYICSSVNDRLIHTLQAEVNDL 147

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

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 69/190 (36%), Positives = 102/190 (53%)

Query:    29 ISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDXXXXXXXXXXXXKKLMHRDVERQRR 88
             IS   ++    ITN +G S++ +S     D                 KK+ HRD+ERQRR
Sbjct:    30 ISYQNNDVFHSITNKIGGSNKKRSLC---DITYGANEANKNDDDRESKKMKHRDIERQRR 86

Query:    89 QEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR-LSNL 147
             QE+++L+  LR LLP ++I+GKRS SD + + VNY+K L+ KIKEL  KR+ +K+ +S  
Sbjct:    87 QEVSSLFKRLRTLLPFQYIQGKRSTSDHIVQAVNYIKDLQIKIKELNEKRNRVKKVISAT 146

Query:   148 SISASQIE--TSDQNDT--SPINR-----------FVVHQSLVGIEIAYSCGYLEQELPL 192
             + + S IE  TS  + +  S ++             VV   LVG+EI  SC     +  L
Sbjct:   147 TTTHSAIEECTSSLSSSAASTLSSSCSCVGDKHITVVVTPCLVGVEIIISCCLGRNKSCL 206

Query:   193 SKVLEVLLDE 202
             S VL++L  E
Sbjct:   207 SSVLQMLAQE 216

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

 Score = 162 (62.1 bits), Expect = 3.8e-11, P = 3.8e-11
 Identities = 53/221 (23%), Positives = 100/221 (45%)

Query:     8 DELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDXXXX 67
             ++LF+   + +     +  D+ SG A +  S    D+      Q  SM      +     
Sbjct:     2 EQLFVDDPAFASSMSSLEADIFSG-AGQLPSSPWLDLDLDDDVQDLSMAPTTANAVSSGY 60

Query:    68 XXXXXXXXKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYL 127
                     +KL H   ER RR+++  LY+SLRALLP      K SI   ++  + Y+  L
Sbjct:    61 GSGGSGSHRKLSHNAYERDRRKQLNELYSSLRALLPDADHTKKLSIPTTVSRVLKYIPEL 120

Query:   128 EKKIKELGVKRDELKRLSNLSISASQIETSDQND-TSPI-NRFVVHQSLVGIEIAYSCGY 185
             +K+++ L  K+ EL   S  +     + +   ++  +PI +   ++   + ++++     
Sbjct:   121 QKQVENLERKKKELTTTSTTNCKPGVLGSQLMSEGMAPIVSATCINDMEIMVQVSLLSNV 180

Query:   186 LEQELPLSKVLEVLLDEGLCVVNC-VSTRVDERLLHTIQAE 225
                 LPLSK ++VL +EGL  ++   S+    R  ++I  +
Sbjct:   181 AGSVLPLSKCIKVLENEGLHFISSSTSSGFGNRTFYSIHLQ 221

GO:0005634 "nucleus" evidence=IC

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

 Score = 149 (57.5 bits), Expect = 3.9e-09, P = 3.9e-09
 Identities = 45/158 (28%), Positives = 84/158 (53%)

Query:    76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
             KKL H   ER+RR+++ T+++SLR+ LP      K S+S  +++ + Y+  L++++K+L 
Sbjct:    62 KKLNHNASERERRKKINTMFSSLRSCLPPTNQTKKLSVSATVSQALKYIPELQEQVKKLM 121

Query:   136 VKRDELK-RLSNLS--ISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQE-LP 191
              K++EL  ++S     +   Q   S++  TS  +  V    L   E+      L+ E   
Sbjct:   122 KKKEELSFQISGQRDLVYTDQNSKSEEGVTSYAST-VSSTRLSETEVMVQISSLQTEKCS 180

Query:   192 LSKVLEVLLDEGLCVVNCVSTRVD-ERLLHTIQAELNN 228
                VL  + ++GL +V   S+R   ERL +++  ++ N
Sbjct:   181 FGNVLSGVEEDGLVLVGASSSRSHGERLFYSMHLQIKN 218

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

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

 Score = 145 (56.1 bits), Expect = 1.3e-08, P = 1.3e-08
 Identities = 54/192 (28%), Positives = 92/192 (47%)

Query:    41 TNDMGKSHRGQSFSMETDKIPSDXXXXXXXXXXXXKKLMHRDVERQRRQEMATLYASLRA 100
             ++++   H   S S  T+   ++            KKL H   ER RR+++  LY+SLRA
Sbjct:    31 SHNINLHHMSLSHSNNTNSNNNNYQEEDRGAVVLEKKLNHNASERDRRRKLNALYSSLRA 90

Query:   101 LLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDEL-KRLSNLSISASQIETS-- 157
             LLPL   K K SI   +   V Y+   +++++ L  +++EL KR+S  +    Q+     
Sbjct:    91 LLPLSDQKRKLSIPMTVARVVKYIPEQKQELQRLSRRKEELLKRISRKT-HQEQLRNKAM 149

Query:   158 -DQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDE 216
              D  D+S   R   +  L   EIA       +   +S +L  L + GL V++ VS+ V  
Sbjct:   150 MDSIDSSSSQRIAANW-LTDTEIAVQIA-TSKWTSVSDMLLRLEENGLNVIS-VSSSVSS 206

Query:   217 --RLLHTIQAEL 226
               R+ +T+  ++
Sbjct:   207 TARIFYTLHLQM 218

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0055072 "iron ion homeostasis" evidence=IGI

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

 Score = 143 (55.4 bits), Expect = 3.2e-08, P = 3.2e-08
 Identities = 43/160 (26%), Positives = 84/160 (52%)

Query:    76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
             KKL H   ER RR+++ TL++SLR+ LP      K SI + +++ + Y+  L++++K L 
Sbjct:    72 KKLNHNASERDRRKKINTLFSSLRSCLPASDQSKKLSIPETVSKSLKYIPELQQQVKRLI 131

Query:   136 VKRDELKRLSNLSISASQIETSDQNDTSPINRFV--VHQSLVG---IEIAYSCGYLEQEL 190
              K++E+  L  +S      E  D+     +  ++  V  + +G   + +  S   +    
Sbjct:   132 QKKEEI--LVRVS-GQRDFELYDKQQPKAVASYLSTVSATRLGDNEVMVQVSSSKIHN-F 187

Query:   191 PLSKVLEVLLDEGLCVVNCVSTRVD-ERLLHTIQAELNNV 229
              +S VL  + ++G  +V+  S+R   ERL +T+  ++ N+
Sbjct:   188 SISNVLGGIEEDGFVLVDVSSSRSQGERLFYTLHLQVENM 227

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

 Score = 130 (50.8 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 43/159 (27%), Positives = 83/159 (52%)

Query:    76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
             KKL H   ER RR+++ +L++SLR+ LP      K SI   ++  + Y+  L++++K+L 
Sbjct:    77 KKLNHNASERDRRRKINSLFSSLRSCLPASGQSKKLSIPATVSRSLKYIPELQEQVKKLI 136

Query:   136 VKRDELK-RLS---NLSISASQIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELP 191
              K++EL  ++S   N      Q   +  N  S ++   +  + V ++I+ S  +      
Sbjct:   137 KKKEELLVQISGQRNTECYVKQPPKAVANYISTVSATRLGDNEVMVQISSSKIH---NFS 193

Query:   192 LSKVLEVLLDEGLCVVNCVSTRVD-ERLLHTIQAELNNV 229
             +S VL  L ++   +V+  S+R   ERL +T+  ++  +
Sbjct:   194 ISNVLSGLEEDRFVLVDMSSSRSQGERLFYTLHLQVEKI 232

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

 Score = 124 (48.7 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 37/154 (24%), Positives = 79/154 (51%)

Query:    81 RDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDE 140
             + VE+ RR +M +LY+ L +LLP        ++ DQ++E  NY+K L+  +++   ++  
Sbjct:    17 KTVEKNRRMQMKSLYSELISLLPHHSSTEPLTLPDQLDEAANYIKKLQVNVEKKRERKRN 76

Query:   141 LKRLSNL----SISASQIETS-DQNDTSPINRFVVHQ--SLVGIEIAYSCGYLEQELPLS 193
             L   + L    S+ +S + +S D +    + +  + +  S+  I +  S   LE +    
Sbjct:    77 LVATTTLEKLNSVGSSSVSSSVDVSVPRKLPKIEIQETGSIFHIFLVTS---LEHKFMFC 133

Query:   194 KVLEVLLDE-GLCVVNCVSTRVDERLLHTIQAEL 226
             +++ VL +E G  + +   + VD+ + HT+  ++
Sbjct:   134 EIIRVLTEELGAEITHAGYSIVDDAVFHTLHCKV 167


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.132   0.363    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      241       229   0.00082  113 3  11 22  0.43    33
                                                     32  0.42    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  584 (62 KB)
  Total size of DFA:  157 KB (2094 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.55u 0.15s 22.70t   Elapsed:  00:00:01
  Total cpu time:  22.55u 0.15s 22.70t   Elapsed:  00:00:01
  Start:  Sat May 11 14:39:46 2013   End:  Sat May 11 14:39:47 2013

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FLI1	BH036_ARATH	No assigned EC number	0.5403	0.6597	0.9137	yes	no

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	241
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-06
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-06

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

 Score = 43.6 bits (104), Expect = 2e-06
 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLE 128
           ++  H + ER+RR  +   +  LR LLP      K S ++ +   + Y+K+L+
Sbjct: 1   RRKAHNERERRRRDRINDAFEELRELLP-TPPNKKLSKAEILRLAIEYIKHLQ 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 = 43.7 bits (104), Expect = 2e-06
 Identities = 16/58 (27%), Positives = 34/58 (58%)

Query: 75  NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK 132
           +++  H   ER+RR+ +   +  LR+LLP      K S ++ + + V+Y+K L++ ++
Sbjct: 3   SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	241
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.35
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.33
smart00353	53	HLH helix loop helix domain.	99.29
KOG1318	411	consensus Helix loop helix transcription factor EB	98.59
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.26
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.09
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.02
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.88
PLN03217	93	transcription factor ATBS1; Provisional	97.68
KOG4304	250	consensus Transcriptional repressors of the hairy/	97.58
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.11
KOG0561	373	consensus bHLH transcription factor [Transcription	97.04
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	96.71
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	96.56
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	96.52
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	96.37
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	96.18
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	96.07
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	95.7
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	95.04
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	94.85
KOG3910	632	consensus Helix loop helix transcription factor [T	94.85
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.84
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	94.55
KOG3898	254	consensus Transcription factor NeuroD and related	93.57
KOG4395	285	consensus Transcription factor Atonal, contains HT	92.11
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	92.09
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	90.95
PRK00275	895	glnD PII uridylyl-transferase; Provisional	90.81
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	90.31
PRK05007	884	PII uridylyl-transferase; Provisional	90.07
PRK04374	869	PII uridylyl-transferase; Provisional	88.29
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	88.19
PRK03059	856	PII uridylyl-transferase; Provisional	87.59
PRK03381	774	PII uridylyl-transferase; Provisional	87.24
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	87.11
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	86.97
PRK01759	854	glnD PII uridylyl-transferase; Provisional	86.93
PRK03381	774	PII uridylyl-transferase; Provisional	86.82
PRK01759	854	glnD PII uridylyl-transferase; Provisional	86.45
PRK03059	856	PII uridylyl-transferase; Provisional	85.91
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	85.84
PRK05092	931	PII uridylyl-transferase; Provisional	85.36
PRK00275	895	glnD PII uridylyl-transferase; Provisional	85.11
PRK05007	884	PII uridylyl-transferase; Provisional	84.62
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	84.28
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	84.11
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	83.53
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	81.53
PRK04374	869	PII uridylyl-transferase; Provisional	80.98
PRK05092	931	PII uridylyl-transferase; Provisional	80.81
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	80.24
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	80.2

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

Probab=99.35  E-value=1.3e-12  Score=91.03  Aligned_cols=53  Identities=28%  Similarity=0.481  Sum_probs=47.7

Q ss_pred             ccccchHHHHHHHHHHHHhHHHHHccCCCC--CcCCCCchhhhHHHHHHHHHHHH
Q 036406           76 KKLMHRDVERQRRQEMATLYASLRALLPLE--FIKGKRSISDQMNEGVNYVKYLE  128 (241)
Q Consensus        76 ~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~--~~~~K~Si~~~l~eAI~YIk~Lq  128 (241)
                      +|..|+..||+||..||..|..|+.+||..  ....|.+..++|..||+||++||
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            467899999999999999999999999995  24567888888999999999997

; 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=99.33  E-value=2.7e-12  Score=89.83  Aligned_cols=58  Identities=28%  Similarity=0.455  Sum_probs=50.1

Q ss_pred             cccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 036406           75 NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        75 ~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      .++..|+..||+||.+||..|..|+++||......|.+.+.+|..||+||+.|+.+++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            4678899999999999999999999999998544455556669999999999998763

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=99.29  E-value=7.6e-12  Score=85.98  Aligned_cols=52  Identities=27%  Similarity=0.466  Sum_probs=44.2

Q ss_pred             hHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 036406           81 RDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        81 ~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      +..||+||.+||..|..|+++||......|.+.+.+|..||+||++|+++++
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            4689999999999999999999975534455555669999999999999876

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

Probab=98.59  E-value=9.4e-08  Score=91.34  Aligned_cols=64  Identities=20%  Similarity=0.364  Sum_probs=52.6

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCC-CCchhhhHHHHHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKG-KRSISDQMNEGVNYVKYLEKKIKELG  135 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~-K~Si~~~l~eAI~YIk~Lq~~v~~L~  135 (241)
                      ....||..||++||+||..||++.-.|.-|||.....+ |..+..+|..+++||++||+..++..
T Consensus       229 rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~  293 (411)
T KOG1318|consen  229 RDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR  293 (411)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence            34688999999999999999999999999999864322 34444459999999999999887444

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

Probab=98.26  E-value=1e-06  Score=78.03  Aligned_cols=67  Identities=28%  Similarity=0.392  Sum_probs=59.4

Q ss_pred             CCcccccccchHHHHHHHHHHHHhHHHHHccCCCCCc-CCCCchhhhHHHHHHHHHHHHHHHHHHHHH
Q 036406           71 NYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFI-KGKRSISDQMNEGVNYVKYLEKKIKELGVK  137 (241)
Q Consensus        71 ~~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~-~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~  137 (241)
                      ......+..+|+.||+|-+.+|..|..||.+||.... ..|.|+.++|..||.||+.|+.-++.-+..
T Consensus       104 ~~~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  104 SQTSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             cchhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            3456788889999999999999999999999999887 778999999999999999999888766633

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

Probab=98.09  E-value=1.1e-05  Score=72.31  Aligned_cols=70  Identities=17%  Similarity=0.315  Sum_probs=56.8

Q ss_pred             cccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 036406           73 NNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELK  142 (241)
Q Consensus        73 ~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~  142 (241)
                      ....+..||+-||+||-+++..|..|+.+||...-..+-....+|+.|..||+.|+....+.+...+++.
T Consensus        56 ~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~  125 (232)
T KOG2483|consen   56 AASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLS  125 (232)
T ss_pred             CCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHH
Confidence            4577889999999999999999999999999865443322456699999999999988877776655544

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.02  E-value=1.2e-05  Score=69.92  Aligned_cols=69  Identities=22%  Similarity=0.400  Sum_probs=58.4

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCC----CCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKG----KRSISDQMNEGVNYVKYLEKKIKELGVKRDELK  142 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~----K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~  142 (241)
                      +-+|..|-.+||+||.-+|.-|..|..|||.....+    |.|..-+|-.||+||.+|..+..+-+++...|.
T Consensus        60 ~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~  132 (229)
T KOG1319|consen   60 DRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR  132 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356899999999999999999999999999766555    777777899999999999988877776655543

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

Probab=97.88  E-value=1.1e-05  Score=82.93  Aligned_cols=58  Identities=16%  Similarity=0.378  Sum_probs=50.4

Q ss_pred             CCCcccccccchHHHHHHHHHHHHhHHHHHccCCCCC----cCCCCchhhhHHHHHHHHHHHHHH
Q 036406           70 SNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEF----IKGKRSISDQMNEGVNYVKYLEKK  130 (241)
Q Consensus        70 ~~~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~----~~~K~Si~~~l~eAI~YIk~Lq~~  130 (241)
                      +++...+|..|+.+||+||.+||.+...|.+|||...    |+||.+|   |..||.+|+.+++.
T Consensus        14 d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tV---Lr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   14 DSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTV---LRMAVDHLRLIKEQ   75 (803)
T ss_pred             cchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHH---HHHHHHHHHHHhhh
Confidence            3556677999999999999999999999999999765    5566666   99999999999885

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.68  E-value=9.7e-05  Score=56.74  Aligned_cols=57  Identities=23%  Similarity=0.348  Sum_probs=50.2

Q ss_pred             HHHHHHhHHHHHccCCCCCc---CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 036406           88 RQEMATLYASLRALLPLEFI---KGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRL  144 (241)
Q Consensus        88 R~~mn~~f~~LrsLlP~~~~---~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~~  144 (241)
                      -.+|+++...|+.|||....   .+|+|.+.+|.|+-+||+.|+.+|..|.++..+|...
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            36899999999999998643   3588889999999999999999999999999888654

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

Probab=97.58  E-value=3.8e-05  Score=69.54  Aligned_cols=62  Identities=21%  Similarity=0.318  Sum_probs=52.4

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCC-----CCchhhhHHHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKG-----KRSISDQMNEGVNYVKYLEKKIKE  133 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~-----K~Si~~~l~eAI~YIk~Lq~~v~~  133 (241)
                      ....+|..|-..||+||-+||+.+..|+.|||...+++     |.-+.|||.-|++|++.|+.....
T Consensus        28 ~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   28 TRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            34688999999999999999999999999999877663     455567799999999999876543

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

Probab=97.11  E-value=0.0013  Score=59.66  Aligned_cols=68  Identities=12%  Similarity=0.204  Sum_probs=54.2

Q ss_pred             cccccccchHHHHHHHHHHHHhHHHHHcc-CCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 036406           73 NNNKKLMHRDVERQRRQEMATLYASLRAL-LPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELK  142 (241)
Q Consensus        73 ~~~~k~~H~~~ER~RR~~mn~~f~~LrsL-lP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~  142 (241)
                      ...+|..--+.||+|=+|+|+.|.+|.-- .++..  -+..+++||.-||.||..||+-++++......+.
T Consensus       115 svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPN--QRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~~  183 (284)
T KOG3960|consen  115 SVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPN--QRLPKVEILRSAIRYIERLQALLQEQDQAEKGLA  183 (284)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc--ccccHHHHHHHHHHHHHHHHHHHHHhhccchhhh
Confidence            45677777899999999999999999644 44433  2555678899999999999999999987666553

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.04  E-value=0.00033  Score=64.99  Aligned_cols=60  Identities=30%  Similarity=0.351  Sum_probs=49.6

Q ss_pred             cccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHH
Q 036406           75 NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG  135 (241)
Q Consensus        75 ~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~  135 (241)
                      .+|..-|--||+|=+-+|.-|.+||+|||.... .|.|+..+|-.+.+||.+|+..--+|-
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~eG-EKLSKAAILQQTa~yI~~Le~~Kt~ll  118 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKEG-EKLSKAAILQQTADYIHQLEGHKTELL  118 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCcccc-hhhHHHHHHHHHHHHHHHHHhcccccc
Confidence            556666778999999999999999999998543 477777779999999999987665554

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

Probab=96.71  E-value=0.009  Score=44.41  Aligned_cols=43  Identities=14%  Similarity=0.158  Sum_probs=39.4

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      +++|+|.+|..+|.++||+|..|-+++.|+++.-+|.+.=.++
T Consensus        10 DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g   52 (72)
T cd04895          10 RKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLG   52 (72)
T ss_pred             CcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCC
Confidence            5899999999999999999999999999999999999875443

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.

>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=96.56  E-value=0.017  Score=41.88  Aligned_cols=48  Identities=15%  Similarity=0.083  Sum_probs=39.7

Q ss_pred             EEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEec
Q 036406          178 EIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRV-DERLLHTIQAELN  227 (241)
Q Consensus       178 eI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~-~~~vl~tI~akv~  227 (241)
                      +|.+.+.  +++++|+++..+|..+|++|++|.+.+. +|.++-+|...-.
T Consensus         3 ~i~v~~~--Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~   51 (73)
T cd04900           3 EVFIYTP--DRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDP   51 (73)
T ss_pred             EEEEEec--CCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECC
Confidence            4444443  5899999999999999999999999776 7999999998643

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.

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=96.52  E-value=0.0013  Score=68.49  Aligned_cols=66  Identities=20%  Similarity=0.322  Sum_probs=54.9

Q ss_pred             cccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 036406           75 NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELK  142 (241)
Q Consensus        75 ~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~  142 (241)
                      .+|.+||.+||+-|.-+|+....|+.+||....+-  ..+..|..||+||++|+...+.|......+.
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl--~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKL--NKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhh--hhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            67999999999999999999999999999765432  2345599999999999998888776655544

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

Probab=96.37  E-value=0.029  Score=42.05  Aligned_cols=45  Identities=11%  Similarity=0.005  Sum_probs=41.1

Q ss_pred             CCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCCc
Q 036406          186 LEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVV  230 (241)
Q Consensus       186 ~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~~  230 (241)
                      .+++++|.+|..+|-++|++|.+|.+++.|+++.-+|...-.++.
T Consensus         9 ~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~   53 (75)
T cd04897           9 RDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGR   53 (75)
T ss_pred             CCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCC
Confidence            369999999999999999999999999999999999998776654

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.

>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=96.18  E-value=0.037  Score=40.82  Aligned_cols=40  Identities=23%  Similarity=0.202  Sum_probs=36.9

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEe
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTR-VDERLLHTIQAEL  226 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~-~~~~vl~tI~akv  226 (241)
                      +++++|+++..+|..+||+|++|.+++ .+|.++.+|.+.=
T Consensus         9 Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d   49 (76)
T cd04927           9 DRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITD   49 (76)
T ss_pred             CCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeC
Confidence            588999999999999999999999986 8999999999863

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

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

Probab=96.07  E-value=0.047  Score=39.61  Aligned_cols=50  Identities=16%  Similarity=0.192  Sum_probs=40.4

Q ss_pred             EEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 036406          177 IEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN  228 (241)
Q Consensus       177 veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~  228 (241)
                      .+|.+.+.  +++++|.++..+|.++|++|+++.+.+.++.++.+|+..-.+
T Consensus         2 tri~V~~~--D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~~~   51 (72)
T cd04926           2 VRLELRTE--DRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTDAN   51 (72)
T ss_pred             eEEEEEEC--CccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEECCC
Confidence            34555442  588999999999999999999999988888888888876433

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

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

Probab=95.70  E-value=0.056  Score=40.50  Aligned_cols=39  Identities=13%  Similarity=0.012  Sum_probs=37.0

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEe--eeCCeEEEEEEEE
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVST--RVDERLLHTIQAE  225 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S--~~~~~vl~tI~ak  225 (241)
                      +++|+|.+|..+|..+|++|.+|-++  +.|+++.-+|...
T Consensus         9 DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~   49 (75)
T cd04896           9 DQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQ   49 (75)
T ss_pred             CcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEe
Confidence            58999999999999999999999999  9999999999983

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.

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

Probab=95.04  E-value=0.17  Score=36.93  Aligned_cols=40  Identities=28%  Similarity=0.179  Sum_probs=37.2

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAEL  226 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv  226 (241)
                      +++++|.+|..+|..+|+.|++|.+++.++.++.+|.+.-
T Consensus         9 Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d   48 (74)
T cd04925           9 DRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRD   48 (74)
T ss_pred             CCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEc
Confidence            5899999999999999999999999999999999998764

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.

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

Probab=94.85  E-value=0.21  Score=36.78  Aligned_cols=49  Identities=22%  Similarity=0.243  Sum_probs=40.3

Q ss_pred             EEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEecC
Q 036406          178 EIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTR-VDERLLHTIQAELNN  228 (241)
Q Consensus       178 eI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~-~~~~vl~tI~akv~~  228 (241)
                      +|.+.+.  +++++|.++..+|..+||.|++|.+.+ .+|.++-+|.+.=.+
T Consensus         3 eI~V~~~--Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~   52 (68)
T cd04928           3 EITFAAG--DKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWK   52 (68)
T ss_pred             EEEEEEC--CCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCC
Confidence            5665553  589999999999999999999998865 788898888887443

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=94.85  E-value=0.017  Score=56.86  Aligned_cols=64  Identities=16%  Similarity=0.319  Sum_probs=49.3

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCC-CchhhhHHHHHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGK-RSISDQMNEGVNYVKYLEKKIKELG  135 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K-~Si~~~l~eAI~YIk~Lq~~v~~L~  135 (241)
                      +..++|+..|+.||-|-+.||+.|..|....=.--+.+| .++.-||..||.-|-.|+++|.+-.
T Consensus       522 REkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN  586 (632)
T KOG3910|consen  522 REKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN  586 (632)
T ss_pred             HHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence            456899999999999999999999999876532222222 2333449999999999999998643

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.84  E-value=0.015  Score=49.38  Aligned_cols=59  Identities=24%  Similarity=0.375  Sum_probs=51.4

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKI  131 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v  131 (241)
                      +-..++..|+..||+|-+-+|+.|..||-.+|-. +-+|.|...+|.-|.-||.-|-.-+
T Consensus        74 E~q~qrv~anvrerqRtqsLn~AF~~lr~iiptl-PsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   74 ELQKQRVMANVRERQRTQSLNEAFAALRKIIPTL-PSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCC-CccccccccchhhcccCCchhhhcc
Confidence            3456899999999999999999999999999985 4578998899999999998886543

>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=94.55  E-value=0.36  Score=33.73  Aligned_cols=44  Identities=18%  Similarity=0.142  Sum_probs=39.2

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCCc
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVV  230 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~~  230 (241)
                      +++++|.+++.+|.++|+.|+++.+.+.++.++.+|++.-.++.
T Consensus         9 d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~   52 (70)
T cd04899           9 DRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQ   52 (70)
T ss_pred             CCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCC
Confidence            48899999999999999999999999988888899998876553

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.

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

Probab=93.57  E-value=0.042  Score=49.88  Aligned_cols=58  Identities=21%  Similarity=0.298  Sum_probs=50.4

Q ss_pred             cccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHH
Q 036406           73 NNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKK  130 (241)
Q Consensus        73 ~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~  130 (241)
                      ...+|..=|..||+|=-.+|+.|..||.++|......|.|+.++|.-|-+||..|++-
T Consensus        69 ~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   69 LTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            3467777889999999999999999999999855566889899999999999998764

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

Probab=92.11  E-value=0.27  Score=44.94  Aligned_cols=59  Identities=19%  Similarity=0.262  Sum_probs=52.9

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      ..++..-+..||+|=..+|..|..||-.+|......|.|.-++|--|-.||--|-..++
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            36778889999999999999999999999999998899999999999999988766553

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

Probab=92.09  E-value=1.6  Score=30.04  Aligned_cols=43  Identities=21%  Similarity=0.232  Sum_probs=36.4

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      ++++.|.++..+|.++|+.|.++.+.+.++.....|++.-.+.
T Consensus         9 d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~~   51 (70)
T cd04873           9 DRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSDG   51 (70)
T ss_pred             CCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCCC
Confidence            4788999999999999999999999887777777777765543

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

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

Probab=90.95  E-value=2.4  Score=30.69  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=37.2

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEee--eCCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTR--VDERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~--~~~~vl~tI~akv~~~  229 (241)
                      +++++|.+|..+|.+.|+.+.+++...  .++.....|.++|.+.
T Consensus        15 dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~   59 (80)
T PF13291_consen   15 DRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDL   59 (80)
T ss_dssp             --TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSH
T ss_pred             cCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCH
Confidence            478999999999999999999999988  4778888999999764

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=90.81  E-value=1.4  Score=46.68  Aligned_cols=51  Identities=12%  Similarity=0.103  Sum_probs=43.0

Q ss_pred             EEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          177 IEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       177 veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      .+|.+.+ . +++++|++|..+|..+||+|++|.|++.|++++-+|.+.-.++
T Consensus       815 T~i~V~a-~-DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g  865 (895)
T PRK00275        815 TVLEIIA-P-DRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADN  865 (895)
T ss_pred             EEEEEEE-C-CCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCC
Confidence            3444444 3 5899999999999999999999999999999999999975544

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

Probab=90.31  E-value=2  Score=31.25  Aligned_cols=41  Identities=12%  Similarity=0.169  Sum_probs=36.3

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELN  227 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~  227 (241)
                      ++++.+..+..+|.++|.+++++..+..++.+...+.+.+.
T Consensus        11 DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~   51 (76)
T PF13740_consen   11 DRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP   51 (76)
T ss_dssp             --TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES
T ss_pred             CCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC
Confidence            58999999999999999999999999999999999888876

>PRK05007 PII uridylyl-transferase; Provisional

Probab=90.07  E-value=0.93  Score=47.85  Aligned_cols=42  Identities=19%  Similarity=0.230  Sum_probs=38.8

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN  228 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~  228 (241)
                      +++|+|++|..+|.++|++|.+|-|++.|+++.-+|.+.-.+
T Consensus       817 DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~~  858 (884)
T PRK05007        817 DQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATAD  858 (884)
T ss_pred             CchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcCC
Confidence            589999999999999999999999999999999999986443

>PRK04374 PII uridylyl-transferase; Provisional

Probab=88.29  E-value=2.2  Score=45.18  Aligned_cols=62  Identities=19%  Similarity=0.088  Sum_probs=46.8

Q ss_pred             CceEEEeee--ceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          166 NRFVVHQSL--VGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       166 ~~V~V~~~~--~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      +.|.+....  .-..|.+.+ . +++++|++|..+|..+|++|++|.|++.|+++.-+|.+.-.++
T Consensus       784 ~~V~~~~~~~~~~t~leI~a-~-DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g  847 (869)
T PRK04374        784 PRVEFSESAGGRRTRISLVA-P-DRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHD  847 (869)
T ss_pred             CeEEEeecCCCCeEEEEEEe-C-CcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCC
Confidence            345554332  223444443 3 5899999999999999999999999999999999999975443

>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=88.19  E-value=5.2  Score=26.99  Aligned_cols=30  Identities=20%  Similarity=0.306  Sum_probs=27.8

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDE  216 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~  216 (241)
                      .++|.|.++..+|.++|+.|.++.....++
T Consensus         9 drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    9 DRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             TSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             CCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            589999999999999999999999988776

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

>PRK03059 PII uridylyl-transferase; Provisional

Probab=87.59  E-value=2.9  Score=44.09  Aligned_cols=46  Identities=17%  Similarity=0.160  Sum_probs=40.1

Q ss_pred             EEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEE
Q 036406          177 IEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQA  224 (241)
Q Consensus       177 veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~a  224 (241)
                      .+|.+.+ . +++++|++|..+|..+|++|++|.+++.|++++-+|.+
T Consensus       787 T~i~V~a-~-DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V  832 (856)
T PRK03059        787 YILSVSA-N-DRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI  832 (856)
T ss_pred             EEEEEEe-C-CcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            3455444 3 58999999999999999999999999999999999998

>PRK03381 PII uridylyl-transferase; Provisional

Probab=87.24  E-value=2.4  Score=44.20  Aligned_cols=52  Identities=17%  Similarity=0.034  Sum_probs=44.4

Q ss_pred             eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 036406          174 LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELN  227 (241)
Q Consensus       174 ~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~  227 (241)
                      ....+|.+.|.  +++++|++|..+|..+|++|++|.+.+.+|.++-+|.+.-.
T Consensus       597 ~~~~~V~V~~~--DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~  648 (774)
T PRK03381        597 PHMVEVTVVAP--DRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPR  648 (774)
T ss_pred             CCeEEEEEEec--CCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECC
Confidence            35677877653  59999999999999999999999999989999999888743

>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=87.11  E-value=3.5  Score=29.02  Aligned_cols=43  Identities=9%  Similarity=0.019  Sum_probs=36.2

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRV-DERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~-~~~vl~tI~akv~~~  229 (241)
                      ++++.|.+|..+|.++|..|.+++.... ++.....|.+++.+.
T Consensus         8 d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~   51 (74)
T cd04887           8 NRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSE   51 (74)
T ss_pred             CCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCH
Confidence            4788999999999999999999998775 466777788887664

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

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

Probab=86.97  E-value=3.6  Score=27.96  Aligned_cols=42  Identities=17%  Similarity=0.258  Sum_probs=33.5

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeee-----CCeEEEEEEEEecC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRV-----DERLLHTIQAELNN  228 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~-----~~~vl~tI~akv~~  228 (241)
                      ++++.|.+|+.+|.+.|++|.+......     ++.....|.+.+.+
T Consensus         7 d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~   53 (73)
T cd04886           7 DRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRG   53 (73)
T ss_pred             CCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCC
Confidence            4788999999999999999998887654     35566667777654

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.

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=86.93  E-value=3.6  Score=43.40  Aligned_cols=62  Identities=18%  Similarity=0.126  Sum_probs=47.8

Q ss_pred             CceEEEee--eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEecCC
Q 036406          166 NRFVVHQS--LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTR-VDERLLHTIQAELNNV  229 (241)
Q Consensus       166 ~~V~V~~~--~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~-~~~~vl~tI~akv~~~  229 (241)
                      |.|.+...  ....+|.+.+.  +++++|++|..+|..+||+|++|.+.+ .+|.++-+|.+.-.++
T Consensus       665 ~~V~i~~~~~~~~t~V~V~~~--DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g  729 (854)
T PRK01759        665 LLVKISNRFSRGGTEIFIYCQ--DQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNG  729 (854)
T ss_pred             CEEEEEecCCCCeEEEEEEec--CCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCC
Confidence            44555433  34456666553  589999999999999999999999866 8999999999875544

>PRK03381 PII uridylyl-transferase; Provisional

Probab=86.82  E-value=3.3  Score=43.14  Aligned_cols=51  Identities=8%  Similarity=0.013  Sum_probs=42.7

Q ss_pred             EEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          177 IEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       177 veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      ..|.+.+ . +++++|.+|..+|.++|++|++|.+++.|++++-+|.+.=.++
T Consensus       708 t~i~V~a-~-DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g  758 (774)
T PRK03381        708 TVLEVRA-A-DRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAG  758 (774)
T ss_pred             EEEEEEe-C-CchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCC
Confidence            3444443 3 5899999999999999999999999999999999999875444

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=86.45  E-value=2.1  Score=45.05  Aligned_cols=43  Identities=16%  Similarity=0.128  Sum_probs=39.1

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      +++|+|.+|..+|.++|++|.+|-|+|.|+++.-+|.+.-.++
T Consensus       792 DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g  834 (854)
T PRK01759        792 DRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQG  834 (854)
T ss_pred             CchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCC
Confidence            5899999999999999999999999999999999999864433

>PRK03059 PII uridylyl-transferase; Provisional

Probab=85.91  E-value=3  Score=43.95  Aligned_cols=54  Identities=13%  Similarity=0.102  Sum_probs=45.1

Q ss_pred             eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEE-eeeCCeEEEEEEEEecCC
Q 036406          174 LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVS-TRVDERLLHTIQAELNNV  229 (241)
Q Consensus       174 ~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~-S~~~~~vl~tI~akv~~~  229 (241)
                      ....+|.+.|.  +++++|+++..+|..+||+|++|.+ |+.+|.++-+|.+.-.++
T Consensus       676 ~~~~~v~i~~~--d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~  730 (856)
T PRK03059        676 GEGLQVMVYTP--DQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEE  730 (856)
T ss_pred             CCeEEEEEEec--CCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCC
Confidence            36678887763  5899999999999999999999998 568899999998875433

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

Probab=85.84  E-value=4.8  Score=29.39  Aligned_cols=47  Identities=11%  Similarity=0.101  Sum_probs=40.3

Q ss_pred             EEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 036406          179 IAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELN  227 (241)
Q Consensus       179 I~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~  227 (241)
                      |.+.|  ++++|...+|-..|.++|..+++++....++.++..+.+.+.
T Consensus         4 ltv~g--~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~   50 (77)
T cd04893           4 ISALG--TDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS   50 (77)
T ss_pred             EEEEe--CCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec
Confidence            34444  368999999999999999999999999999999888888765

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

>PRK05092 PII uridylyl-transferase; Provisional

Probab=85.36  E-value=4.6  Score=42.86  Aligned_cols=62  Identities=13%  Similarity=-0.010  Sum_probs=47.4

Q ss_pred             CceEEEee--eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          166 NRFVVHQS--LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       166 ~~V~V~~~--~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      |.|.+...  .....|.|.+  .+++++|.+|..+|.++|++|.+|.+++.++++.-+|.+.-.++
T Consensus       831 ~~V~~~~~~s~~~t~i~I~~--~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g  894 (931)
T PRK05092        831 PRVTIDNEASNRFTVIEVNG--RDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFG  894 (931)
T ss_pred             CEEEEeeCCCCCeEEEEEEE--CCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCC
Confidence            34555433  2223444444  25899999999999999999999999999999999999976554

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=85.11  E-value=3.2  Score=43.96  Aligned_cols=54  Identities=13%  Similarity=0.004  Sum_probs=45.3

Q ss_pred             ceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEE-eeeCCeEEEEEEEEecCCc
Q 036406          175 VGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVS-TRVDERLLHTIQAELNNVV  230 (241)
Q Consensus       175 ~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~-S~~~~~vl~tI~akv~~~~  230 (241)
                      .+.+|.|.|.  +++++|.++..+|..+||+|++|.+ |+.+|.++-+|.+.-.++.
T Consensus       703 ~~t~V~V~~~--DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~  757 (895)
T PRK00275        703 GGTQIFIYAP--DQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGE  757 (895)
T ss_pred             CeEEEEEEeC--CCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCC
Confidence            5678887763  5899999999999999999999997 5678889999988765543

>PRK05007 PII uridylyl-transferase; Provisional

Probab=84.62  E-value=5.6  Score=42.12  Aligned_cols=62  Identities=15%  Similarity=0.034  Sum_probs=46.9

Q ss_pred             CceEEEee--eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEecCC
Q 036406          166 NRFVVHQS--LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTR-VDERLLHTIQAELNNV  229 (241)
Q Consensus       166 ~~V~V~~~--~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~-~~~~vl~tI~akv~~~  229 (241)
                      |.|.+...  ....+|.|.+.  +++++|.+|..+|..+||+|++|.+.+ .+|.++-+|.+.-.++
T Consensus       689 p~V~i~~~~~~~~t~V~V~a~--DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g  753 (884)
T PRK05007        689 PLVLLSKQATRGGTEIFIWSP--DRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDG  753 (884)
T ss_pred             CeEEEEecCCCCeEEEEEEec--CCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCC
Confidence            44555443  34567776553  589999999999999999999999766 5668988888875554

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=84.28  E-value=4.5  Score=42.44  Aligned_cols=54  Identities=20%  Similarity=0.030  Sum_probs=44.9

Q ss_pred             eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEe-eeCCeEEEEEEEEecCC
Q 036406          174 LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVST-RVDERLLHTIQAELNNV  229 (241)
Q Consensus       174 ~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S-~~~~~vl~tI~akv~~~  229 (241)
                      ....+|.|.+.  +++++|++|..+|..+||+|++|.+. +.+|.++-+|.++-.++
T Consensus       666 ~~~t~i~V~~~--DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g  720 (850)
T TIGR01693       666 SGGTEVFIYAP--DQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFG  720 (850)
T ss_pred             CCeEEEEEEeC--CCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCC
Confidence            34456666553  58999999999999999999999998 68999999999986654

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.

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

Probab=84.11  E-value=6.4  Score=27.63  Aligned_cols=43  Identities=21%  Similarity=0.108  Sum_probs=33.8

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeee-CCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRV-DERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~-~~~vl~tI~akv~~~  229 (241)
                      .+++.|.+|+..|.++|++|...+.+.. ++..-..|.+.+.+.
T Consensus         9 d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~   52 (76)
T cd04888           9 HRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTM   52 (76)
T ss_pred             CCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCch
Confidence            3678999999999999999999887653 465666677766554

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.

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

Probab=83.53  E-value=5.2  Score=28.55  Aligned_cols=42  Identities=14%  Similarity=0.188  Sum_probs=34.5

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCC-eEEEEEEEEecC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDE-RLLHTIQAELNN  228 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~-~vl~tI~akv~~  228 (241)
                      .++|.|.+++..+.++|+.+++..+.+..+ ..-|.|.+.+..
T Consensus         8 d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~   50 (75)
T cd04880           8 NKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEG   50 (75)
T ss_pred             CcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEEC
Confidence            478999999999999999999998887655 466777777654

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

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

Probab=81.53  E-value=11  Score=26.89  Aligned_cols=41  Identities=7%  Similarity=0.067  Sum_probs=33.9

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeC------CeEEEEEEEEec
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVD------ERLLHTIQAELN  227 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~------~~vl~tI~akv~  227 (241)
                      ++++.+.+|-+.|.++|+++.+....+.+      +.+...+.+.+.
T Consensus         8 D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p   54 (81)
T cd04869           8 DRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALP   54 (81)
T ss_pred             CCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecC
Confidence            58899999999999999999999998876      555556666654

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

>PRK04374 PII uridylyl-transferase; Provisional

Probab=80.98  E-value=6.6  Score=41.61  Aligned_cols=54  Identities=6%  Similarity=0.091  Sum_probs=44.9

Q ss_pred             eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEecCC
Q 036406          174 LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTR-VDERLLHTIQAELNNV  229 (241)
Q Consensus       174 ~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~-~~~~vl~tI~akv~~~  229 (241)
                      ....+|.+.+.  +++++|+++.-+|..+||+|++|.+.+ .+|.++-+|.+.-.+.
T Consensus       688 ~~~~~v~v~~~--d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~  742 (869)
T PRK04374        688 NDALEVFVYSP--DRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDT  742 (869)
T ss_pred             CCeEEEEEEeC--CCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCC
Confidence            46678887763  589999999999999999999998876 7899999999864333

>PRK05092 PII uridylyl-transferase; Provisional

Probab=80.81  E-value=9.8  Score=40.44  Aligned_cols=62  Identities=15%  Similarity=0.021  Sum_probs=47.6

Q ss_pred             CceEEEee--eceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEee-eCCeEEEEEEEEecCC
Q 036406          166 NRFVVHQS--LVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTR-VDERLLHTIQAELNNV  229 (241)
Q Consensus       166 ~~V~V~~~--~~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~-~~~~vl~tI~akv~~~  229 (241)
                      +.|.+...  ....+|.+.+.  +++++|.+|..+|..+|++|++|.+.+ .+|.++-+|.+.-.++
T Consensus       720 ~~v~~~~~~~~~~t~v~I~~~--Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g  784 (931)
T PRK05092        720 LATEVRPDPARGVTEVTVLAA--DHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFG  784 (931)
T ss_pred             cEEEEEecCCCCeEEEEEEeC--CCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCC
Confidence            33445443  35678887763  589999999999999999999999876 7888888888765443

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

Probab=80.24  E-value=4.2  Score=42.88  Aligned_cols=60  Identities=17%  Similarity=0.175  Sum_probs=47.3

Q ss_pred             CceEEEeee----ceEEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          166 NRFVVHQSL----VGIEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       166 ~~V~V~~~~----~~veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      |.|++....    ..+||.   +. +++|+|.+|-.+|.+++|++++|.|+++|.++.-+|.+.....
T Consensus       779 p~v~i~~t~~~~~t~lEv~---al-DRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~  842 (867)
T COG2844         779 PRVTILPTASNDKTVLEVR---AL-DRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADG  842 (867)
T ss_pred             CceeeccccCCCceEEEEE---eC-CcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEecccc
Confidence            556665542    335554   23 5899999999999999999999999999999988887776555

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=80.20  E-value=6.1  Score=41.43  Aligned_cols=43  Identities=16%  Similarity=0.054  Sum_probs=39.3

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      +++|+|.+|..+|.++|++|.+|.+++.++++.-+|.+....+
T Consensus       788 DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g  830 (850)
T TIGR01693       788 DRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFG  830 (850)
T ss_pred             CccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCC
Confidence            5899999999999999999999999999999999998876544

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.

---

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	241
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	4e-07
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	9e-07
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-06
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	7e-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 = 49.3 bits (118), Expect = 3e-08
 Identities = 17/71 (23%), Positives = 34/71 (47%)

Query: 73  NNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK 132
            N K+  H  +ERQRR E+   + +LR  +P      K      + +   Y+  ++ + +
Sbjct: 3   MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ 62

Query: 133 ELGVKRDELKR 143
           +L  + D L++
Sbjct: 63  KLISEEDLLRK 73

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

 Score = 51.8 bits (123), Expect = 6e-08
 Identities = 39/224 (17%), Positives = 67/224 (29%), Gaps = 61/224 (27%)

Query: 56  ETDKIPSDN---YNSNNSN-YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIK--- 108
              + PS     Y       YN+N+     +V   R Q    L  +L  L P + +    
Sbjct: 100 TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV--SRLQPYLKLRQALLELRPAKNVLIDG 157

Query: 109 ----GK----------RSISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSNLS--ISAS 152
               GK            +  +M+  + ++      +K        L+ L  L   I  +
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWL-----NLKNCNSPETVLEMLQKLLYQIDPN 212

Query: 153 QIETSDQNDTSPINRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLDEGLCV------ 206
               SD +    +    +   L           L +  P    L VLL+    V      
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELR---------RLLKSKPYENCLLVLLN----VQNAKAW 259

Query: 207 ----VNC---VSTR---VDERL--LHTIQAELNNVVPKFDADAT 238
               ++C   ++TR   V + L    T    L++       D  
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

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

 Score = 42.1 bits (98), Expect = 9e-05
 Identities = 41/219 (18%), Positives = 70/219 (31%), Gaps = 50/219 (22%)

Query: 9   ELFIKVSSNSHQQDKIPQDLISGHASEASSIITNDMGKSHRGQSFSMETDKIPSDNYNSN 68
            L +K      Q   +P+++++ +     SII          +S          DN+   
Sbjct: 305 SLLLKYLDCRPQ--DLPREVLTTNP-RRLSII---------AESIRDGLATW--DNWK-- 348

Query: 69  NSNYNNNKKLMHRDVERQRRQEMATLYASLRALLP---------LEFIKGKRSISDQMNE 119
           + N +    ++   +      E   ++  L ++ P         L  I      SD M  
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRL-SVFPPSAHIPTILLSLIWFDVIKSDVMVV 407

Query: 120 GVNYVKY--LEKKIKE-----------LGVKRDELKRLSNLSISASQI-ETSDQNDTSPI 165
                KY  +EK+ KE           L VK +    L    +    I +T D +D  P 
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467

Query: 166 ---NRFVVHQSLVGIEIAYSCGYLEQELPLSKVLEVLLD 201
                F  H       I +    +E    ++    V LD
Sbjct: 468 YLDQYFYSH-------IGHHLKNIEHPERMTLFRMVFLD 499

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

 Score = 39.5 bits (91), Expect = 7e-04
 Identities = 46/305 (15%), Positives = 92/305 (30%), Gaps = 103/305 (33%)

Query: 3   PLHSGDELFIKVSSNSHQQ-DKIPQDLISGHASEASSIITNDM---GKS----------- 47
            L++ +++F K + +  Q   K+ Q L+      A +++ + +   GK+           
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLRQALLE--LRPAKNVLIDGVLGSGKTWVALDVCLSYK 175

Query: 48  -HRGQSF-----SMETDKIPSD--------------NYNSNNSNYNNNKKLMHRDVERQR 87
                 F     +++    P                N+ S + + +N K  +H      R
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR 235

Query: 88  RQEMATLYASLRALLPLE----------F-IKGK-------RSISDQMNEGVNYVKYLEK 129
           R   +  Y     LL L           F +  K       + ++D ++        L+ 
Sbjct: 236 RLLKSKPYE--NCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 130 KIKELGVKRDELKRL--SNLSISASQI--ETSDQNDTSPINRFVVHQSLVGIEIAYSCGY 185
                 +  DE+K L    L      +  E      T+P     +  S++          
Sbjct: 294 HSM--TLTPDEVKSLLLKYLDCRPQDLPREVLT---TNP---RRL--SIIA--------- 334

Query: 186 LEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNVVPK-----------FD 234
                         + +GL   +       ++L   I++ LN + P            F 
Sbjct: 335 ------------ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP 382

Query: 235 ADATI 239
             A I
Sbjct: 383 PSAHI 387

>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 = 45.8 bits (109), Expect = 4e-07
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 75  NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKEL 134
           +K+  H  +ER+RR  +   + SLR  +P      K S +  +++   Y++Y+ +K    
Sbjct: 1   DKRAHHNALERKRRDHIKDSFHSLRDSVP-SLQGEKASRAQILDKATEYIQYMRRKNHTH 59

Query: 135 GVKRDELKR 143
               D+LKR
Sbjct: 60  QQDIDDLKR 68

>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 = 44.7 bits (106), Expect = 9e-07
 Identities = 12/69 (17%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           K+  H  +E++ R  +      L+ L+     + K + S  + + ++Y+++L+   ++L 
Sbjct: 6   KRTAHNAIEKRYRSSINDKIIELKDLVV--GTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

Query: 136 VKRDELKRL 144
            +   L+  
Sbjct: 64  QENLSLRTA 72

>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 = 42.7 bits (101), Expect = 4e-06
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 66  NSNNSNYNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVK 125
           +      + +K+  H  +ER+RR  +   + SLR  +P      K S +  +++   Y++
Sbjct: 2   DDIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVP-SLQGEKASRAQILDKATEYIQ 60

Query: 126 YLEKKIKELGVKRDELKR 143
           Y+ +K        D+LKR
Sbjct: 61  YMRRKNHTHQQDIDDLKR 78

>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 = 39.4 bits (92), Expect = 7e-05
 Identities = 14/64 (21%), Positives = 31/64 (48%)

Query: 80  HRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRD 139
           H ++E+ RR  +      L+ L+PL     + +    + +   ++K LE   ++   + D
Sbjct: 5   HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQID 64

Query: 140 ELKR 143
           +L+R
Sbjct: 65  QLQR 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	241
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.59
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.58
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.56
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.56
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.56
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.49
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.47
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.46
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.4
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.4
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.4
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.28
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.24
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.89
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.75
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.58
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.55
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.95
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	90.49
2nyi_A	195	Unknown protein; protein structure initiative, PSI	86.32
1u8s_A	192	Glycine cleavage system transcriptional repressor,	84.13
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	83.37

>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=99.59  E-value=1.2e-15  Score=114.50  Aligned_cols=69  Identities=17%  Similarity=0.322  Sum_probs=59.7

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRL  144 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~~  144 (241)
                      ..++..|+.+||+||.+||+.|..|++|||...  .|.+.+++|.+||+||++||.+++.|+.+.+.+...
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~--~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   72 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999852  244444559999999999999999999998888754

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

Probab=99.58  E-value=5.1e-15  Score=110.86  Aligned_cols=67  Identities=21%  Similarity=0.318  Sum_probs=62.2

Q ss_pred             cccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           77 KLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        77 k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      +..||..||+||..||..|..|+++||......|+|.+++|..|++||++|+++.++|..+++.+..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999999877788898999999999999999999999998887754

>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=99.56  E-value=5.7e-15  Score=110.64  Aligned_cols=67  Identities=28%  Similarity=0.472  Sum_probs=60.0

Q ss_pred             ccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        76 ~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      +|..|+.+||+||..||..|..|+++||... ..|.|.+++|..||+||+.|++++++|+.+++++..
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            6889999999999999999999999999753 346777788999999999999999999998888765

>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=99.56  E-value=3.4e-15  Score=111.29  Aligned_cols=71  Identities=27%  Similarity=0.440  Sum_probs=63.4

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      ....++..|+.+||+||..||..|..|+++||.... .|.|.+++|..||+||++|++++++|+.+.+.|..
T Consensus         8 ~~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~-~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~   78 (80)
T 1hlo_A            8 SDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQG-EKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   78 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTT-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             chHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345789999999999999999999999999997542 47888888999999999999999999999888764

>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=99.56  E-value=4.7e-15  Score=112.83  Aligned_cols=71  Identities=24%  Similarity=0.302  Sum_probs=62.8

Q ss_pred             cccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           73 NNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        73 ~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      +..++..|+..||+||..||+.|..|+++||......|.|.+.+|..||+||++|+++.+.|...++.+..
T Consensus         3 d~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~   73 (88)
T 1nkp_A            3 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK   73 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35688999999999999999999999999998766668888888999999999999999998877766543

>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=99.49  E-value=4.2e-15  Score=106.65  Aligned_cols=57  Identities=23%  Similarity=0.426  Sum_probs=49.3

Q ss_pred             ccccchHHHHHHHHHHHHhHHHHHccCCCCCcC----CCCchhhhHHHHHHHHHHHHHHHH
Q 036406           76 KKLMHRDVERQRRQEMATLYASLRALLPLEFIK----GKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        76 ~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~----~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      +|.+|+.+||.||.+||..|..|++|||...+.    .|.|.+++|+.||+||++||++++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            688999999999999999999999999976443    356666779999999999998753

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

Probab=99.47  E-value=1.4e-14  Score=107.61  Aligned_cols=62  Identities=19%  Similarity=0.360  Sum_probs=51.2

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCC-chhhhHHHHHHHHHHHHHHHHHHH
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKR-SISDQMNEGVNYVKYLEKKIKELG  135 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~-Si~~~l~eAI~YIk~Lq~~v~~L~  135 (241)
                      ..+|..||..||+||..||+.|..||.+||.....+|+ |..++|..||+||+.||+++++++
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            46889999999999999999999999999965556676 788889999999999999999876

>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=99.46  E-value=2.4e-14  Score=102.58  Aligned_cols=58  Identities=19%  Similarity=0.420  Sum_probs=48.8

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcC---CCCchhhhHHHHHHHHHHHHHHH
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIK---GKRSISDQMNEGVNYVKYLEKKI  131 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~---~K~Si~~~l~eAI~YIk~Lq~~v  131 (241)
                      ..++..|+.+||+||..||..|..|++|||.....   .|.+.+++|..||+||++||++.
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            46889999999999999999999999999987632   24444444999999999999764

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

Probab=99.40  E-value=2.6e-13  Score=108.35  Aligned_cols=69  Identities=19%  Similarity=0.252  Sum_probs=51.4

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcC-CCCchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIK-GKRSISDQMNEGVNYVKYLEKKIKELGVKRDE  140 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~-~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~e  140 (241)
                      ....++..|+.+||+||.+||+.|..|++|||..... .|.+.+++|..||+||++||.+++.|+....+
T Consensus        23 k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~~   92 (118)
T 4ati_A           23 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENR   92 (118)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4457899999999999999999999999999987653 36666777999999999999999999865433

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

Probab=99.40  E-value=3.1e-13  Score=96.07  Aligned_cols=58  Identities=19%  Similarity=0.279  Sum_probs=53.7

Q ss_pred             cccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 036406           75 NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        75 ~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      +++..||..||+|+..||..|..||.+||......|.|+.++|..||+||..|++.++
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            3678899999999999999999999999998777899999999999999999998764

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

Probab=99.40  E-value=1.7e-13  Score=100.64  Aligned_cols=61  Identities=16%  Similarity=0.339  Sum_probs=52.7

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCC-CcCCCCchhhhHHHHHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLE-FIKGKRSISDQMNEGVNYVKYLEKKIKELG  135 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~-~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~  135 (241)
                      ....++.+|+.+||+||.+||..|..|++|||.. .+.+|++|   |..||+||++||+++.=|+
T Consensus         4 k~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sI---L~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            4 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTV---LQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHH---HHHHHHHHHHHHHHHHHTC
T ss_pred             hhhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHH---HHHHHHHHHHHHHhhhHHH
Confidence            4568899999999999999999999999999963 35566666   9999999999999887654

>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=99.28  E-value=2.7e-12  Score=93.42  Aligned_cols=59  Identities=12%  Similarity=0.249  Sum_probs=52.9

Q ss_pred             cccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 036406           73 NNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        73 ~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      ...++..||..||+|+..||+.|..||.+||... ..|.|..++|..||+||..|++.++
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~-~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCT-TSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            4578889999999999999999999999999754 5689999999999999999998653

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

Probab=99.24  E-value=1.1e-12  Score=96.67  Aligned_cols=55  Identities=24%  Similarity=0.342  Sum_probs=48.2

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCC----CcCCCCchhhhHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLE----FIKGKRSISDQMNEGVNYVKYLEK  129 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~----~~~~K~Si~~~l~eAI~YIk~Lq~  129 (241)
                      +...++..|+.+||+||.+||..|..|++|||..    .+.+|++|   |..||+||+.|+.
T Consensus         5 k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasI---L~~tV~ylk~l~~   63 (73)
T 4h10_A            5 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTV---LRMAVQHMKTLRG   63 (73)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHH---HHHHHHHHHHHSC
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHH---HHHHHHHHHHHhc
Confidence            4567889999999999999999999999999965    46667766   9999999999974

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

Probab=98.89  E-value=4.5e-10  Score=81.55  Aligned_cols=49  Identities=18%  Similarity=0.209  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHH
Q 036406           81 RDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEK  129 (241)
Q Consensus        81 ~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~  129 (241)
                      ++.||+|+..||..|..||.+||......|.|+.++|.-||+||..||+
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            4569999999999999999999998888899999999999999999984

>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=4e-09  Score=96.35  Aligned_cols=57  Identities=16%  Similarity=0.403  Sum_probs=40.8

Q ss_pred             CCcccccccchHHHHHHHHHHHHhHHHHHccCC-CCCcCCCCchhhhHHHHHHHHHHHHHH
Q 036406           71 NYNNNKKLMHRDVERQRRQEMATLYASLRALLP-LEFIKGKRSISDQMNEGVNYVKYLEKK  130 (241)
Q Consensus        71 ~~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP-~~~~~~K~Si~~~l~eAI~YIk~Lq~~  130 (241)
                      .....++..|+.+||+||.+||..|..|++||| ...+.+|++|   |..||.||+.|+..
T Consensus         7 ~~~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~i---l~~~~~~~~~~~~~   64 (361)
T 4f3l_A            7 DKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTV---LQKSIDFLRKHKET   64 (361)
T ss_dssp             ------------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHH---HHHHHHHHHHHHHH
T ss_pred             cccchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHH---HHHHHHHHHHHHhh
Confidence            345688999999999999999999999999999 4557778877   99999999999864

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

Probab=98.58  E-value=2e-08  Score=92.90  Aligned_cols=57  Identities=23%  Similarity=0.373  Sum_probs=49.3

Q ss_pred             CCcccccccchHHHHHHHHHHHHhHHHHHccCC----CCCcCCCCchhhhHHHHHHHHHHHHHH
Q 036406           71 NYNNNKKLMHRDVERQRRQEMATLYASLRALLP----LEFIKGKRSISDQMNEGVNYVKYLEKK  130 (241)
Q Consensus        71 ~~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP----~~~~~~K~Si~~~l~eAI~YIk~Lq~~  130 (241)
                      .+...+|.+|+.+||+||.+||..|..|++|||    ...+.+|+||   |..||.|||.|+..
T Consensus         8 ~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~i---l~~~~~~l~~~~~~   68 (387)
T 4f3l_B            8 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTV---LRMAVQHMKTLRGA   68 (387)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHH---HHHHHHHHHHHHCC
T ss_pred             chhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHH---HHHHHHHHHHhhcc
Confidence            445678999999999999999999999999999    5667888888   99999999999843

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

Probab=98.55  E-value=1.1e-07  Score=73.43  Aligned_cols=52  Identities=19%  Similarity=0.224  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHH
Q 036406           82 DVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKE  133 (241)
Q Consensus        82 ~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~  133 (241)
                      ..||+|-..||..|..||.+||......|.|+.++|.-||+||..|++-+++
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            3468899999999999999999987777999999999999999999988764

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

Probab=97.95  E-value=2.5e-05  Score=58.67  Aligned_cols=55  Identities=15%  Similarity=0.219  Sum_probs=44.6

Q ss_pred             HHHHHHhHHHHHccCCCCC-cCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 036406           88 RQEMATLYASLRALLPLEF-IKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELK  142 (241)
Q Consensus        88 R~~mn~~f~~LrsLlP~~~-~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~  142 (241)
                      |-.+|..+..|..|||... +..|.+...+|..||+||++||..++.+.+.-....
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r~k   59 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQK   59 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999753 444778888899999999999998887776544433

>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=90.49  E-value=1.9  Score=30.53  Aligned_cols=49  Identities=14%  Similarity=0.078  Sum_probs=39.9

Q ss_pred             EEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 036406          178 EIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN  228 (241)
Q Consensus       178 eI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~  228 (241)
                      .+.+.|  .+++|.+.+|..+|-++|..|.+.+....++..+..+.+.+.+
T Consensus         7 ~l~v~~--~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~~   55 (91)
T 1zpv_A            7 IITVVG--KDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE   55 (91)
T ss_dssp             EEEEEE--SCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS
T ss_pred             EEEEEE--CCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeCC
Confidence            344444  3589999999999999999999999888778777777777765

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

Probab=86.32  E-value=3.9  Score=33.71  Aligned_cols=49  Identities=8%  Similarity=-0.008  Sum_probs=40.7

Q ss_pred             EEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEec
Q 036406          177 IEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELN  227 (241)
Q Consensus       177 veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~  227 (241)
                      +.|.+.|.  ++++++.+|..+|.++|+.|+.+...+..|.++-.+.+...
T Consensus         6 ~~ltv~~~--DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~~~   54 (195)
T 2nyi_A            6 FVVSVAGS--DRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVSLN   54 (195)
T ss_dssp             EEEEEEEE--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES
T ss_pred             EEEEEEeC--CCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEEec
Confidence            45666653  58999999999999999999999999988887777777654

>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=84.13  E-value=5.5  Score=32.34  Aligned_cols=48  Identities=6%  Similarity=0.054  Sum_probs=40.0

Q ss_pred             EEEEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEe
Q 036406          177 IEIAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAEL  226 (241)
Q Consensus       177 veI~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv  226 (241)
                      ..|.+.|.  +++|++.+|..+|.++|+.|+.+......|.++.++.+..
T Consensus         7 ~~itv~~~--DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~   54 (192)
T 1u8s_A            7 LVITAVGT--DRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG   54 (192)
T ss_dssp             EEEEEEEE--CCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEcC--CCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEec
Confidence            44555553  5899999999999999999999999888888877777764

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

Probab=83.37  E-value=4.3  Score=28.14  Aligned_cols=42  Identities=10%  Similarity=0.026  Sum_probs=34.1

Q ss_pred             CCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 036406          187 EQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN  228 (241)
Q Consensus       187 ~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~  228 (241)
                      +++|.|.+|..+|.+.|+.|.+......++.....+.+.+.+
T Consensus        14 Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~~~~   55 (88)
T 2ko1_A           14 DKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIFVKN   55 (88)
T ss_dssp             CCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEEESS
T ss_pred             CCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEEECC
Confidence            588999999999999999999999887666444566666654

---

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	241
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-13
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	5e-09
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	3e-08
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	4e-08
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	7e-07
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	8e-07
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	2e-05
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	0.004

>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 = 61.8 bits (150), Expect = 2e-13
 Identities = 17/70 (24%), Positives = 34/70 (48%)

Query: 74  NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKE 133
           N K+  H  +ERQRR E+   + +LR  +P      K      + +   Y+  ++ + ++
Sbjct: 4   NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQK 63

Query: 134 LGVKRDELKR 143
           L  + D L++
Sbjct: 64  LISEEDLLRK 73

>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 = 49.5 bits (118), Expect = 5e-09
 Identities = 14/64 (21%), Positives = 31/64 (48%)

Query: 80  HRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRD 139
           H ++E+ RR  +      L+ L+PL     + +    + +   ++K LE   ++   + D
Sbjct: 5   HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQID 64

Query: 140 ELKR 143
           +L+R
Sbjct: 65  QLQR 68

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

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

 Score = 47.6 bits (113), Expect = 3e-08
 Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 75  NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKEL 134
           +K+  H  +ER+RR  +   + SLR  +P    + K S +  +++   Y++Y+ +K    
Sbjct: 1   DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKNHTH 59

Query: 135 GVKRDELKR 143
               D+LKR
Sbjct: 60  QQDIDDLKR 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 = 46.8 bits (111), Expect = 4e-08
 Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIK----GKRSISDQMNEGVNYVKYLEKKI 131
           K+  H+  E+ RR  +A     L +L+P E+ +       S +  +     Y+++L++  
Sbjct: 2   KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

Query: 132 K 132
            
Sbjct: 62  S 62

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

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

 Score = 43.8 bits (103), Expect = 7e-07
 Identities = 12/71 (16%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 76  KKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELG 135
           K+  H  +E++ R  +      L+ L+       K + S  + + ++Y+++L+   ++L 
Sbjct: 6   KRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLK 63

Query: 136 VKRDELKRLSN 146
            +   L+   +
Sbjct: 64  QENLSLRTAVH 74

>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 = 43.3 bits (102), Expect = 8e-07
 Identities = 7/61 (11%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 73  NNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK 132
           N +++      ER+R  ++   + +L+        +      + +   + Y++ L+  ++
Sbjct: 9   NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRL-PKVEILRNAIRYIEGLQALLR 67

Query: 133 E 133
           +
Sbjct: 68  D 68

>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 = 39.4 bits (92), Expect = 2e-05
 Identities = 11/59 (18%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 75  NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKG---KRSISDQMNEGVNYVKYLEKK 130
            ++  H +VER+RR ++      L  ++P   ++     +S    +++  +Y++ L + 
Sbjct: 4   KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS 62

>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 = 32.4 bits (74), Expect = 0.004
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 88  RQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRLSN 146
           R  +      L+ L+       K   S  + + ++Y+KYL++   +L  +   LK  + 
Sbjct: 1   RSSINDKIIELKDLVM--GTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQ 57

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	241
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.61
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.59
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.47
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.46
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.37
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.21
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	88.01
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	87.2

>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=99.61  E-value=9.8e-16  Score=111.95  Aligned_cols=67  Identities=21%  Similarity=0.318  Sum_probs=61.6

Q ss_pred             cccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           77 KLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        77 k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      +..|+.+||+||..||+.|..|+++||......|+|.+++|..||+||+.|+..++.|..+++.+..
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~   68 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999999998877778888888999999999999999999988887754

>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=99.59  E-value=1.4e-15  Score=113.32  Aligned_cols=70  Identities=24%  Similarity=0.317  Sum_probs=63.7

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      ..+|..|+.+||+||..||+.|..|+++||......|.|.+++|..||+||++|+++++.|..+++.+..
T Consensus         4 ~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   73 (88)
T d1nkpa_           4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK   73 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4578899999999999999999999999998777778888899999999999999999999988877654

>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=99.52  E-value=1.2e-14  Score=107.06  Aligned_cols=68  Identities=28%  Similarity=0.475  Sum_probs=59.0

Q ss_pred             cccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036406           75 NKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKR  143 (241)
Q Consensus        75 ~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~  143 (241)
                      .+|..|+.+||+||.+||+.|..|+++||... ..|.|.+++|..||+||+.|+++++.|..+.+.+..
T Consensus         1 ~rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~-~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   68 (83)
T d1nkpb_           1 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36889999999999999999999999999643 236777777999999999999999999988777654

>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=99.51  E-value=9.3e-15  Score=107.14  Aligned_cols=69  Identities=17%  Similarity=0.322  Sum_probs=59.7

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRL  144 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~~  144 (241)
                      ..++..|+.+||+||..||+.|..|++|||...  .|.|.+++|..||+||++|+++++.|..+...+...
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~--~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~   72 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467889999999999999999999999999744  255556669999999999999999999888877543

>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=99.47  E-value=9.1e-15  Score=102.81  Aligned_cols=56  Identities=23%  Similarity=0.416  Sum_probs=47.4

Q ss_pred             ccccchHHHHHHHHHHHHhHHHHHccCCCC----CcCCCCchhhhHHHHHHHHHHHHHHH
Q 036406           76 KKLMHRDVERQRRQEMATLYASLRALLPLE----FIKGKRSISDQMNEGVNYVKYLEKKI  131 (241)
Q Consensus        76 ~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~----~~~~K~Si~~~l~eAI~YIk~Lq~~v  131 (241)
                      +|..|+.+||+||.+||..|..|++|||..    ....|.|.+++|..||+||++||+++
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            678999999999999999999999999952    23345555666999999999999865

>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=99.46  E-value=1.2e-14  Score=103.86  Aligned_cols=60  Identities=12%  Similarity=0.215  Sum_probs=52.6

Q ss_pred             CcccccccchHHHHHHHHHHHHhHHHHHccCCCCCcCCCCchhhhHHHHHHHHHHHHHHHH
Q 036406           72 YNNNKKLMHRDVERQRRQEMATLYASLRALLPLEFIKGKRSISDQMNEGVNYVKYLEKKIK  132 (241)
Q Consensus        72 ~~~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~~K~Si~~~l~eAI~YIk~Lq~~v~  132 (241)
                      ....++..|+..||+||..||+.|..|++|||.... +|.|.+++|..||+||++||+.|+
T Consensus         8 ~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~-~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPN-QRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTT-SCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHhh
Confidence            345788999999999999999999999999998654 377778889999999999998764

>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=99.37  E-value=1.3e-13  Score=97.36  Aligned_cols=58  Identities=19%  Similarity=0.420  Sum_probs=48.6

Q ss_pred             ccccccchHHHHHHHHHHHHhHHHHHccCCCCCcC---CCCchhhhHHHHHHHHHHHHHHH
Q 036406           74 NNKKLMHRDVERQRRQEMATLYASLRALLPLEFIK---GKRSISDQMNEGVNYVKYLEKKI  131 (241)
Q Consensus        74 ~~~k~~H~~~ER~RR~~mn~~f~~LrsLlP~~~~~---~K~Si~~~l~eAI~YIk~Lq~~v  131 (241)
                      ..++..|+.+||+||..||..|..|++|||.....   .|.|.+++|..||+||++||++.
T Consensus         3 ~~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            46788999999999999999999999999975422   25555566999999999999753

>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=99.21  E-value=4.2e-12  Score=88.49  Aligned_cols=54  Identities=20%  Similarity=0.277  Sum_probs=47.4

Q ss_pred             HHHHHHhHHHHHccCCCCC-cCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 036406           88 RQEMATLYASLRALLPLEF-IKGKRSISDQMNEGVNYVKYLEKKIKELGVKRDELKRL  144 (241)
Q Consensus        88 R~~mn~~f~~LrsLlP~~~-~~~K~Si~~~l~eAI~YIk~Lq~~v~~L~~~k~el~~~  144 (241)
                      |.+||++|..||++||+.. +.+|++|   |.+||+||+.||.++++|+++...+...
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~i---L~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   55 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGV---LRKAIDYIKYLQQVNHKLRQENMVLKLA   55 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5689999999999999865 5667777   9999999999999999999988887654

>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=88.01  E-value=1.3  Score=30.21  Aligned_cols=48  Identities=6%  Similarity=0.046  Sum_probs=40.8

Q ss_pred             EEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecC
Q 036406          179 IAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNN  228 (241)
Q Consensus       179 I~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~  228 (241)
                      |.+.|  ++++|.+.+|...|-+.|..++.+..+..++.+...+.+.+.+
T Consensus         8 itv~G--~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~~   55 (86)
T d1u8sa1           8 ITAVG--TDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP   55 (86)
T ss_dssp             EEEEE--ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH
T ss_pred             EEEEe--CCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcCc
Confidence            44444  3699999999999999999999999999999988888877653

>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=87.20  E-value=2.4  Score=28.47  Aligned_cols=49  Identities=14%  Similarity=0.085  Sum_probs=40.8

Q ss_pred             EEEeecCCCCCchHHHHHHHHHhCCcEEEEEEEeeeCCeEEEEEEEEecCC
Q 036406          179 IAYSCGYLEQELPLSKVLEVLLDEGLCVVNCVSTRVDERLLHTIQAELNNV  229 (241)
Q Consensus       179 I~i~~~~~~~~~~Lsrvl~aLeelgLdVvsa~~S~~~~~vl~tI~akv~~~  229 (241)
                      |++.|  ++++|.+.+|-..|-++|..+.+++-...++.++..+.+.+...
T Consensus         5 itv~g--~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~~~~   53 (83)
T d1zpva1           5 ITVVG--KDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDEK   53 (83)
T ss_dssp             EEEEE--SCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESSC
T ss_pred             EEEEc--CCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEEecC
Confidence            34444  46999999999999999999999999999998887777777644