Psyllid ID: psy8988

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130---
Protein Sequence
MNKSKAILECLFNGRLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQMSQREYIPYTALVPTYPAIN
Secondary Structure (PSIPRED)
cccccHHHHHcccccccccccccccccccccccccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MNKSKAILECLfngrlsghggsstgtngghtkkTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSEllhgtpngstsgspiyqmsqreyipytalvptypain
Flexible Loop (DISEMBL)
MNKSKAILECLFngrlsghggsstgtngghtkktrrrvATLAQrraanirerrrmfnlneafdklrrkvptfayekrlsrIETLRLAITYISFMSELLHGTPNGSTSGSPIYQMSQREYIPYTALVPTYPAIN
Low Complexity Region (SEG)
MNKSKAILECLFNgrlsghggsstgtngghtkktrrrVATLaqrraanirerrrMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQMSQREYIPYTALVPTYPAIN
Disordered region (IsUnstruct)
******ILECLFN***************************************RRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHG***********YQMSQREYIPYTALVPTY****
Disordered Region (DISOPRED)
*************************************************RERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE*************************************
Disordered Region (DISEMBL)
MNKSKAILECLFNGRLSGHGG*******************LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQMSQREYIPYTALVPTYPAIN
Disordered Region (DISPRO)
*********CLFN**********************RRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGT*******SPIYQ***REYIPYTALVPTYPAIN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNKSKAILECLFNGRLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQMSQREYIPYTALVPTYPAIN
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	133	2.2.26 [Sep-21-2011]
Q9VGJ5	195	Protein Fer3 OS=Drosophil	yes	N/A	0.721	0.492	0.734	1e-31
Q96RJ6	166	Fer3-like protein OS=Homo	yes	N/A	0.503	0.403	0.835	6e-26
Q923Z4	168	Fer3-like protein OS=Mus	yes	N/A	0.548	0.434	0.780	8e-26
Q4ZHW1	270	Pancreas transcription fa	N/A	N/A	0.699	0.344	0.466	2e-17
Q9QX98	324	Pancreas transcription fa	no	N/A	0.661	0.271	0.454	6e-16
Q64305	326	Pancreas transcription fa	no	N/A	0.496	0.202	0.582	1e-15
Q7ZSX3	265	Pancreas transcription fa	yes	N/A	0.563	0.283	0.512	1e-15
Q7RTS3	328	Pancreas transcription fa	no	N/A	0.473	0.192	0.593	2e-15
Q5IS79	356	Protein atonal homolog 1	no	N/A	0.503	0.188	0.550	8e-13
Q92858	354	Protein atonal homolog 1	no	N/A	0.503	0.189	0.550	9e-13

>sp|Q9VGJ5|FER3_DROME Protein Fer3 OS=Drosophila melanogaster GN=fer3 PE=2 SV=2

 Score =  134 bits (338), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 72/98 (73%), Positives = 79/98 (80%), Gaps = 2/98 (2%)

Query: 34  TRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISF 93
           TRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI F
Sbjct: 78  TRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYIGF 137

Query: 94  MSELLHGTP-NGSTSGSPIY-QMSQREYIPYTALVPTY 129
           M+ELL GTP N   S S +Y  M+     P  A+ P +
Sbjct: 138 MAELLSGTPSNSHKSRSDVYGSMNGHHQAPPPAIHPHH 175

Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E proteins.
Drosophila melanogaster (taxid: 7227)

>sp|Q96RJ6|FER3L_HUMAN Fer3-like protein OS=Homo sapiens GN=FERD3L PE=2 SV=1

 Score =  115 bits (289), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 56/67 (83%), Positives = 61/67 (91%)

Query: 35  RRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
           R+RV T AQR+AANIRER+RMFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM
Sbjct: 94  RKRVITYAQRQAANIRERKRMFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFM 153

Query: 95  SELLHGT 101
           +ELL   
Sbjct: 154 TELLESC 160

Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E proteins.

Homo sapiens (taxid: 9606)

>sp|Q923Z4|FER3L_MOUSE Fer3-like protein OS=Mus musculus GN=Ferd3l PE=1 SV=1

 Score =  115 bits (288), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 57/73 (78%), Positives = 62/73 (84%)

Query: 35  RRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
           R+RV T AQR+AANIRER+RMFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM
Sbjct: 96  RKRVITYAQRQAANIRERKRMFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFM 155

Query: 95  SELLHGTPNGSTS 107
           +ELL        S
Sbjct: 156 TELLQSKEEKEAS 168

Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E proteins.

Mus musculus (taxid: 10090)

>sp|Q4ZHW1|PTF1A_XENLA Pancreas transcription factor 1 subunit alpha OS=Xenopus laevis GN=ptf1a PE=2 SV=1

 Score = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 49/105 (46%), Positives = 67/105 (63%), Gaps = 12/105 (11%)

Query: 18  GHGGS--STGTNGGH-TKKTRRRVATLAQ----RRAANIRERRRMFNLNEAFDKLRRKVP 70
           G GG   S G  GG    K RRR+ + A+    R+AAN+RERRRM ++N+AF+ LR  +P
Sbjct: 88  GDGGCDLSPGMKGGSLVMKRRRRLRSDAEMQQLRQAANVRERRRMQSINDAFEGLRSHIP 147

Query: 71  TFAYEKRLSRIETLRLAITYISFMSELLHGT-----PNGSTSGSP 110
           T  YEKRLS+++TLRLAI YI+F+SE++        PN  +   P
Sbjct: 148 TLPYEKRLSKVDTLRLAIGYINFLSEMVQSDLPLRNPNSDSGNQP 192

Transcriptional activator (By similarity). Acts together with pdx1 to induce the pancreatic lineage within the endoderm.

Xenopus laevis (taxid: 8355)

>sp|Q9QX98|PTF1A_MOUSE Pancreas transcription factor 1 subunit alpha OS=Mus musculus GN=Ptf1a PE=1 SV=1

 Score = 82.8 bits (203), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 40/88 (45%), Positives = 57/88 (64%)

Query: 14  GRLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFA 73
            RL G  G++        ++ R        R+AAN+RERRRM ++N+AF+ LR  +PT  
Sbjct: 132 ARLGGLNGAAAAAAARRRRRVRSEAELQQLRQAANVRERRRMQSINDAFEGLRSHIPTLP 191

Query: 74  YEKRLSRIETLRLAITYISFMSELLHGT 101
           YEKRLS+++TLRLAI YI+F+SEL+   
Sbjct: 192 YEKRLSKVDTLRLAIGYINFLSELVQAD 219

Transcriptional activator. Binds to the E-box consensus sequence 5'-CANNTG-3'. May play a role in early and late pancreas development and differentiation. Plays an important role in determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates. May be involved in the maintenance of exocrine pancreas-specific gene expression including ELA1 and amylase. Required for the formation of pancreatic acinar and ductal cells. Plays an important role in cerebellar development.

Mus musculus (taxid: 10090)

>sp|Q64305|PTF1A_RAT Pancreas transcription factor 1 subunit alpha OS=Rattus norvegicus GN=Ptf1a PE=1 SV=1

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/67 (58%), Positives = 52/67 (77%), Gaps = 1/67 (1%)

Query: 36  RRVATLAQ-RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
           R  A L Q R+AAN+RERRRM ++N+AF+ LR  +PT  YEKRLS+++TLRLAI YI+F+
Sbjct: 155 RSEAELQQLRQAANVRERRRMQSINDAFEGLRSHIPTLPYEKRLSKVDTLRLAIGYINFL 214

Query: 95  SELLHGT 101
           SEL+   
Sbjct: 215 SELVQAD 221

Transcriptional activator. Binds to the E-box consensus sequence 5'-CANNTG-3'. Plays an important role in determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates. May be involved in the maintenance of exocrine pancreas-specific gene expression including ELA1 and amylase. Required for the formation of pancreatic acinar and ductal cells. Plays an important role in cerebellar development.

Rattus norvegicus (taxid: 10116)

>sp|Q7ZSX3|PTF1A_DANRE Pancreas transcription factor 1 subunit alpha OS=Danio rerio GN=ptf1a PE=2 SV=1

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/78 (51%), Positives = 56/78 (71%), Gaps = 3/78 (3%)

Query: 27  NGGHTKKTRR---RVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIET 83
           +GG  K+ RR    V     R+AAN+RERRRM ++N+AF+ LR  +PT  YEKRLS+++T
Sbjct: 97  DGGLLKRRRRMRSEVEMQQLRQAANVRERRRMQSINDAFEGLRSHIPTLPYEKRLSKVDT 156

Query: 84  LRLAITYISFMSELLHGT 101
           LRLAI YI+F++EL+   
Sbjct: 157 LRLAIGYINFLAELVQSD 174

Transcriptional activator. Required for exocrine pancreatic development.

Danio rerio (taxid: 7955)

>sp|Q7RTS3|PTF1A_HUMAN Pancreas transcription factor 1 subunit alpha OS=Homo sapiens GN=PTF1A PE=1 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 51/64 (79%), Gaps = 1/64 (1%)

Query: 39  ATLAQ-RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSEL 97
           A L Q R+AAN+RERRRM ++N+AF+ LR  +PT  YEKRLS+++TLRLAI YI+F+SEL
Sbjct: 159 AELQQLRQAANVRERRRMQSINDAFEGLRSHIPTLPYEKRLSKVDTLRLAIGYINFLSEL 218

Query: 98  LHGT 101
           +   
Sbjct: 219 VQAD 222

Transcriptional activator. Binds to the E-box consensus sequence 5'-CANNTG-3'. Plays an important role in determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates. May be involved in the maintenance of exocrine pancreas-specific gene expression including ELA1 and amylase. Required for the formation of pancreatic acinar and ductal cells (By similarity). Plays an important role in cerebellar development.

Homo sapiens (taxid: 9606)

>sp|Q5IS79|ATOH1_PANTR Protein atonal homolog 1 OS=Pan troglodytes GN=ATOH1 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 38/69 (55%), Positives = 49/69 (71%), Gaps = 2/69 (2%)

Query: 43  QRR-AANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGT 101
           QRR AAN RERRRM  LN AFD+LR  +P+F  +K+LS+ ETL++A  YI+ +SELL  T
Sbjct: 161 QRRLAANARERRRMHGLNHAFDQLRNVIPSFNNDKKLSKYETLQMAQIYINALSELLQ-T 219

Query: 102 PNGSTSGSP 110
           P+G     P
Sbjct: 220 PSGGEQPPP 228

Transcriptional regulator. Activates E box-dependent transcription in collaboration with TCF3/E47, but the activity is completely antagonized by the negative regulator of neurogenesis HES1. Plays a role in the differentiation of subsets of neural cells by activating E box-dependent transcription.

Pan troglodytes (taxid: 9598)

>sp|Q92858|ATOH1_HUMAN Protein atonal homolog 1 OS=Homo sapiens GN=ATOH1 PE=2 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 38/69 (55%), Positives = 49/69 (71%), Gaps = 2/69 (2%)

Query: 43  QRR-AANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGT 101
           QRR AAN RERRRM  LN AFD+LR  +P+F  +K+LS+ ETL++A  YI+ +SELL  T
Sbjct: 159 QRRLAANARERRRMHGLNHAFDQLRNVIPSFNNDKKLSKYETLQMAQIYINALSELLQ-T 217

Query: 102 PNGSTSGSP 110
           P+G     P
Sbjct: 218 PSGGEQPPP 226

Transcriptional regulator. Activates E box-dependent transcription in collaboration with TCF3/E47, but the activity is completely antagonized by the negative regulator of neurogenesis HES1. Plays a role in the differentiation of subsets of neural cells by activating E box-dependent transcription.

Homo sapiens (taxid: 9606)

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	133
91095215	178	PREDICTED: similar to n-twist [Tribolium	0.744	0.556	0.757	7e-34
347970547	287	AGAP003756-PA [Anopheles gambiae str. PE	0.624	0.289	0.843	2e-32
242007238	168	protein lin-32, putative [Pediculus huma	0.706	0.559	0.75	6e-32
170049966	152	n-twist [Culex quinquefasciatus] gi|1678	0.796	0.697	0.650	8e-32
194744397	195	GF16621 [Drosophila ananassae] gi|190627	0.669	0.456	0.8	1e-31
170056166	389	n-twist [Culex quinquefasciatus] gi|1678	0.721	0.246	0.744	1e-31
157112594	152	n-twist [Aedes aegypti] gi|108878027|gb|	0.766	0.671	0.669	2e-31
357629572	155	putative n-twist [Danaus plexippus]	0.639	0.548	0.816	2e-31
125777650	205	GA19952 [Drosophila pseudoobscura pseudo	0.684	0.443	0.793	2e-31
195445425	198	GK11993 [Drosophila willistoni] gi|19416	0.639	0.429	0.823	2e-31

>gi|91095215|ref|XP_969233.1| PREDICTED: similar to n-twist [Tribolium castaneum] gi|270015990|gb|EFA12438.1| hypothetical protein TcasGA2_TC001473 [Tribolium castaneum]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 81/107 (75%), Positives = 82/107 (76%), Gaps = 8/107 (7%)

Query: 21  GSSTGTNGGHT-----KKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYE 75
           G+  G NG        KK RRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYE
Sbjct: 71  GNRLGRNGPQNGPQSQKKPRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYE 130

Query: 76  KRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQMSQREYIPY 122
           KRLSRIETLRLAITYISFMSELLHG P    S        QREYIPY
Sbjct: 131 KRLSRIETLRLAITYISFMSELLHGHPPDHKSPD---MYPQREYIPY 174

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347970547|ref|XP_310293.3| AGAP003756-PA [Anopheles gambiae str. PEST] gi|333466722|gb|EAA45190.3| AGAP003756-PA [Anopheles gambiae str. PEST]

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 70/83 (84%), Positives = 74/83 (89%)

Query: 21  GSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 80
           G+    + G TKKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR
Sbjct: 59  GAQPAPSSGSTKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 118

Query: 81  IETLRLAITYISFMSELLHGTPN 103
           IETLRLAITYI FMSELL GTP 
Sbjct: 119 IETLRLAITYIGFMSELLAGTPT 141

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007238|ref|XP_002424449.1| protein lin-32, putative [Pediculus humanus corporis] gi|212507849|gb|EEB11711.1| protein lin-32, putative [Pediculus humanus corporis]

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 72/96 (75%), Positives = 80/96 (83%), Gaps = 2/96 (2%)

Query: 32  KKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI 91
           KK RRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI
Sbjct: 71  KKPRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI 130

Query: 92  SFMSELLHGTPNGSTSGSPIYQMS--QREYIPYTAL 125
           SFM+ELL G P      SPI   +  + +++PY+ +
Sbjct: 131 SFMAELLDGGPKNGRIDSPICHFTNPRSDFLPYSLI 166

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170049966|ref|XP_001858896.1| n-twist [Culex quinquefasciatus] gi|167871606|gb|EDS34989.1| n-twist [Culex quinquefasciatus]

 Score =  141 bits (356), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 80/123 (65%), Positives = 86/123 (69%), Gaps = 17/123 (13%)

Query: 15  RLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY 74
           RLS  G     T+   +KKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY
Sbjct: 27  RLSPRGAQPASTSS--SKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY 84

Query: 75  EKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIY--------------QMSQREYI 120
           EKRLSRIETLRLAITYI FMSELL+GTP        +Y                 QREYI
Sbjct: 85  EKRLSRIETLRLAITYIGFMSELLNGTPTHDGRSPELYPNLVHPHHPNHIHPSFHQREYI 144

Query: 121 -PY 122
            PY
Sbjct: 145 SPY 147

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194744397|ref|XP_001954681.1| GF16621 [Drosophila ananassae] gi|190627718|gb|EDV43242.1| GF16621 [Drosophila ananassae]

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 77/90 (85%), Gaps = 1/90 (1%)

Query: 21  GSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 80
           G S GT+    KKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR
Sbjct: 67  GRSNGTSSS-AKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 125

Query: 81  IETLRLAITYISFMSELLHGTPNGSTSGSP 110
           IETLRLAITYI FM+ELL GTP+ S    P
Sbjct: 126 IETLRLAITYIGFMAELLSGTPSNSHKSRP 155

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170056166|ref|XP_001863909.1| n-twist [Culex quinquefasciatus] gi|167875978|gb|EDS39361.1| n-twist [Culex quinquefasciatus]

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 73/98 (74%), Positives = 79/98 (80%), Gaps = 2/98 (2%)

Query: 15  RLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY 74
           RLS  G     T+   +KKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY
Sbjct: 55  RLSPRGAQPASTSS--SKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY 112

Query: 75  EKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIY 112
           EKRLSRIETLRLAITYI FMSELL+GTP        +Y
Sbjct: 113 EKRLSRIETLRLAITYIGFMSELLNGTPTHDGRSPELY 150

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157112594|ref|XP_001657582.1| n-twist [Aedes aegypti] gi|108878027|gb|EAT42252.1| AAEL006206-PA [Aedes aegypti]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 79/118 (66%), Positives = 85/118 (72%), Gaps = 16/118 (13%)

Query: 21  GSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 80
           G+    +   TKKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR
Sbjct: 30  GAQPAPSQSTTKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 89

Query: 81  IETLRLAITYISFMSELLHGTPNGSTSGSP-IY--------------QMSQREYI-PY 122
           IETLRLAITYI FMSELL+GTP      SP +Y                 QREYI PY
Sbjct: 90  IETLRLAITYIGFMSELLNGTPTHHDGRSPELYPNLVHPHHTNHLHPSFHQREYITPY 147

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357629572|gb|EHJ78260.1| putative n-twist [Danaus plexippus]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 71/87 (81%), Positives = 76/87 (87%), Gaps = 2/87 (2%)

Query: 17  SGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEK 76
           +G G SS  +  G  KK RRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEK
Sbjct: 51  AGCGRSSARSTPG--KKPRRRVASVAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEK 108

Query: 77  RLSRIETLRLAITYISFMSELLHGTPN 103
           RLSRIETLRLAITYISFM ELLHG+P 
Sbjct: 109 RLSRIETLRLAITYISFMCELLHGSPQ 135

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125777650|ref|XP_001359681.1| GA19952 [Drosophila pseudoobscura pseudoobscura] gi|54639429|gb|EAL28831.1| GA19952 [Drosophila pseudoobscura pseudoobscura]

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 73/92 (79%), Positives = 79/92 (85%), Gaps = 1/92 (1%)

Query: 11  LFNGRLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVP 70
           L   R S HG  S G++   +KKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVP
Sbjct: 58  LVPQRPSTHG-RSNGSSSSSSKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVP 116

Query: 71  TFAYEKRLSRIETLRLAITYISFMSELLHGTP 102
           TFAYEKRLSRIETLRLAITYI FM+ELL GTP
Sbjct: 117 TFAYEKRLSRIETLRLAITYIGFMAELLSGTP 148

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195445425|ref|XP_002070318.1| GK11993 [Drosophila willistoni] gi|194166403|gb|EDW81304.1| GK11993 [Drosophila willistoni]

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 70/85 (82%), Positives = 77/85 (90%)

Query: 21  GSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 80
           G S G++   +KKTRRRVA++AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR
Sbjct: 65  GRSHGSSSSSSKKTRRRVASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSR 124

Query: 81  IETLRLAITYISFMSELLHGTPNGS 105
           IETLRLAITYI FM+ELL GTP+ S
Sbjct: 125 IETLRLAITYIGFMAELLSGTPSNS 149

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	133
FB|FBgn0037937	195	Fer3 "48 related 3" [Drosophil	0.706	0.482	0.581	1e-20
UNIPROTKB|F1NJS8	163	FERD3L "Uncharacterized protei	0.345	0.282	0.891	6.7e-17
UNIPROTKB|E2R686	167	FERD3L "Uncharacterized protei	0.390	0.311	0.807	1.4e-16
UNIPROTKB|F1MFN4	164	FERD3L "Uncharacterized protei	0.330	0.268	0.931	1.8e-16
UNIPROTKB|Q96RJ6	166	FERD3L "Fer3-like protein" [Ho	0.330	0.265	0.931	1.8e-16
UNIPROTKB|F1SEI0	164	FERD3L "Uncharacterized protei	0.330	0.268	0.931	1.8e-16
MGI|MGI:2150010	168	Ferd3l "Fer3-like (Drosophila)	0.330	0.261	0.931	1.8e-16
RGD|1311812	166	Ferd3l "Fer3-like (Drosophila)	0.330	0.265	0.931	1.8e-16
ZFIN|ZDB-GENE-081104-461	81	ferd3l "Fer3-like (Drosophila)	0.330	0.543	0.818	6.9e-15
FB|FBgn0037475	251	Fer1 "48 related 1" [Drosophil	0.481	0.254	0.468	1.1e-11

FB|FBgn0037937 Fer3 "48 related 3" [Drosophila melanogaster (taxid:7227)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 57/98 (58%), Positives = 65/98 (66%)

Query:    38 VATLXXXXXXXXXXXXXMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSEL 97
             VA++             MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI FM+EL
Sbjct:    82 VASMAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYIGFMAEL 141

Query:    98 LHGTPNGS-TSGSPIY-QMSQREYIPYTALVP--TYPA 131
             L GTP+ S  S S +Y  M+     P  A+ P   +PA
Sbjct:   142 LSGTPSNSHKSRSDVYGSMNGHHQAPPPAIHPHHLHPA 179

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F1NJS8 FERD3L "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 41/46 (89%), Positives = 45/46 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHG 100
             MFNLNEAFD+LR+KVPTFAYEKRLSRIETLRLAI YISFM+ELL+G
Sbjct:   111 MFNLNEAFDQLRKKVPTFAYEKRLSRIETLRLAIVYISFMTELLNG 156

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

UNIPROTKB|E2R686 FERD3L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 42/52 (80%), Positives = 44/52 (84%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGST 106
             MFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM+ELL       T
Sbjct:   115 MFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFMTELLESCAKKET 166

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F1MFN4 FERD3L "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 41/44 (93%), Positives = 43/44 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
             MFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM+ELL
Sbjct:   113 MFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFMTELL 156

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|Q96RJ6 FERD3L "Fer3-like protein" [Homo sapiens (taxid:9606)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 41/44 (93%), Positives = 43/44 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
             MFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM+ELL
Sbjct:   114 MFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFMTELL 157

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

UNIPROTKB|F1SEI0 FERD3L "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 41/44 (93%), Positives = 43/44 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
             MFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM+ELL
Sbjct:   112 MFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFMTELL 155

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

MGI|MGI:2150010 Ferd3l "Fer3-like (Drosophila)" [Mus musculus (taxid:10090)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 41/44 (93%), Positives = 43/44 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
             MFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM+ELL
Sbjct:   116 MFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFMTELL 159

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP

GO:0046983 "protein dimerization activity" evidence=IEA

RGD|1311812 Ferd3l "Fer3-like (Drosophila)" [Rattus norvegicus (taxid:10116)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 41/44 (93%), Positives = 43/44 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
             MFNLNEAFD+LRRKVPTFAYEKRLSRIETLRLAI YISFM+ELL
Sbjct:   114 MFNLNEAFDQLRRKVPTFAYEKRLSRIETLRLAIVYISFMTELL 157

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA;ISO

GO:0046983 "protein dimerization activity" evidence=IEA

ZFIN|ZDB-GENE-081104-461 ferd3l "Fer3-like (Drosophila)" [Danio rerio (taxid:7955)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 36/44 (81%), Positives = 43/44 (97%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
             MF+LNEAFD+LRR+VPTFAYEKRLSRIETLRLAI YI+FM+++L
Sbjct:    37 MFSLNEAFDRLRRRVPTFAYEKRLSRIETLRLAIVYIAFMTDIL 80

GO:0046983 "protein dimerization activity" evidence=IEA

FB|FBgn0037475 Fer1 "48 related 1" [Drosophila melanogaster (taxid:7227)]

 Score = 159 (61.0 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 30/64 (46%), Positives = 47/64 (73%)

Query:    55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQM 114
             M ++NEAF+ LR  +PT  YEKRLS+++TL+LAI+YI+F+SE++    NG+  G  + + 
Sbjct:    94 MQSINEAFEGLRTHIPTLPYEKRLSKVDTLKLAISYITFLSEMVKKDKNGNEPGLSLQRN 153

Query:   115 SQRE 118
              Q+E
Sbjct:   154 YQKE 157

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

---

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)
Q9VGJ5	FER3_DROME	No assigned EC number	0.7346	0.7218	0.4923	yes	N/A
Q20561	HLH13_CAEEL	No assigned EC number	0.5396	0.4661	0.4217	yes	N/A
Q96RJ6	FER3L_HUMAN	No assigned EC number	0.8358	0.5037	0.4036	yes	N/A
Q7ZSX3	PTF1A_DANRE	No assigned EC number	0.5128	0.5639	0.2830	yes	N/A
Q923Z4	FER3L_MOUSE	No assigned EC number	0.7808	0.5488	0.4345	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	133
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-16
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-16
smart00353	53	smart00353, HLH, helix loop helix domain	2e-15

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

 Score = 67.5 bits (166), Expect = 2e-16
 Identities = 26/52 (50%), Positives = 36/52 (69%), Gaps = 1/52 (1%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
          +R+A N RERRR   +N+AF++LR  +PT    K+LS+ E LRLAI YI  +
Sbjct: 1  RRKAHNERERRRRDRINDAFEELRELLPT-PPNKKLSKAEILRLAIEYIKHL 51

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 = 67.6 bits (166), Expect = 2e-16
 Identities = 28/57 (49%), Positives = 38/57 (66%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          +R A N+RERRR   +N+AFD+LR  +PT    K+LS+ E LR A+ YI  + ELL 
Sbjct: 4  RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 64.9 bits (159), Expect = 2e-15
 Identities = 28/52 (53%), Positives = 34/52 (65%)

Query: 48 NIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          N RERRR   +NEAFD+LR  +PT    K+LS+ E LRLAI YI  + E L 
Sbjct: 1  NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	133
KOG3960|consensus	284		99.8
KOG4029|consensus	228		99.77
KOG3898|consensus	254		99.62
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.61
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.54
KOG4395|consensus	285		99.5
smart00353	53	HLH helix loop helix domain.	99.46
KOG4447|consensus	173		99.4
KOG3910|consensus	632		99.12
KOG0561|consensus	373		99.07
KOG1319|consensus	229		98.59
KOG1318|consensus	411		98.41
KOG2483|consensus	232		98.28
KOG4304|consensus	250		97.71
KOG3561|consensus	803		97.4
KOG2588|consensus	953		96.95
KOG4447|consensus	173		96.87
PLN03217	93	transcription factor ATBS1; Provisional	95.02
KOG3560|consensus	712		93.46
KOG3558|consensus	768		85.85

>KOG3960|consensus

Probab=99.80  E-value=2.9e-19  Score=145.02  Aligned_cols=75  Identities=36%  Similarity=0.632  Sum_probs=66.5

Q ss_pred             CcccccchhhHHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q psy8988          31 TKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGST  106 (133)
Q Consensus        31 ~k~~rrr~~~~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~~~  106 (133)
                      -|..+|+..+++||++|.+|||+|.++||+|||.|+++.-. +++++|.||||||.||+||..||++|++.+....
T Consensus       106 ckackrks~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~-NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~  180 (284)
T KOG3960|consen  106 CKACKRKSTSVDRRKAATMRERRRLKKVNEAFETLKRRTSS-NPNQRLPKVEILRSAIRYIERLQALLQEQDQAEK  180 (284)
T ss_pred             hhhccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCC-CccccccHHHHHHHHHHHHHHHHHHHHHhhccch
Confidence            46677888899999999999999999999999999988743 5789999999999999999999999997655433

>KOG4029|consensus

Probab=99.77  E-value=5.4e-19  Score=140.51  Aligned_cols=67  Identities=45%  Similarity=0.634  Sum_probs=62.2

Q ss_pred             hHHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q psy8988          40 TLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY-EKRLSRIETLRLAITYISFMSELLHGTPNGST  106 (133)
Q Consensus        40 ~~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~-~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~~~  106 (133)
                      ...+|.++|+|||+||+.||.+|..||.+||..+. ++|||||+||+.||.||.+|+++|+.+.....
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~~  173 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPLN  173 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCCC
Confidence            44688999999999999999999999999999988 99999999999999999999999998876653

>KOG3898|consensus

Probab=99.62  E-value=3.7e-16  Score=127.02  Aligned_cols=63  Identities=46%  Similarity=0.600  Sum_probs=58.2

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNG  104 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~  104 (133)
                      .+|.++|+|||+||++||+||+.||.+||.+..+.|+|||+||++|-+||..|++++......
T Consensus        71 ~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~ls~~~~  133 (254)
T KOG3898|consen   71 LRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVLLSGIAP  133 (254)
T ss_pred             hhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccccccCCCc
Confidence            588999999999999999999999999998889999999999999999999999988754444

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

Probab=99.61  E-value=2.2e-15  Score=95.35  Aligned_cols=53  Identities=38%  Similarity=0.616  Sum_probs=49.5

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCC--CCCCCCCHHHHHHHHHHHHHHHH
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTF--AYEKRLSRIETLRLAITYISFMS   95 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~--~~~~klSKi~tL~~Ai~YI~~L~   95 (133)
                      +|..||.+||.|+..||++|+.|+..||..  ....|++|++||..||+||..||
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            588999999999999999999999999995  26888999999999999999996

; 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=99.54  E-value=4e-14  Score=89.81  Aligned_cols=58  Identities=48%  Similarity=0.743  Sum_probs=53.5

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      .+|..+|..||.|+..||.+|+.|+..||....+.+++|+.||..|++||..|+..++
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            4678899999999999999999999999997678999999999999999999998653

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

>KOG4395|consensus

Probab=99.50  E-value=5.9e-14  Score=114.25  Aligned_cols=65  Identities=48%  Similarity=0.585  Sum_probs=59.2

Q ss_pred             hHHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy8988          40 TLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNG  104 (133)
Q Consensus        40 ~~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~  104 (133)
                      ...+|.++|+|||+||..||.||+.||..+|....+++|||.+||++|-.||..|..+|+.....
T Consensus       171 ~~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~~~~~~  235 (285)
T KOG4395|consen  171 NSHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLDLPMSG  235 (285)
T ss_pred             HHhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhcCcccc
Confidence            34578899999999999999999999999999999999999999999999999999999754433

>smart00353 HLH helix loop helix domain

Probab=99.46  E-value=3e-13  Score=84.32  Aligned_cols=52  Identities=54%  Similarity=0.776  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          48 NIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        48 n~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      |..||.|+..||++|+.|+..||....+.+++|+.||..|++||..|+..++
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            5789999999999999999999986668999999999999999999998765

>KOG4447|consensus

Probab=99.40  E-value=3.8e-13  Score=102.73  Aligned_cols=59  Identities=47%  Similarity=0.764  Sum_probs=55.3

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCC
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGT  101 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~  101 (133)
                      .+|.-||.|||+|-+.||+||..||..+|+.|. .|+|||.||++|..||.+|..+|...
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPs-dklSkiqtLklA~ryidfl~~vl~s~  135 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPS-DKLSKIQTLKLAARYIDFLYQVLQSD  135 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCc-cccccccchhhcccCCchhhhccccc
Confidence            489999999999999999999999999999764 67999999999999999999999976

>KOG3910|consensus

Probab=99.12  E-value=5.7e-11  Score=104.36  Aligned_cols=59  Identities=31%  Similarity=0.414  Sum_probs=52.8

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHhcC
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKV-PTFAYEKRLSRIETLRLAITYISFMSELLHG  100 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~l-P~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~  100 (133)
                      +||++.|+|||.|+++||+||++|-+.+ -++..+|-.+|+-||.+|+..|..|++.+++
T Consensus       525 ERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  525 ERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             HHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999995544 4445799999999999999999999999985

>KOG0561|consensus

Probab=99.07  E-value=4.1e-10  Score=94.17  Aligned_cols=54  Identities=33%  Similarity=0.512  Sum_probs=49.9

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE   96 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~   96 (133)
                      -||.-||-.||+||+.||.+|..||.+||. ..+.||||..||+...+||..|+.
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr-~eGEKLSKAAILQQTa~yI~~Le~  112 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPR-KEGEKLSKAAILQQTADYIHQLEG  112 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCc-ccchhhHHHHHHHHHHHHHHHHHh
Confidence            367789999999999999999999999998 568999999999999999999875

>KOG1319|consensus

Probab=98.59  E-value=2.1e-07  Score=73.67  Aligned_cols=58  Identities=29%  Similarity=0.457  Sum_probs=50.6

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCC----CCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAY----EKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~----~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      .||.+|..-||+|+.-||.+|+.|+.+||...+    +.|+||.-||..+|+||.+|..-..
T Consensus        61 rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~  122 (229)
T KOG1319|consen   61 RRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKK  122 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356679999999999999999999999998753    4599999999999999999976443

>KOG1318|consensus

Probab=98.41  E-value=1.2e-06  Score=75.91  Aligned_cols=58  Identities=24%  Similarity=0.358  Sum_probs=52.5

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      +||-.||+-||+|+-.||+...+|...||... .+-++.|--||+.+++||..|++.++
T Consensus       232 ~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  232 RKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            35567999999999999999999999999875 57788899999999999999998877

>KOG2483|consensus

Probab=98.28  E-value=2.3e-06  Score=69.31  Aligned_cols=59  Identities=25%  Similarity=0.353  Sum_probs=51.4

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ...|..||+-||+|+..|.++|+.|++.||..+.+++-+-+.||+.|..||..|+....
T Consensus        57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~  115 (232)
T KOG2483|consen   57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSA  115 (232)
T ss_pred             CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHH
Confidence            35789999999999999999999999999997666655589999999999999876543

>KOG4304|consensus

Probab=97.71  E-value=3.9e-05  Score=62.69  Aligned_cols=57  Identities=16%  Similarity=0.342  Sum_probs=48.3

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCC-----CCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAY-----EKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~~-----~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ++..+=.-||+|+.-||.++++|+++||....     -.||-|.+||.++++|.+.|+..-.
T Consensus        32 rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   32 RKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             hhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            44457788999999999999999999998642     2688999999999999999988433

>KOG3561|consensus

Probab=97.40  E-value=0.00043  Score=64.53  Aligned_cols=54  Identities=26%  Similarity=0.430  Sum_probs=50.1

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHHH
Q psy8988          44 RRAANIRERRRMFNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMSEL   97 (133)
Q Consensus        44 R~~an~RER~R~~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~~~   97 (133)
                      |..+|.-||+|+.++|...++|-..||... -.+|+.|..||+.||..|+.+.++
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            788999999999999999999999999854 479999999999999999998885

>KOG2588|consensus

Probab=96.95  E-value=0.00079  Score=63.46  Aligned_cols=61  Identities=30%  Similarity=0.351  Sum_probs=54.1

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNG  104 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~  104 (133)
                      .+|.+||.-|++=+-.||+-..+|++.+|.  .+-|+.|-++|+.||+||.+|+...+....+
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g--~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~  335 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPG--TEAKLNKSAVLRKAIDYIEDLQGYNQKLKLE  335 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCc--cHhhhhhhhhHHHHHHHHHHhhccccccchh
Confidence            579999999999999999999999999997  5678999999999999999999876644333

>KOG4447|consensus

Probab=96.87  E-value=0.00065  Score=52.39  Aligned_cols=58  Identities=24%  Similarity=0.243  Sum_probs=48.2

Q ss_pred             hHHHHHHhHHH-HHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Q psy8988          40 TLAQRRAANIR-ERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL   98 (133)
Q Consensus        40 ~~~rR~~an~R-ER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L   98 (133)
                      ....+.-+|.+ ||.|.+.+|++|..|+..+|..+. .+.+++.+|+.+..||.+|.++-
T Consensus        18 ~~~~~~~~r~~~e~~R~~~ls~~s~l~g~l~pgspa-~gk~~~ktlr~~~~~~~~~dE~q   76 (173)
T KOG4447|consen   18 GVSEEECDRQRKERGRKRRLSDASTLLGKLEPGSPA-DGKRGKKTLRIGTDSIQSLDELQ   76 (173)
T ss_pred             chhhhhhhhhHHHHhHHhhhhhhhhhccccCCCCCC-cccccccccccCCCchhhHHHHH
Confidence            34556666666 999999999999999999999764 55788999999999999998753

>PLN03217 transcription factor ATBS1; Provisional

Probab=95.02  E-value=0.056  Score=38.06  Aligned_cols=45  Identities=18%  Similarity=0.263  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHhhCCCCC---CCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          55 MFNLNEAFDKLRRKVPTFA---YEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        55 ~~~in~aF~~LR~~lP~~~---~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      -.+||+-...|+..||...   ...|.|-..+|+.+++||..|..-++
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvD   66 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVD   66 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHH
Confidence            4579999999999999864   34567778999999999999877655

>KOG3560|consensus

Probab=93.46  E-value=0.12  Score=47.18  Aligned_cols=64  Identities=27%  Similarity=0.503  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHH---HHHHHhcCCCCCCCCCCCCCCCCCCCCCCcc
Q psy8988          56 FNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYIS---FMSELLHGTPNGSTSGSPIYQMSQREYIPYT  123 (133)
Q Consensus        56 ~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~---~L~~~L~~~~~~~~~~~p~~~~~~~~~~p~~  123 (133)
                      ..||.-+|.|-.+||... --.||.|+.+||+++.|+.   +.+.+|..+.....+..+.+    ..++||.
T Consensus        38 dRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~KSfFqvvl~~s~~~~~gg~~s~----~a~~~yr  105 (712)
T KOG3560|consen   38 DRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRVKSFFQVVLHQSSRQPAGGPPSP----HASCPYR  105 (712)
T ss_pred             HHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHhcCccccCCCCCCc----cccchhh
Confidence            448999999999999843 3568999999999999986   67788887777777766543    3344554

>KOG3558|consensus

Probab=85.85  E-value=2.7  Score=39.39  Aligned_cols=46  Identities=28%  Similarity=0.413  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHH
Q psy8988          51 ERRRMFNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMSE   96 (133)
Q Consensus        51 ER~R~~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~~   96 (133)
                      -|-|+.+=|+-|.+|..+||-.. -..-|.|+.|+|++|.|.+.=.-
T Consensus        54 ARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk~  100 (768)
T KOG3558|consen   54 ARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRKF  100 (768)
T ss_pred             hhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHHH
Confidence            36788899999999999999432 46679999999999999875443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	133
2ql2_B	60	Crystal Structure Of The Basic-Helix-Loop-Helix Dom		1e-06

>pdb|2QL2|B Chain B, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of The Heterodimer E47NEUROD1 BOUND TO DNA Length = 60

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 31/44 (70%)
Query: 55 MFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELL 98
          M  LN A D LR+ VP ++  ++LS+IETLRLA  YI  +SE+L
Sbjct: 14 MHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL 57

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	133
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	3e-27
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	4e-25
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	4e-15
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	4e-09
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	7e-08
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	3e-07
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	1e-06
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	2e-05
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus} Length = 60

 Score = 94.6 bits (236), Expect = 3e-27
 Identities = 30/58 (51%), Positives = 40/58 (68%)

Query: 42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          ++R  AN RER RM  LN A D LR+ VP ++  ++LS+IETLRLA  YI  +SE+L 
Sbjct: 1  SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR 58

>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* Length = 68

 Score = 89.7 bits (223), Expect = 4e-25
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 33 KTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYIS 92
          + +R+     +R+AA +RERRR+  +NEAF+ L+R   +    +RL ++E LR AI YI 
Sbjct: 2  ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIE 60

Query: 93 FMSELLH 99
           +  LL 
Sbjct: 61 GLQALLR 67

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A* Length = 76

 Score = 64.5 bits (157), Expect = 4e-15
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRK-VPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          +R   N  ER+R  ++NEAF +L R        +K  +++  L+ A+  I  + + + 
Sbjct: 5  KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVR 62

>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 = 4e-09
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
          RR  N+ ER+R   L  +F  LR ++P     ++  ++  L+ A  YI  +
Sbjct: 7  RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 57

>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 = 45.8 bits (109), Expect = 7e-08
 Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
          R   N  ER+R  ++ ++F  LR  VP+   EK  SR + L  A  YI +M
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEK-ASRAQILDKATEYIQYM 62

>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 = 44.7 bits (106), Expect = 2e-07
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
          +R   N  ER+R  ++ ++F  LR  VP+   EK  SR + L  A  YI +M
Sbjct: 2  KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKA-SRAQILDKATEYIQYM 52

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

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 13/53 (24%), Positives = 23/53 (43%)

Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE 96
          R   N  E+ R  +L  + +KL+  VP      R + +  L  A  +I  + +
Sbjct: 2  RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLED 54

>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 = 42.4 bits (100), Expect = 1e-06
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
           +R A N  E+R   ++N+   +L+  V     E +L++   LR AI YI F+
Sbjct: 5  EKRTAHNAIEKRYRSSINDKIIELKDLVV--GTEAKLNKSAVLRKAIDYIRFL 55

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 68

 Score = 39.3 bits (91), Expect = 2e-05
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 36 RRVATLAQRRAANIRERRRM-FNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI 91
             + +   +     E   +  ++N  + +LR  VP      +LS++E L+  I YI
Sbjct: 6  HHHSHMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYI 62

>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 Length = 65

 Score = 38.9 bits (91), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 43 QRRAA-NIRERRRMFNLNEAFDKLRRKVPTFAYE---KRLSRIETLRLAITYISFM 94
          +RRA  N  ERRR   +N    +L + +P  + E      S+   L  A  YI  +
Sbjct: 4  KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

>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 = 37.1 bits (85), Expect = 8e-04
 Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 19/58 (32%)

Query: 49  IRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAI------TYISFMSELLHG 100
           I +R R++N N+ F K    V       RL     LR A+        +     L+ G
Sbjct: 113 IEQRDRLYNDNQVFAK--YNVS------RLQPYLKLRQALLELRPAKNV-----LIDG 157

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	133
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.92
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.91
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.84
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	99.83
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.75
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.66
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.66
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.63
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.62
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.49
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.44
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.36
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.36
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.3
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.28
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.73
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.48
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.0
3muj_A	138	Transcription factor COE3; immunoglobulin like fol	93.25

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

Probab=99.92  E-value=5.5e-25  Score=143.03  Aligned_cols=58  Identities=52%  Similarity=0.766  Sum_probs=56.1

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcC
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHG  100 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~  100 (133)
                      +|.+||+|||+||++||+||+.||.+||..+.++||||++||+.||+||.+|+++|++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~~   59 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILRS   59 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTTC
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHhc
Confidence            6889999999999999999999999999998999999999999999999999999975

>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=99.91  E-value=9e-25  Score=145.28  Aligned_cols=65  Identities=40%  Similarity=0.661  Sum_probs=59.1

Q ss_pred             ccchhhHHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcC
Q psy8988          35 RRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHG  100 (133)
Q Consensus        35 rrr~~~~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~  100 (133)
                      +++..+.++|.+||+|||+||++||+||+.||++||.. +++|+||++||+.||+||.+|+++|++
T Consensus         4 kr~~~~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~-~~~KlSKi~tLr~Ai~YI~~L~~~L~~   68 (68)
T 1mdy_A            4 KRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD   68 (68)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSC-TTSCCCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CcCCCchhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCC-CCCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence            34456778999999999999999999999999999985 489999999999999999999999974

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

Probab=99.84  E-value=2.1e-22  Score=133.81  Aligned_cols=50  Identities=26%  Similarity=0.367  Sum_probs=48.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy8988          47 ANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE   96 (133)
Q Consensus        47 an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~   96 (133)
                      +|+|||+||+.||+||+.||++||..+.++||||||||+.||+||.+||+
T Consensus        18 a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           18 AAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            58999999999999999999999999999999999999999999999985

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

Probab=99.83  E-value=5.3e-21  Score=134.86  Aligned_cols=65  Identities=23%  Similarity=0.369  Sum_probs=54.5

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTS  107 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~~~~  107 (133)
                      |+.....+||.||+.||+||+.||.+||..+.++||||||||++||+||.+|+++|++.+.....
T Consensus        25 R~k~~~~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~~~~~~   89 (97)
T 4aya_A           25 RSKTPVDDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPSFL   89 (97)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTTSTTCC
T ss_pred             HHhcccccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCCCCcch
Confidence            33344566799999999999999999999999999999999999999999999999987765544

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

Probab=99.75  E-value=7e-19  Score=119.01  Aligned_cols=64  Identities=23%  Similarity=0.290  Sum_probs=52.0

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPT-FAYEKRLSRIETLRLAITYISFMSELLHGTPNG  104 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~-~~~~~klSKi~tL~~Ai~YI~~L~~~L~~~~~~  104 (133)
                      .++|..||++||+|+..||++|+.||.+||. .+.++.+||++||+.||+||..|++.|++....
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~~   67 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLN   67 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4578999999999999999999999999995 445666699999999999999999999975544

>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=99.66  E-value=1.7e-16  Score=109.63  Aligned_cols=60  Identities=25%  Similarity=0.393  Sum_probs=55.3

Q ss_pred             hHHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          40 TLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        40 ~~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ...+|..||+.||+|+..||++|+.||.+||..+.+.|+||+.||..||+||.+|+....
T Consensus         3 d~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~   62 (88)
T 1nkp_A            3 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ   62 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            346899999999999999999999999999998788999999999999999999997643

>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=99.66  E-value=2.1e-16  Score=106.94  Aligned_cols=58  Identities=31%  Similarity=0.499  Sum_probs=53.2

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ..+|..||++||+|+..||++|+.|+.+||..+ +.|+||++||+.|++||.+|+..++
T Consensus        10 ~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~~~~~   67 (80)
T 1hlo_A           10 ADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNH   67 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCC-CCCccHHHHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999999999854 5689999999999999999998765

>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=99.63  E-value=7.6e-16  Score=104.60  Aligned_cols=56  Identities=32%  Similarity=0.525  Sum_probs=51.4

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      +|..||.+||+|+..||++|+.|+.+||..+ +.|+||++||+.||+||..|+..++
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~~~~~   57 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKNH   57 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            6889999999999999999999999999854 6789999999999999999996554

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

Probab=99.62  E-value=1.1e-15  Score=104.04  Aligned_cols=56  Identities=23%  Similarity=0.204  Sum_probs=52.8

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        44 R~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      |..||+.||+|+..||++|+.||+.||..+.+.|+||+.||+.|++||..|++...
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~   57 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDR   57 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            78899999999999999999999999998889999999999999999999987543

>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=99.49  E-value=8.3e-14  Score=94.77  Aligned_cols=57  Identities=30%  Similarity=0.366  Sum_probs=52.4

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ..+|..||..||+|+..||++|..|+..||.  .+.|++|+.||..||+||.+|+..++
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~--~~~k~~Ka~IL~~Ai~YI~~Lq~~~~   60 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQ   60 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--SSCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccC--CCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3578899999999999999999999999997  46899999999999999999998765

>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=99.44  E-value=1.4e-14  Score=94.23  Aligned_cols=55  Identities=27%  Similarity=0.277  Sum_probs=49.4

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCC---CCCCHHHHHHHHHHHHHHHHHH
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYE---KRLSRIETLRLAITYISFMSEL   97 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~---~klSKi~tL~~Ai~YI~~L~~~   97 (133)
                      +|..||..||.|+..||++|+.|+.+||.....   .|++|+.||..||+||..|+..
T Consensus         5 rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~   62 (65)
T 1an4_A            5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHH
Confidence            466799999999999999999999999986543   5899999999999999999864

>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=99.36  E-value=9.4e-14  Score=90.56  Aligned_cols=57  Identities=21%  Similarity=0.208  Sum_probs=50.1

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCC----CCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFA----YEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~----~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      +|..|+.-||.|+..||.+|+.|+.+||...    .+.++||.+||..||+||..|++.+.
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            3567899999999999999999999999753    25799999999999999999987553

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

Probab=99.36  E-value=3.1e-12  Score=85.41  Aligned_cols=57  Identities=19%  Similarity=0.317  Sum_probs=52.0

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ..+|..+|..||+|+..||+.|..|+..||.  ...|++|..||+.||+||..|+..+.
T Consensus         6 ~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~--~~~K~dK~sIL~~aI~yik~Lq~~~~   62 (71)
T 4h10_B            6 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPG--NARKMDKSTVLQKSIDFLRKHKEITA   62 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSS--CCSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHhhhhhHHHhhHHHHHHHHHHHHHHhCCC--CCCCCcHHHHHHHHHHHHHHHHHhhh
Confidence            4578899999999999999999999999995  46799999999999999999998764

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

Probab=99.30  E-value=5.2e-12  Score=91.29  Aligned_cols=57  Identities=25%  Similarity=0.424  Sum_probs=47.4

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      +|..||.-||+|+..||+.|..|+..||... .+.|++|+.||..||+||.+|+..++
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~   84 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQ   84 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHH
Confidence            5778999999999999999999999999865 36799999999999999999987655

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

Probab=99.28  E-value=3.6e-12  Score=85.36  Aligned_cols=58  Identities=26%  Similarity=0.383  Sum_probs=50.4

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      .+|..|+..||+|+..||.+|+.|+..||... ...|++|+.||+.||+||..|+..-.
T Consensus         8 ~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~~~~   66 (73)
T 4h10_A            8 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGAWL   66 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSCC--
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhcCcc
Confidence            46788999999999999999999999999743 46899999999999999999876443

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

Probab=98.73  E-value=2.1e-08  Score=82.07  Aligned_cols=56  Identities=20%  Similarity=0.310  Sum_probs=44.5

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      .+|..||..||+|+..||..|..|+..||.  ...||.|+.||++||.||..|+.+-.
T Consensus        11 ~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~--~~~~~dk~~il~~~~~~~~~~~~~~~   66 (361)
T 4f3l_A           11 AKRVSRNKSEKKRRDQFNVLIKELGSMLPG--NARKMDKSTVLQKSIDFLRKHKETTA   66 (361)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHTCCS--SSCCCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHhCCC--CCCCcCHHHHHHHHHHHHHHHHhhcc
Confidence            357789999999999999999999999993  56899999999999999999998654

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

Probab=98.48  E-value=1.5e-07  Score=78.00  Aligned_cols=54  Identities=28%  Similarity=0.440  Sum_probs=49.0

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHH
Q psy8988          42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMS   95 (133)
Q Consensus        42 ~rR~~an~RER~R~~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~   95 (133)
                      .+|..||.-||+|+..||..|.+|+.+||... ...|+.|..||++||+||..|+
T Consensus        12 ~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~   66 (387)
T 4f3l_B           12 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR   66 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHH
T ss_pred             hhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhh
Confidence            35778999999999999999999999999643 4689999999999999999987

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

Probab=98.00  E-value=1.7e-05  Score=54.12  Aligned_cols=43  Identities=21%  Similarity=0.375  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHh
Q psy8988          56 FNLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMSELL   98 (133)
Q Consensus        56 ~~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~~~L   98 (133)
                      -.||+.|.+|...||... .+-|.+|-.||+.|++||.+|++-.
T Consensus         5 ~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~   48 (83)
T 4ath_A            5 FNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQ   48 (83)
T ss_dssp             HHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTH
T ss_pred             hhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHH
Confidence            469999999999999753 6789999999999999999997743

>3muj_A Transcription factor COE3; immunoglobulin like fold, helix-loop-helix, structural genom consortium, SGC, DNA binding protein; 1.92A {Homo sapiens} PDB: 3mqi_A

Probab=93.25  E-value=0.19  Score=36.95  Aligned_cols=39  Identities=18%  Similarity=0.368  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHH
Q psy8988          57 NLNEAFDKLRRKVPTFA-YEKRLSRIETLRLAITYISFMS   95 (133)
Q Consensus        57 ~in~aF~~LR~~lP~~~-~~~klSKi~tL~~Ai~YI~~L~   95 (133)
                      .|+-+|+.|.+.+|-++ ...+|.|-.||+.|.++...|-
T Consensus        95 tId~gfqrl~k~~pr~pgdpe~lpk~~~lkraa~l~e~~~  134 (138)
T 3muj_A           95 TIDYGFQRLQKVIPRHPGDPERLPKEVLLKRAADLVEALY  134 (138)
T ss_dssp             CHHHHHHHHHHHSCCCTTCCSSCCHHHHHHHHHHHHHHHH
T ss_pred             ccccchhhhccccCCCCCChhhhhHHHHHHHHHHHHHHHh
Confidence            58899999999999987 4688999999999999888763

---

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	133
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	8e-16
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	3e-12
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	8e-12
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-11
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	5e-11
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	3e-10
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-07

>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 = 64.9 bits (158), Expect = 8e-16
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 33 KTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYIS 92
          + +R+     +R+AA +RERRR+  +NEAF+ L+R   +    +RL ++E LR AI YI 
Sbjct: 2  ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIE 60

Query: 93 FMSELLH 99
           +  LL 
Sbjct: 61 GLQALLR 67

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

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

 Score = 56.1 bits (135), Expect = 3e-12
 Identities = 15/58 (25%), Positives = 27/58 (46%)

Query: 42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
           +RR  N+ ER+R   L  +F  LR ++P     ++  ++  L+ A  YI  +     
Sbjct: 5  VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ 62

>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 = 54.9 bits (132), Expect = 8e-12
 Identities = 13/56 (23%), Positives = 23/56 (41%)

Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          R   N  E+ R  +L  + +KL+  VP      R + +  L  A  +I  + +   
Sbjct: 2  RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDR 57

>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 = 54.4 bits (131), Expect = 1e-11
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 3/57 (5%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYE---KRLSRIETLRLAITYISFMSE 96
          +R   N  ERRR   +N    +L + +P  + E      S+   L  A  YI  + +
Sbjct: 5  RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61

>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 = 52.2 bits (125), Expect = 5e-11
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 4/58 (6%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYE----KRLSRIETLRLAITYISFMSE 96
          +R +    E+ R   L  A  +L   +P    +       S+  T+  A  YI  + +
Sbjct: 2  KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQ 59

>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 = 51.0 bits (122), Expect = 3e-10
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          +R   N  ER+R  ++ ++F  LR  VP+    ++ SR + L  A  YI +M    H
Sbjct: 2  KRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNH 57

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

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

 Score = 44.2 bits (104), Expect = 1e-07
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
          +R A N  E+R   ++N+   +L+  V     E +L++   LR AI YI F+     
Sbjct: 6  KRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQ 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	133
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.78
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.63
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.57
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.48
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.86

>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=99.78  E-value=4e-19  Score=115.91  Aligned_cols=63  Identities=40%  Similarity=0.661  Sum_probs=56.8

Q ss_pred             chhhHHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhcC
Q psy8988          37 RVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHG  100 (133)
Q Consensus        37 r~~~~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~~  100 (133)
                      +.....+|..||.+||.|+..||++|+.|+..||..+ .+|+||++||+.||+||.+|+++|++
T Consensus         6 ~~~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~-~~k~sK~~iL~~Ai~YI~~Lq~~l~e   68 (68)
T d1mdya_           6 KTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALLRD   68 (68)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCT-TSCCCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHhhC
Confidence            3455678999999999999999999999999999854 56999999999999999999999874

>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=99.63  E-value=3.8e-16  Score=103.48  Aligned_cols=56  Identities=23%  Similarity=0.204  Sum_probs=53.0

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        44 R~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      |..||+.||+|+..||++|+.|+.+||..+...|+||++||..|++||..|+..+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~   57 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDR   57 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            78899999999999999999999999998888899999999999999999998765

>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=99.63  E-value=3.1e-16  Score=105.82  Aligned_cols=59  Identities=25%  Similarity=0.403  Sum_probs=54.8

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ..+|..||++||+|+..||++|+.|+.+||..+.+.|+||++||..|++||..|++.++
T Consensus         4 ~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~   62 (88)
T d1nkpa_           4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ   62 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999987788899999999999999999998765

>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=99.60  E-value=9.1e-16  Score=102.48  Aligned_cols=56  Identities=32%  Similarity=0.516  Sum_probs=51.5

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      +|..||.+||.|+..||++|+.|+.+||.. .+.|+||++||+.|++||..|++.++
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~-~~~k~sK~~iL~~A~~yI~~L~~~~~   57 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNH   57 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGG-TTSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999964 56799999999999999999987654

>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=99.57  E-value=3.5e-16  Score=100.10  Aligned_cols=56  Identities=21%  Similarity=0.233  Sum_probs=50.7

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCC----CCCCCCCHHHHHHHHHHHHHHHHHHh
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTF----AYEKRLSRIETLRLAITYISFMSELL   98 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~----~~~~klSKi~tL~~Ai~YI~~L~~~L   98 (133)
                      +|..||..||+|+..||++|+.|+.+||..    ..+.|+||.+||+.|++||.+|++.+
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            467899999999999999999999999952    36789999999999999999998754

>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=99.50  E-value=3e-14  Score=94.65  Aligned_cols=57  Identities=30%  Similarity=0.366  Sum_probs=51.9

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          41 LAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        41 ~~rR~~an~RER~R~~~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      ..+|..||..||+|+..||++|+.|+.+||.  ...|++|++||..|++||..|+..++
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~--~~~k~~K~~iL~~a~~yI~~L~~~~~   60 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQ   60 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--SSCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3578899999999999999999999999996  45689999999999999999998664

>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=99.48  E-value=2.2e-15  Score=96.88  Aligned_cols=54  Identities=26%  Similarity=0.270  Sum_probs=49.3

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhhCCCCC---CCCCCCHHHHHHHHHHHHHHHHH
Q psy8988          43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFA---YEKRLSRIETLRLAITYISFMSE   96 (133)
Q Consensus        43 rR~~an~RER~R~~~in~aF~~LR~~lP~~~---~~~klSKi~tL~~Ai~YI~~L~~   96 (133)
                      +|..||..||+|+..||++|+.|+..||...   .+.++||++||..|++||..|++
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~   61 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ   61 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            4677999999999999999999999999764   46799999999999999999986

>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=98.86  E-value=7.7e-10  Score=69.64  Aligned_cols=41  Identities=24%  Similarity=0.468  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q psy8988          57 NLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH   99 (133)
Q Consensus        57 ~in~aF~~LR~~lP~~~~~~klSKi~tL~~Ai~YI~~L~~~L~   99 (133)
                      .||+.|..||+.||..  ..|.+|++||..||+||..|+..+.
T Consensus         3 ~in~~f~~L~~lvP~~--~~K~~Ka~iL~~Ai~YI~~Lq~~~~   43 (61)
T d1uklc_           3 SINDKIIELKDLVMGT--DAKMHKSGVLRKAIDYIKYLQQVNH   43 (61)
T ss_dssp             CHHHHHHHHHHHHSCS--SCCCCTTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCCC--CCcccHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999963  5689999999999999999998765