Psyllid ID: psy8078

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-----
Protein Sequence
MFLQREKFSETHGASRQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccHcccccccccHHHccccccccccccccccHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHcHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mflqrekfsethgaSRQNLFRLldksdgstqaLSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKllptlppdkklskIEILRLAICYIAYLNNVLET
Flexible Loop (DISEMBL)
mflqrekfsethgasrqnlfrlldksdgstqalsreerrrrrratqkyrtahatrervrveafnsafgelrkllptlppdkklskIEILRLAICYIAYLNNVLET
Low Complexity Region (SEG)
MFLQREKFSETHGASRQNLFRLLDKSDGSTQALSreerrrrrrATQKYRTAHATRERVRVEAFNSAFGElrkllptlppdkklSKIEILRLAICYIAYLNNVLET
Disordered region (IsUnstruct)
*********************************************************VRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL**
Disordered Region (DISOPRED)
********************************************************RVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE*
Disordered Region (DISEMBL)
*************ASRQNLFRLLDKS**************************ATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET
Disordered Region (DISPRO)
********************************************TQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFLQREKFSETHGASRQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET
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	105	2.2.26 [Sep-21-2011]
Q02576	133	Helix-loop-helix protein	yes	N/A	0.714	0.563	0.88	2e-26
Q02575	133	Helix-loop-helix protein	yes	N/A	0.714	0.563	0.88	4e-26
Q64221	135	Helix-loop-helix protein	no	N/A	0.885	0.688	0.69	4e-23
Q02577	135	Helix-loop-helix protein	no	N/A	0.885	0.688	0.69	5e-23
Q90YI8	371	T-cell acute lymphocytic	N/A	N/A	0.485	0.137	0.666	1e-12
P79782	183	Transcription factor 15 O	no	N/A	0.742	0.426	0.494	9e-11
O93507	324	T-cell acute lymphocytic	no	N/A	0.476	0.154	0.64	9e-11
P24899	311	T-cell acute lymphocytic	no	N/A	0.476	0.160	0.64	1e-10
P17542	331	T-cell acute lymphocytic	no	N/A	0.476	0.151	0.64	2e-10
O73823	394	T-cell acute lymphocytic	N/A	N/A	0.485	0.129	0.627	2e-10

>sp|Q02576|HEN1_MOUSE Helix-loop-helix protein 1 OS=Mus musculus GN=Nhlh1 PE=2 SV=1

 Score =  117 bits (292), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query: 31  QALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILR 90
           Q LSREERRRRRRAT KYRTAHATRER+RVEAFN AF ELRKLLPTLPPDKKLSKIEILR
Sbjct: 59  QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query: 91  LAICYIAYLNNVLET 105
           LAICYI+YLN+VL+ 
Sbjct: 119 LAICYISYLNHVLDV 133

May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.
Mus musculus (taxid: 10090)

>sp|Q02575|HEN1_HUMAN Helix-loop-helix protein 1 OS=Homo sapiens GN=NHLH1 PE=1 SV=1

 Score =  116 bits (291), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query: 31  QALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILR 90
           Q LSREERRRRRRAT KYRTAHATRER+RVEAFN AF ELRKLLPTLPPDKKLSKIEILR
Sbjct: 59  QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query: 91  LAICYIAYLNNVLET 105
           LAICYI+YLN+VL+ 
Sbjct: 119 LAICYISYLNHVLDV 133

May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

Homo sapiens (taxid: 9606)

>sp|Q64221|HEN2_MOUSE Helix-loop-helix protein 2 OS=Mus musculus GN=Nhlh2 PE=1 SV=2

 Score =  106 bits (265), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 69/100 (69%), Positives = 77/100 (77%), Gaps = 7/100 (7%)

Query: 6   EKFSETHGASRQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNS 65
           E   +  G SR  L+          Q LSREE+RRRRRAT KYR+AHATRER+RVEAFN 
Sbjct: 43  EADGDGKGGSRAALYP-------HPQQLSREEKRRRRRATAKYRSAHATRERIRVEAFNL 95

Query: 66  AFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
           AF ELRKLLPTLPPDKKLSKIEILRLAICYI+YLN+VL+ 
Sbjct: 96  AFAELRKLLPTLPPDKKLSKIEILRLAICYISYLNHVLDV 135

May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

Mus musculus (taxid: 10090)

>sp|Q02577|HEN2_HUMAN Helix-loop-helix protein 2 OS=Homo sapiens GN=NHLH2 PE=1 SV=1

 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 69/100 (69%), Positives = 77/100 (77%), Gaps = 7/100 (7%)

Query: 6   EKFSETHGASRQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNS 65
           E   +  G SR  L+          Q LSREE+RRRRRAT KYR+AHATRER+RVEAFN 
Sbjct: 43  EAEGDGKGGSRAALYP-------HPQQLSREEKRRRRRATAKYRSAHATRERIRVEAFNL 95

Query: 66  AFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
           AF ELRKLLPTLPPDKKLSKIEILRLAICYI+YLN+VL+ 
Sbjct: 96  AFAELRKLLPTLPPDKKLSKIEILRLAICYISYLNHVLDV 135

May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

Homo sapiens (taxid: 9606)

>sp|Q90YI8|TAL1_TAKRU T-cell acute lymphocytic leukemia protein 1 OS=Takifugu rubripes GN=tal1 PE=2 SV=1

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query: 54  TRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE 104
           +RER R +  N AF ELRKL+PT PPDKKLSK EILRLA+ YI++L+N+LE
Sbjct: 211 SRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYISFLSNLLE 261

Transcription factor that plays a pivotal role in hemopoietic and endothelial development.

Takifugu rubripes (taxid: 31033)

>sp|P79782|TCF15_CHICK Transcription factor 15 OS=Gallus gallus GN=TCF15 PE=2 SV=2

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 42/85 (49%), Positives = 51/85 (60%), Gaps = 7/85 (8%)

Query: 24  DKSDGSTQALSREERRRRRRATQ-----KYRTAHATRERVRVEAFNSAFGELRKLLPTLP 78
           D+S G  +    E RR+  R T      K R A   RER R ++ N+AF  LR L+PT P
Sbjct: 35  DQSYGCCEGA--EARRKVPRKTGPMVMVKQRQAANARERDRTQSVNTAFTALRTLIPTEP 92

Query: 79  PDKKLSKIEILRLAICYIAYLNNVL 103
            D+KLSKIE LRLA  YIA+L NVL
Sbjct: 93  VDRKLSKIETLRLASSYIAHLANVL 117

May function as an early transcriptional regulator, involved in the patterning of the mesoderm and in lineage determination of cell types derived from the mesoderm.

Gallus gallus (taxid: 9031)

>sp|O93507|TAL1_DANRE T-cell acute lymphocytic leukemia protein 1 homolog OS=Danio rerio GN=tal1 PE=1 SV=1

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 32/50 (64%), Positives = 38/50 (76%)

Query: 54  TRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL 103
           +RER R +  N AF ELRKL+PT PPDKKLSK EILRLA+ YI +L  +L
Sbjct: 192 SRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLL 241

Transcription factor that plays a pivotal role in hemopoietic and endothelial development, acting synergistically with lmo2 and downstream of clo. Specifies mesodermal precursors to a hemangioblast cell fate. Hemangioblasts are bipotential precursors of blood and endothelium, and in the absence of hemopoietic induction cues such as gata1, tal1/scl-lmo2-induced hemangioblasts differentiate into endothelial cells. Isoform alpha and isoform beta are redundant for the initiation of primitive hemopoiesis but have distinct roles in the regulation of primitive erythroid differentiation and definitive hemopoietic stem cell specification, most likely due to differences in expression levels. Specification of definitive hemopoietic stem cells requires isoform beta. DNA binding is required for erythroid maturation, but not for its other hemopoietic functions. Endothelial roles include development of the dorsal aorta, the site of definitive hemopoiesis in the embryo. Required for angiogenesis but not angioblast specification. Has an additional role in endocardium formation during heart development. May play a role in central nervous system development.

Danio rerio (taxid: 7955)

>sp|P24899|TAL1_CHICK T-cell acute lymphocytic leukemia protein 1 homolog OS=Gallus gallus GN=TAL1 PE=2 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/50 (64%), Positives = 38/50 (76%)

Query: 54  TRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL 103
           +RER R +  N AF ELRKL+PT PPDKKLSK EILRLA+ YI +L  +L
Sbjct: 186 SRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLL 235

Implicated in the genesis of hemopoietic malignancies. It may play an important role in hemopoietic differentiation.

Gallus gallus (taxid: 9031)

>sp|P17542|TAL1_HUMAN T-cell acute lymphocytic leukemia protein 1 OS=Homo sapiens GN=TAL1 PE=1 SV=2

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/50 (64%), Positives = 38/50 (76%)

Query: 54  TRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL 103
           +RER R +  N AF ELRKL+PT PPDKKLSK EILRLA+ YI +L  +L
Sbjct: 194 SRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLL 243

Implicated in the genesis of hemopoietic malignancies. It may play an important role in hemopoietic differentiation. Serves as a positive regulator of erythroid differentiation.

Homo sapiens (taxid: 9606)

>sp|O73823|TAL1_XENLA T-cell acute lymphocytic leukemia protein 1 OS=Xenopus laevis GN=tal1 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 39/51 (76%)

Query: 54  TRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE 104
           +RER R +  N AF ELRKL+PT PPDKKLSK EILRLA+ YI +L  +L+
Sbjct: 269 SRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLLD 319

Transcription factor that acts synergistically with lmo2 and gata1 to specify embryonic dorsal mesoderm to a hematopoietic fate.

Xenopus laevis (taxid: 8355)

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	105
355558310	99	hypothetical protein EGK_01133 [Macaca m	0.638	0.676	0.865	2e-26
345491490	91	PREDICTED: helix-loop-helix protein 1-li	0.790	0.912	0.843	2e-26
270005642	176	hypothetical protein TcasGA2_TC007725 [T	0.695	0.414	0.931	3e-26
241832872	103	helix-loop-helix protein, putative [Ixod	0.761	0.776	0.792	9e-26
157105998	133	salivary gland-expressed bHLH, putative	0.761	0.601	0.833	1e-25
340718816	93	PREDICTED: helix-loop-helix protein 1-li	0.752	0.849	0.886	1e-25
383848819	93	PREDICTED: helix-loop-helix protein 1-li	0.685	0.774	0.958	1e-25
110759754	93	PREDICTED: helix-loop-helix protein 1-li	0.685	0.774	0.958	1e-25
307174828	109	Helix-loop-helix protein 1 [Camponotus f	0.752	0.724	0.873	2e-25
307205014	109	Helix-loop-helix protein 1 [Harpegnathos	0.685	0.660	0.944	2e-25

>gi|355558310|gb|EHH15090.1| hypothetical protein EGK_01133 [Macaca mulatta]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/67 (86%), Positives = 63/67 (94%)

Query: 39  RRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAY 98
           RRRRRAT KYR+AHATRER+RVEAFN AF ELRKLLPTLPPDKKLSKIEILRLAICYI+Y
Sbjct: 33  RRRRRATAKYRSAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILRLAICYISY 92

Query: 99  LNNVLET 105
           LN+VL+ 
Sbjct: 93  LNHVLDV 99

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345491490|ref|XP_001605861.2| PREDICTED: helix-loop-helix protein 1-like [Nasonia vitripennis]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 70/83 (84%), Positives = 74/83 (89%)

Query: 22  LLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDK 81
           ++      T +LSREERRRRRRATQKYRTAHATRERVRVEAFN AF ELRKLLPTLPPDK
Sbjct: 8   IVSGVTSGTGSLSREERRRRRRATQKYRTAHATRERVRVEAFNLAFAELRKLLPTLPPDK 67

Query: 82  KLSKIEILRLAICYIAYLNNVLE 104
           KLSKIEILRLAICYIAYLN+VLE
Sbjct: 68  KLSKIEILRLAICYIAYLNHVLE 90

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270005642|gb|EFA02090.1| hypothetical protein TcasGA2_TC007725 [Tribolium castaneum]

 Score =  122 bits (305), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 68/73 (93%), Positives = 71/73 (97%)

Query: 32  ALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRL 91
           ALSREERRRRRRATQKYRTAHATRER+RVEAFN AF ELRKLLPTLPPDKKLSKIEILRL
Sbjct: 103 ALSREERRRRRRATQKYRTAHATRERIRVEAFNVAFAELRKLLPTLPPDKKLSKIEILRL 162

Query: 92  AICYIAYLNNVLE 104
           AICYIAYLN+VL+
Sbjct: 163 AICYIAYLNHVLD 175

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241832872|ref|XP_002414911.1| helix-loop-helix protein, putative [Ixodes scapularis] gi|215509123|gb|EEC18576.1| helix-loop-helix protein, putative [Ixodes scapularis]

 Score =  120 bits (302), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 65/82 (79%), Positives = 74/82 (90%), Gaps = 2/82 (2%)

Query: 26  SDG--STQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKL 83
           SDG  +  +LSRE+RRRRRRATQKYR AHATRER+RVEAFN AF +LR+LLPTLPPDKKL
Sbjct: 22  SDGHQAVVSLSREDRRRRRRATQKYRLAHATRERIRVEAFNVAFAQLRRLLPTLPPDKKL 81

Query: 84  SKIEILRLAICYIAYLNNVLET 105
           SKIEILRLAICYI+YLN+VL+ 
Sbjct: 82  SKIEILRLAICYISYLNHVLDV 103

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157105998|ref|XP_001649119.1| salivary gland-expressed bHLH, putative [Aedes aegypti] gi|108879945|gb|EAT44170.1| AAEL004428-PA [Aedes aegypti]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 70/84 (83%), Positives = 75/84 (89%), Gaps = 4/84 (4%)

Query: 25  KSDGSTQA----LSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPD 80
           K DGS Q+    L+REERRRRRRAT KYRTAHATRER+RVEAFN AF ELRKLLPTLPPD
Sbjct: 49  KHDGSVQSELAGLTREERRRRRRATLKYRTAHATRERIRVEAFNVAFTELRKLLPTLPPD 108

Query: 81  KKLSKIEILRLAICYIAYLNNVLE 104
           KKLSKIEIL+LAICYIAYLN+VLE
Sbjct: 109 KKLSKIEILKLAICYIAYLNHVLE 132

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340718816|ref|XP_003397859.1| PREDICTED: helix-loop-helix protein 1-like [Bombus terrestris]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 70/79 (88%), Positives = 71/79 (89%)

Query: 26  SDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSK 85
           S      LSREERRRRRRATQKYRTAHATRERVRVEAFN AF ELRKLLPTLPPDKKLSK
Sbjct: 14  SAPGAGTLSREERRRRRRATQKYRTAHATRERVRVEAFNLAFAELRKLLPTLPPDKKLSK 73

Query: 86  IEILRLAICYIAYLNNVLE 104
           IEILRLAICYIAYLN+VLE
Sbjct: 74  IEILRLAICYIAYLNHVLE 92

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383848819|ref|XP_003700045.1| PREDICTED: helix-loop-helix protein 1-like [Megachile rotundata]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/72 (95%), Positives = 70/72 (97%)

Query: 33  LSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLA 92
           LSREERRRRRRATQKYRTAHATRERVRVEAFN AF ELRKLLPTLPPDKKLSKIEILRLA
Sbjct: 21  LSREERRRRRRATQKYRTAHATRERVRVEAFNLAFAELRKLLPTLPPDKKLSKIEILRLA 80

Query: 93  ICYIAYLNNVLE 104
           ICYIAYLN+VLE
Sbjct: 81  ICYIAYLNHVLE 92

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110759754|ref|XP_001122281.1| PREDICTED: helix-loop-helix protein 1-like [Apis mellifera] gi|350419807|ref|XP_003492307.1| PREDICTED: helix-loop-helix protein 1-like [Bombus impatiens] gi|380012301|ref|XP_003690224.1| PREDICTED: helix-loop-helix protein 1-like [Apis florea]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/72 (95%), Positives = 70/72 (97%)

Query: 33  LSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLA 92
           LSREERRRRRRATQKYRTAHATRERVRVEAFN AF ELRKLLPTLPPDKKLSKIEILRLA
Sbjct: 21  LSREERRRRRRATQKYRTAHATRERVRVEAFNLAFAELRKLLPTLPPDKKLSKIEILRLA 80

Query: 93  ICYIAYLNNVLE 104
           ICYIAYLN+VLE
Sbjct: 81  ICYIAYLNHVLE 92

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307174828|gb|EFN65122.1| Helix-loop-helix protein 1 [Camponotus floridanus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 69/79 (87%), Positives = 72/79 (91%)

Query: 26  SDGSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSK 85
           S   +  LSREERRRRRRATQKYRTAHATRERVRVEAFN AF ELRKLLPTLPPDKKLSK
Sbjct: 30  SAPGSGTLSREERRRRRRATQKYRTAHATRERVRVEAFNLAFAELRKLLPTLPPDKKLSK 89

Query: 86  IEILRLAICYIAYLNNVLE 104
           IEILRLAICYIAYLN+VL+
Sbjct: 90  IEILRLAICYIAYLNHVLQ 108

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307205014|gb|EFN83537.1| Helix-loop-helix protein 1 [Harpegnathos saltator]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 68/72 (94%), Positives = 70/72 (97%)

Query: 33  LSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLA 92
           LSREERRRRRRATQKYRTAHATRERVRVEAFN AF ELRKLLPTLPPDKKLSKIEILRLA
Sbjct: 37  LSREERRRRRRATQKYRTAHATRERVRVEAFNLAFAELRKLLPTLPPDKKLSKIEILRLA 96

Query: 93  ICYIAYLNNVLE 104
           ICYIAYLN+VL+
Sbjct: 97  ICYIAYLNHVLQ 108

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

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	105
FB|FBgn0011277	167	HLH4C "Helix loop helix protei	0.590	0.371	0.661	3.3e-15
UNIPROTKB|H9L3K7	130	NHLH1 "Uncharacterized protein	0.704	0.569	0.581	4.2e-15
UNIPROTKB|H9L3K8	131	NHLH1 "Uncharacterized protein	0.704	0.564	0.581	4.2e-15
UNIPROTKB|E1BPH8	133	NHLH1 "Uncharacterized protein	0.704	0.556	0.581	5.4e-15
UNIPROTKB|E2QW01	132	NHLH1 "Uncharacterized protein	0.704	0.560	0.581	5.4e-15
UNIPROTKB|Q02575	133	NHLH1 "Helix-loop-helix protei	0.704	0.556	0.581	5.4e-15
UNIPROTKB|F1RJY2	133	NHLH1 "Uncharacterized protein	0.704	0.556	0.581	5.4e-15
MGI|MGI:98481	133	Nhlh1 "nescient helix loop hel	0.704	0.556	0.581	5.4e-15
RGD|1310261	133	Nhlh1 "nescient helix loop hel	0.704	0.556	0.581	5.4e-15
ZFIN|ZDB-GENE-040426-1809	122	nhlh2 "nescient helix loop hel	0.780	0.672	0.517	5.4e-15

FB|FBgn0011277 HLH4C "Helix loop helix protein 4C" [Drosophila melanogaster (taxid:7227)]

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 41/62 (66%), Positives = 45/62 (72%)

Query:    44 ATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILRLAICYIAYLNNVL 103
             AT KYRTAHATRER+RVEAFN +F E              SKIEIL+LAICYIAYLN+VL
Sbjct:   105 ATLKYRTAHATRERIRVEAFNVSFAELRKLLPTLPPDKKLSKIEILKLAICYIAYLNHVL 164

Query:   104 ET 105
             ET
Sbjct:   165 ET 166

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|H9L3K7 NHLH1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 191 (72.3 bits), Expect = 4.2e-15, P = 4.2e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    56 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNMAFAELRKLLPTLPPDKKLSKIEILR 115

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   116 LAICYISYLNHVLD 129

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|H9L3K8 NHLH1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 191 (72.3 bits), Expect = 4.2e-15, P = 4.2e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    57 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNMAFAELRKLLPTLPPDKKLSKIEILR 116

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   117 LAICYISYLNHVLD 130

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|E1BPH8 NHLH1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    59 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   119 LAICYISYLNHVLD 132

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|E2QW01 NHLH1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    58 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 117

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   118 LAICYISYLNHVLD 131

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|Q02575 NHLH1 "Helix-loop-helix protein 1" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    59 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   119 LAICYISYLNHVLD 132

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0030154 "cell differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007417 "central nervous system development" evidence=TAS

UNIPROTKB|F1RJY2 NHLH1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    59 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   119 LAICYISYLNHVLD 132

GO:0046983 "protein dimerization activity" evidence=IEA

MGI|MGI:98481 Nhlh1 "nescient helix loop helix 1" [Mus musculus (taxid:10090)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    59 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   119 LAICYISYLNHVLD 132

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

RGD|1310261 Nhlh1 "nescient helix loop helix 1" [Rattus norvegicus (taxid:10116)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/74 (58%), Positives = 47/74 (63%)

Query:    31 QALSXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILR 90
             Q LS         AT KYRTAHATRER+RVEAFN AF E              SKIEILR
Sbjct:    59 QHLSREERRRRRRATAKYRTAHATRERIRVEAFNLAFAELRKLLPTLPPDKKLSKIEILR 118

Query:    91 LAICYIAYLNNVLE 104
             LAICYI+YLN+VL+
Sbjct:   119 LAICYISYLNHVLD 132

GO:0046983 "protein dimerization activity" evidence=IEA

ZFIN|ZDB-GENE-040426-1809 nhlh2 "nescient helix loop helix 2" [Danio rerio (taxid:7955)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 45/87 (51%), Positives = 53/87 (60%)

Query:    23 LDKSDGSTQAL-----SXXXXXXXXXATQKYRTAHATRERVRVEAFNSAFGEXXXXXXXX 77
             L+  DG T+AL     +         AT KYR+AHATRER+RVEAFN AF E        
Sbjct:    35 LEADDGKTRALVPAALTREEKRRRRRATAKYRSAHATRERIRVEAFNVAFAELRKLLPTL 94

Query:    78 XXXXXXSKIEILRLAICYIAYLNNVLE 104
                   SKIEILRLAICYI+YLN+VL+
Sbjct:    95 PPDKKLSKIEILRLAICYISYLNHVLD 121

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)
Q02576	HEN1_MOUSE	No assigned EC number	0.88	0.7142	0.5639	yes	N/A
Q02575	HEN1_HUMAN	No assigned EC number	0.88	0.7142	0.5639	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	105
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-14
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-13
smart00353	53	smart00353, HLH, helix loop helix domain	4e-13

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

 Score = 61.3 bits (150), Expect = 2e-14
 Identities = 34/52 (65%), Positives = 38/52 (73%), Gaps = 1/52 (1%)

Query: 48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
           R AH  RER R +  N AF ELR+LLPT PP+KKLSK EILRLAI YI +L
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 = 59.1 bits (144), Expect = 2e-13
 Identities = 35/58 (60%), Positives = 38/58 (65%)

Query: 47  KYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE 104
             R AH  RER R E  N AF ELR LLPTLPP KKLSK EILR A+ YI  L  +L+
Sbjct: 3   SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 58.0 bits (141), Expect = 4e-13
 Identities = 32/51 (62%), Positives = 34/51 (66%)

Query: 55  RERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
           RER R    N AF ELR LLPTLP +KKLSK EILRLAI YI  L   L+ 
Sbjct: 3   RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	105
KOG4029|consensus	228		99.7
KOG3960|consensus	284		99.7
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.65
KOG3898|consensus	254		99.63
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.59
smart00353	53	HLH helix loop helix domain.	99.52
KOG4395|consensus	285		99.37
KOG4447|consensus	173		99.32
KOG0561|consensus	373		99.3
KOG3910|consensus	632		99.03
KOG1319|consensus	229		98.89
KOG1318|consensus	411		98.6
KOG2483|consensus	232		98.55
KOG4304|consensus	250		97.62
KOG3561|consensus	803		97.56
KOG2588|consensus	953		97.55
KOG4447|consensus	173		96.88
PLN03217	93	transcription factor ATBS1; Provisional	96.8
KOG3558|consensus	768		93.49
KOG3560|consensus	712		89.88

>KOG4029|consensus

Probab=99.70  E-value=7.7e-18  Score=127.31  Aligned_cols=61  Identities=61%  Similarity=0.868  Sum_probs=57.6

Q ss_pred             cHHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCC-CCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          45 TQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPP-DKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        45 ~~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~-~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      ...+|..+|.|||.|++.||.+|..||.+||+.+. ++|+||++||+.||.||.+|+++|++
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~  167 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLAT  167 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcc
Confidence            45688899999999999999999999999999888 99999999999999999999999974

>KOG3960|consensus

Probab=99.70  E-value=3.3e-17  Score=126.76  Aligned_cols=72  Identities=35%  Similarity=0.528  Sum_probs=63.6

Q ss_pred             ccHHHHhhhhhhcHHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          33 LSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        33 ~~~~~~r~~~~~~~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      .+.++-.+|+..+..+|++|..|||+|.++||+||++|++..-. .++++|.||||||.||+||..||.+|.+
T Consensus       103 ~wackackrks~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~-NPNQRLPKVEILRsAI~YIE~Lq~LL~~  174 (284)
T KOG3960|consen  103 LWACKACKRKSTSVDRRKAATMRERRRLKKVNEAFETLKRRTSS-NPNQRLPKVEILRSAIRYIERLQALLQE  174 (284)
T ss_pred             HHhhhhccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCC-CccccccHHHHHHHHHHHHHHHHHHHHH
Confidence            35566666777889999999999999999999999999888743 5789999999999999999999999964

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

Probab=99.65  E-value=8.1e-16  Score=92.91  Aligned_cols=53  Identities=47%  Similarity=0.660  Sum_probs=49.0

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCC--CCCCCCCHHHHHHHHHHHHHHHH
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTL--PPDKKLSKIEILRLAICYIAYLN  100 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~--~~~~klSKi~~Lr~Ai~YI~~L~  100 (105)
                      +|..||.+||.|+..||.+|+.|+.+||..  ....+++|++||..||+||..||
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            478899999999999999999999999984  36789999999999999999996

; 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 ....

>KOG3898|consensus

Probab=99.63  E-value=1.8e-16  Score=122.53  Aligned_cols=59  Identities=44%  Similarity=0.543  Sum_probs=55.6

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      ..+|..+|+|||.||++||+||+.||.+||+++.+.|++||+||++|-+||+.|+.++.
T Consensus        70 ~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~l  128 (254)
T KOG3898|consen   70 TLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVLL  128 (254)
T ss_pred             hhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccccc
Confidence            34889999999999999999999999999999999999999999999999999998764

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

Probab=99.59  E-value=1.1e-14  Score=88.25  Aligned_cols=58  Identities=60%  Similarity=0.836  Sum_probs=53.0

Q ss_pred             HHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          47 KYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        47 ~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      ..|..||..||.|+..||.+|+.|+..||....+.+++|+.||..|++||.+|+..++
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            3577899999999999999999999999987668999999999999999999998653

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

>smart00353 HLH helix loop helix domain

Probab=99.52  E-value=6.9e-14  Score=83.27  Aligned_cols=53  Identities=60%  Similarity=0.815  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          53 ATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        53 n~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      |..||.|+..||.+|+.|+..||....+.+++|+.||..|++||..|+..+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~~   53 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQK   53 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            57899999999999999999999865689999999999999999999987753

>KOG4395|consensus

Probab=99.37  E-value=7.5e-13  Score=102.71  Aligned_cols=59  Identities=44%  Similarity=0.583  Sum_probs=56.0

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      +.+|.++|+|||+||+.||.|||.||.+||....+++|||.+||+.|--||..|..+|.
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            45789999999999999999999999999999999999999999999999999998874

>KOG4447|consensus

Probab=99.32  E-value=9.3e-13  Score=95.85  Aligned_cols=58  Identities=52%  Similarity=0.798  Sum_probs=54.1

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      +++|.-||.+||+|.+.+|+||..||+.+|++|. .|+|||.||+.|..||.+|..+|.
T Consensus        76 q~qrv~anvrerqRtqsLn~AF~~lr~iiptlPs-dklSkiqtLklA~ryidfl~~vl~  133 (173)
T KOG4447|consen   76 QKQRVMANVRERQRTQSLNEAFAALRKIIPTLPS-DKLSKIQTLKLAARYIDFLYQVLQ  133 (173)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCc-cccccccchhhcccCCchhhhccc
Confidence            4689999999999999999999999999999765 599999999999999999999875

>KOG0561|consensus

Probab=99.30  E-value=5.8e-12  Score=100.08  Aligned_cols=53  Identities=38%  Similarity=0.529  Sum_probs=49.6

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNN  101 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~  101 (105)
                      +|..||..||+||+.||.+|..||.+||.. .+.||||..||+.+.+||..|..
T Consensus        60 RReIANsNERRRMQSINAGFqsLr~LlPr~-eGEKLSKAAILQQTa~yI~~Le~  112 (373)
T KOG0561|consen   60 RREIANSNERRRMQSINAGFQSLRALLPRK-EGEKLSKAAILQQTADYIHQLEG  112 (373)
T ss_pred             HHHhhcchHHHHHHhhhHHHHHHHHhcCcc-cchhhHHHHHHHHHHHHHHHHHh
Confidence            588899999999999999999999999984 67899999999999999999975

>KOG3910|consensus

Probab=99.03  E-value=3e-10  Score=95.12  Aligned_cols=60  Identities=35%  Similarity=0.463  Sum_probs=55.0

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHH-HhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGEL-RKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~L-R~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      +.+|++.|+|||.|+.+||+||.+| |.|.-++..+|.-+|+-||..|+..|..|++.++|
T Consensus       524 kERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  524 KERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             HHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            4589999999999999999999999 77777788899999999999999999999998864

>KOG1319|consensus

Probab=98.89  E-value=5.8e-09  Score=78.53  Aligned_cols=55  Identities=36%  Similarity=0.573  Sum_probs=48.8

Q ss_pred             HHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCC----CCCCCCHHHHHHHHHHHHHHHHH
Q psy8078          47 KYRTAHATRERVRVEAFNSAFGELRKLLPTLP----PDKKLSKIEILRLAICYIAYLNN  101 (105)
Q Consensus        47 ~~R~~an~rER~R~~~in~af~~LR~~vP~~~----~~~klSKi~~Lr~Ai~YI~~L~~  101 (105)
                      .+|.+|..-||+|+.-||.+|++|+.+||.-.    .+.|+||.-||+.+|+||.+|..
T Consensus        61 rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~  119 (229)
T KOG1319|consen   61 RRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHK  119 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHH
Confidence            35678999999999999999999999999633    34699999999999999999975

>KOG1318|consensus

Probab=98.60  E-value=2e-07  Score=76.72  Aligned_cols=57  Identities=35%  Similarity=0.431  Sum_probs=50.6

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCC-CCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTL-PPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~-~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      +|-.||+-||+|+..||..+..|...||.. ..+-+..|-.||..+++||..|++.++
T Consensus       233 Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  233 KRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            467799999999999999999999999963 356788899999999999999998764

>KOG2483|consensus

Probab=98.55  E-value=1.6e-07  Score=72.20  Aligned_cols=58  Identities=22%  Similarity=0.315  Sum_probs=50.8

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      ...|..||+.|+.|+..|.+||+.|+..||.++..++-.-+.||..|..||..|+...
T Consensus        57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~  114 (232)
T KOG2483|consen   57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS  114 (232)
T ss_pred             CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence            4578999999999999999999999999998755544448999999999999998754

>KOG4304|consensus

Probab=97.62  E-value=5.1e-05  Score=58.95  Aligned_cols=52  Identities=27%  Similarity=0.392  Sum_probs=44.6

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHhhCCCCC-----CCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          51 AHATRERVRVEAFNSAFGELRKLLPTLP-----PDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        51 ~an~rER~R~~~in~af~~LR~~vP~~~-----~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      .+-..||+|+.-||.|++.||.+||..-     .-.||-|.+||.++.+|.+.|+..
T Consensus        35 ~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~   91 (250)
T KOG4304|consen   35 RKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRS   91 (250)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcc
Confidence            3567899999999999999999999521     237999999999999999999863

>KOG3561|consensus

Probab=97.56  E-value=0.00014  Score=64.27  Aligned_cols=54  Identities=24%  Similarity=0.415  Sum_probs=49.1

Q ss_pred             hHHhhHHHHHHHHHHHHHHHHHHhhCCC-CCCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          49 RTAHATRERVRVEAFNSAFGELRKLLPT-LPPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        49 R~~an~rER~R~~~in~af~~LR~~vP~-~~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      |..+|.-|++|+.++|.-+++|-..||+ ..-..|+.|..||+.|+..|+.+..+
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            7889999999999999999999999997 33579999999999999999988764

>KOG2588|consensus

Probab=97.55  E-value=6.1e-05  Score=67.22  Aligned_cols=54  Identities=37%  Similarity=0.467  Sum_probs=49.8

Q ss_pred             HHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          47 KYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        47 ~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      .+|.+||.-|++-+..||+-...|+..||.  ...|+.|-++|+.||+||.+|+..
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g--~~aKl~kSavLr~ai~~i~dl~~~  328 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPG--TEAKLNKSAVLRKAIDYIEDLQGY  328 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCc--cHhhhhhhhhHHHHHHHHHHhhcc
Confidence            579999999999999999999999999985  457999999999999999999864

>KOG4447|consensus

Probab=96.88  E-value=0.00051  Score=50.47  Aligned_cols=54  Identities=26%  Similarity=0.254  Sum_probs=46.2

Q ss_pred             HhHHhhHH-HHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          48 YRTAHATR-ERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        48 ~R~~an~r-ER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      .+..+|.+ |+.|.+.+|++|.-|++.+|..|. .+.+++.+|+.+.+||.+|.++
T Consensus        21 ~~~~~r~~~e~~R~~~ls~~s~l~g~l~pgspa-~gk~~~ktlr~~~~~~~~~dE~   75 (173)
T KOG4447|consen   21 EEECDRQRKERGRKRRLSDASTLLGKLEPGSPA-DGKRGKKTLRIGTDSIQSLDEL   75 (173)
T ss_pred             hhhhhhhHHHHhHHhhhhhhhhhccccCCCCCC-cccccccccccCCCchhhHHHH
Confidence            45556666 999999999999999999998654 5788999999999999999875

>PLN03217 transcription factor ATBS1; Provisional

Probab=96.80  E-value=0.0027  Score=42.49  Aligned_cols=43  Identities=28%  Similarity=0.419  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHhhCCCCC---CCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          61 EAFNSAFGELRKLLPTLP---PDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        61 ~~in~af~~LR~~vP~~~---~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      ..||+-...|+.++|...   ...+.|-..+|+.+|.||..|+.-+
T Consensus        20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEv   65 (93)
T PLN03217         20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREV   65 (93)
T ss_pred             HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHH
Confidence            569999999999999743   3468888899999999999998654

>KOG3558|consensus

Probab=93.49  E-value=0.16  Score=44.90  Aligned_cols=44  Identities=43%  Similarity=0.639  Sum_probs=37.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhCCCCCC--CCCCCHHHHHHHHHHHHH
Q psy8078          53 ATRERVRVEAFNSAFGELRKLLPTLPP--DKKLSKIEILRLAICYIA   97 (105)
Q Consensus        53 n~rER~R~~~in~af~~LR~~vP~~~~--~~klSKi~~Lr~Ai~YI~   97 (105)
                      -.--|.|+.+=|.-|.+|..+|| +|.  ..-|.|+.|+|+||.|.+
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lP-lp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLP-LPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCC-CcchhhhhhhhHHHHHHHHHHHH
Confidence            34468889999999999999999 553  578999999999999976

>KOG3560|consensus

Probab=89.88  E-value=0.22  Score=43.25  Aligned_cols=36  Identities=39%  Similarity=0.783  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHhhCCCCCCC--CCCCHHHHHHHHHHHHH
Q psy8078          61 EAFNSAFGELRKLLPTLPPD--KKLSKIEILRLAICYIA   97 (105)
Q Consensus        61 ~~in~af~~LR~~vP~~~~~--~klSKi~~Lr~Ai~YI~   97 (105)
                      .-+|.-+|.|..+||. +++  .||.|+.|||+++.|++
T Consensus        38 dRLNaELD~lAsLLPf-pqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   38 DRLNAELDHLASLLPF-PQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             HHhhhHHHHHHHhcCC-CHHHHhhhhhhhhhhhhHHHHH
Confidence            3489999999999995 554  79999999999999976

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	105
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	4e-20
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	5e-18
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	4e-09
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	6e-07
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	6e-06
4f3l_A	361	Mclock, circadian locomoter output cycles protein	7e-06
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	9e-06
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-05
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	1e-04
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-04

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

 Score = 75.8 bits (187), Expect = 4e-20
 Identities = 25/57 (43%), Positives = 33/57 (57%)

Query: 49  RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
           R     RER R+   N+A   LRK++P     +KLSKIE LRLA  YI  L+ +L +
Sbjct: 3   RMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILRS 59

>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 = 70.5 bits (173), Expect = 5e-18
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 40  RRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
           +R+      R A   RER R+   N AF  L++   +  P+++L K+EILR AI YI  L
Sbjct: 4   KRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGL 62

Query: 100 NNVLE 104
             +L 
Sbjct: 63  QALLR 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 = 48.3 bits (115), Expect = 4e-09
 Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 49  RTAHATRERVRVEAFNSAFGEL-RKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL 103
           R  H   ER R    N AF EL R     L  DK  +K+ IL+ A+  I  L   +
Sbjct: 6   RAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQV 61

>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 = 42.4 bits (99), Expect = 6e-07
 Identities = 17/65 (26%), Positives = 28/65 (43%)

Query: 38  RRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIA 97
                      +   A      ++  N  +  LR+L+P +P   +LS++EIL+  I YI 
Sbjct: 4   HHHHHSHMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYIL 63

Query: 98  YLNNV 102
            L  V
Sbjct: 64  DLQVV 68

>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 = 40.0 bits (94), Expect = 6e-06
 Identities = 17/51 (33%), Positives = 24/51 (47%)

Query: 49 RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
          R  H   ER R      +F  LR  +P L  ++K  K+ IL+ A  YI  +
Sbjct: 7  RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 57

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 41.9 bits (98), Expect = 7e-06
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 6/63 (9%)

Query: 34 SREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAI 93
          + EE  + +      R +    E+ R + FN    EL  +LP     +K+ K  +L+ +I
Sbjct: 2  AVEEDDKDKAK----RVSRNKSEKKRRDQFNVLIKELGSMLPG--NARKMDKSTVLQKSI 55

Query: 94 CYI 96
           ++
Sbjct: 56 DFL 58

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score = 41.5 bits (97), Expect = 9e-06
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 34 SREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDK-KLSKIEILRLA 92
            E + R + A + +       E+ R +  NS   EL  L+PT      KL K+ +LR+A
Sbjct: 3  YAEHQGRIKNAREAHSQI----EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMA 58

Query: 93 ICYI 96
          + ++
Sbjct: 59 VQHM 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 = 38.5 bits (90), Expect = 2e-05
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 49 RTAHATRERVRVEAFNSAFGELRKLLPTL---PPDKKLSKIEILRLAICYIAYL 99
          R  H   ER R +  N+   +L K++P           SK  IL  A  YI  L
Sbjct: 6  RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

>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 = 36.5 bits (85), Expect = 1e-04
 Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 49 RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
          R  H   ER R +    +F  LR  +P+L   +K S+ +IL  A  YI Y+
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYM 62

>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 = 36.2 bits (84), Expect = 2e-04
 Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 49 RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
          RTAH   E+    + N    EL+ L+     + KL+K  +LR AI YI +L
Sbjct: 7  RTAHNAIEKRYRSSINDKIIELKDLVVGT--EAKLNKSAVLRKAIDYIRFL 55

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	105
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	99.85
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	99.82
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.77
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.71
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.69
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.68
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.67
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.54
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.51
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.49
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.43
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.38
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.38
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.8
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.55
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.26
3muj_A	138	Transcription factor COE3; immunoglobulin like fol	94.7

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

Probab=99.92  E-value=3.3e-25  Score=137.45  Aligned_cols=58  Identities=43%  Similarity=0.616  Sum_probs=55.6

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      +|..||++||.||++||.||+.||.+||+.+.++||||++||+.||+||.+|+++|++
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            5788999999999999999999999999999999999999999999999999999974

>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=1.2e-24  Score=137.91  Aligned_cols=62  Identities=37%  Similarity=0.545  Sum_probs=57.2

Q ss_pred             hhcHHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          43 RATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        43 ~~~~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      .....+|.+||++||.||+.||+||+.||++||.. +++|+||++||+.||+||.+|+++|++
T Consensus         7 ~~~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~-~~~KlSKi~tLr~Ai~YI~~L~~~L~~   68 (68)
T 1mdy_A            7 TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD   68 (68)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSC-TTSCCCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCchhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCC-CCCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence            44567899999999999999999999999999975 589999999999999999999999974

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

Probab=99.85  E-value=1.1e-22  Score=128.89  Aligned_cols=50  Identities=32%  Similarity=0.515  Sum_probs=48.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy8078          52 HATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNN  101 (105)
Q Consensus        52 an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~  101 (105)
                      +|+|||.||+.||+||+.||++||++|.++|||||+||+.||+||.+|+.
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            79999999999999999999999999999999999999999999999985

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

Probab=99.82  E-value=1e-20  Score=127.18  Aligned_cols=54  Identities=31%  Similarity=0.535  Sum_probs=49.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          52 HATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        52 an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      ...+||.||+.||.||+.||.+||+.+.++|||||+||+.||+||.+|+++|++
T Consensus        29 ~~~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           29 PVDDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            356679999999999999999999999999999999999999999999999974

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

Probab=99.77  E-value=1.1e-19  Score=117.23  Aligned_cols=60  Identities=32%  Similarity=0.383  Sum_probs=49.4

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCC-CCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPT-LPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~-~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      ..+|..||++||.|+..||++|+.|+.+||. .+.++.+||++||+.||+||.+|++.|++
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e   63 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRE   63 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHH
Confidence            4578899999999999999999999999994 55666669999999999999999998863

>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=99.71  E-value=2.3e-17  Score=108.65  Aligned_cols=57  Identities=30%  Similarity=0.422  Sum_probs=53.4

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      ..+|..||..||.|+..||.+|+.|+.+||..+.+.|+||+.||..||+||.+|+..
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~   60 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAE   60 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            346889999999999999999999999999988889999999999999999999875

>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=99.69  E-value=6.4e-17  Score=104.33  Aligned_cols=58  Identities=31%  Similarity=0.466  Sum_probs=52.4

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      ..+|..||.+||.|+..||.+|+.|+.+||..+ +.|+||++||+.||+||.+|+..++
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            457889999999999999999999999999864 4689999999999999999997653

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

Probab=99.68  E-value=8e-17  Score=104.54  Aligned_cols=54  Identities=22%  Similarity=0.343  Sum_probs=51.6

Q ss_pred             hHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          49 RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        49 R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      |..||..||.|+..||.+|+.|+++||.++.+.|+||+.||+.|++||..|+..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~   55 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDS   55 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999988899999999999999999999874

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

Probab=99.67  E-value=1.5e-16  Score=103.02  Aligned_cols=55  Identities=33%  Similarity=0.488  Sum_probs=50.4

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      +|..||..||.|+..||.+|+.|+.+||..+ +.|+||++||+.||+||..|+..+
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~~~~   56 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMRRKN   56 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHH
Confidence            4788999999999999999999999999854 578999999999999999999654

>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=99.54  E-value=1.6e-14  Score=93.73  Aligned_cols=56  Identities=34%  Similarity=0.443  Sum_probs=51.0

Q ss_pred             HHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          47 KYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        47 ~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      .+|..||..||.|+..||++|.+|+.+||.  .+.|++|++||..||+||.+|+..+.
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~--~~~k~~Ka~IL~~Ai~YI~~Lq~~~~   60 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQ   60 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--SSCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccC--CCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            457889999999999999999999999996  46899999999999999999997653

>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=99.51  E-value=2.7e-15  Score=93.11  Aligned_cols=56  Identities=30%  Similarity=0.293  Sum_probs=49.8

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCC---CCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPD---KKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~---~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      +|..||..||.|+..||.+|+.|+.+||.....   .+++|+.||..||+||..|+...
T Consensus         5 rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            467799999999999999999999999976543   58999999999999999998743

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

Probab=99.49  E-value=8.1e-15  Score=91.19  Aligned_cols=57  Identities=28%  Similarity=0.275  Sum_probs=50.7

Q ss_pred             hHHhhHHHHHHHHHHHHHHHHHHhhCCCCC----CCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          49 RTAHATRERVRVEAFNSAFGELRKLLPTLP----PDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        49 R~~an~rER~R~~~in~af~~LR~~vP~~~----~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      |..|+.-||.|+..||.+|+.|+.+||...    ++.++||.+||..||+||..|++.+.+
T Consensus         3 r~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~~   63 (63)
T 1a0a_A            3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST   63 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSCC
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhhC
Confidence            667999999999999999999999999532    257999999999999999999987653

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

Probab=99.43  E-value=6.8e-13  Score=84.49  Aligned_cols=55  Identities=24%  Similarity=0.403  Sum_probs=50.0

Q ss_pred             HHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          47 KYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        47 ~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      ..|..||..||.|+..||..|..|+..||.  .+.|++|..||+.||+||..|+..+
T Consensus         7 ~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~--~~~K~dK~sIL~~aI~yik~Lq~~~   61 (71)
T 4h10_B            7 AKRVSRNKSEKKRRDQFNVLIKELGSMLPG--NARKMDKSTVLQKSIDFLRKHKEIT   61 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSSS--CCSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhhHHHhhHHHHHHHHHHHHHHhCCC--CCCCCcHHHHHHHHHHHHHHHHHhh
Confidence            357789999999999999999999999994  4579999999999999999999764

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

Probab=99.38  E-value=5.7e-13  Score=85.11  Aligned_cols=56  Identities=34%  Similarity=0.501  Sum_probs=49.8

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCC-CCCCCCCHHHHHHHHHHHHHHHHH
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTL-PPDKKLSKIEILRLAICYIAYLNN  101 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~-~~~~klSKi~~Lr~Ai~YI~~L~~  101 (105)
                      ..+|..||..||.|+..||.+|++|+.+||.. ....|++|++||+.||+||..|+.
T Consensus         7 ~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            7 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            34678899999999999999999999999952 346899999999999999999864

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

Probab=99.38  E-value=9.9e-13  Score=90.52  Aligned_cols=56  Identities=30%  Similarity=0.379  Sum_probs=46.3

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLP-PDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~-~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      .|..||..||.|+..||..|..|+.+||... .+.|++|+.||..||+||.+|+..+
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~   83 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQ   83 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999753 4679999999999999999998654

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

Probab=98.80  E-value=7.7e-09  Score=80.36  Aligned_cols=53  Identities=25%  Similarity=0.406  Sum_probs=42.9

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      .|..||..||+|+..||..|..|+.+||  ....||.|+.||+.||.||..|+.+
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~p--~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSMLP--GNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCC--SSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhCC--CCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            4677999999999999999999999999  3567999999999999999999864

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

Probab=98.55  E-value=7.4e-08  Score=75.76  Aligned_cols=54  Identities=35%  Similarity=0.498  Sum_probs=48.0

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHHHHHHHHHH
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLP-PDKKLSKIEILRLAICYIAYLNN  101 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~-~~~klSKi~~Lr~Ai~YI~~L~~  101 (105)
                      .|..||..||+|+..||..|.+|+.+||... ...|+.|..||+.||.||..|+.
T Consensus        13 ~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            4678999999999999999999999999522 45899999999999999998873

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

Probab=98.26  E-value=2.7e-06  Score=55.38  Aligned_cols=42  Identities=31%  Similarity=0.429  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHhhCCCC-CCCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          61 EAFNSAFGELRKLLPTL-PPDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        61 ~~in~af~~LR~~vP~~-~~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      ..||..+.+|...||.. .++.+.+|-.||+.|++||.+|++.
T Consensus         5 ~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e   47 (83)
T 4ath_A            5 FNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQRE   47 (83)
T ss_dssp             HHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHT
T ss_pred             hhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHH
Confidence            46999999999999963 4678999999999999999999763

>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=94.70  E-value=0.073  Score=37.31  Aligned_cols=41  Identities=24%  Similarity=0.399  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHhhCCCCCC-CCCCCHHHHHHHHHHHHHHHHH
Q psy8078          61 EAFNSAFGELRKLLPTLPP-DKKLSKIEILRLAICYIAYLNN  101 (105)
Q Consensus        61 ~~in~af~~LR~~vP~~~~-~~klSKi~~Lr~Ai~YI~~L~~  101 (105)
                      ..|+-+|+.|.+.||-++. ..+|.|--||+.|.++...|-.
T Consensus        94 PtId~gfqrl~k~~pr~pgdpe~lpk~~~lkraa~l~e~~~~  135 (138)
T 3muj_A           94 PTIDYGFQRLQKVIPRHPGDPERLPKEVLLKRAADLVEALYG  135 (138)
T ss_dssp             CCHHHHHHHHHHHSCCCTTCCSSCCHHHHHHHHHHHHHHHHC
T ss_pred             CccccchhhhccccCCCCCChhhhhHHHHHHHHHHHHHHHhC
Confidence            4589999999999998765 4899999999999999998753

---

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	105
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-11
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	3e-09
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	5e-09
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	8e-09
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-08
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	5e-07
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-04
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	0.004

>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 = 53.0 bits (127), Expect = 2e-11
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 40  RRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
           +R+      R A   RER R+   N AF  L++   +  P+++L K+EILR AI YI  L
Sbjct: 4   KRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGL 62

Query: 100 NNVLE 104
             +L 
Sbjct: 63  QALLR 67

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

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

 Score = 46.8 bits (111), Expect = 3e-09
 Identities = 16/61 (26%), Positives = 21/61 (34%), Gaps = 4/61 (6%)

Query: 49  RTAHATRERVRVEAFNSAFGELRKLLPTLP----PDKKLSKIEILRLAICYIAYLNNVLE 104
           R +H   E+ R      A  EL  L+P            SK   +  A  YI +L     
Sbjct: 3   RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

Query: 105 T 105
           T
Sbjct: 63  T 63

>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 = 46.3 bits (110), Expect = 5e-09
 Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 45 TQKYRTAHATRERVRVEAFNSAFGELRKLLPTL---PPDKKLSKIEILRLAICYIAYL 99
           +K R  H   ER R +  N+   +L K++P           SK  IL  A  YI  L
Sbjct: 2  DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

>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 = 46.4 bits (110), Expect = 8e-09
 Identities = 12/56 (21%), Positives = 24/56 (42%)

Query: 49  RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE 104
           R+ H   E+ R      +  +L+ L+P  P   + + + +L  A  +I  L +   
Sbjct: 2   RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDR 57

>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 = 46.1 bits (109), Expect = 1e-08
 Identities = 17/57 (29%), Positives = 25/57 (43%)

Query: 49  RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
           R  H   ER R      +F  LR  +P L  ++K  K+ IL+ A  YI  +    + 
Sbjct: 7   RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQK 63

>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 = 41.8 bits (98), Expect = 5e-07
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 49  RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
           R  H   ER R +    +F  LR  +P+L   +K S+ +IL  A  YI Y+     T
Sbjct: 3   RAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHT 58

>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 = 35.3 bits (81), Expect = 1e-04
 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 49  RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE 104
           RTAH   E+    + N    EL+ L+     + KL+K  +LR AI YI +L +  +
Sbjct: 7   RTAHNAIEKRYRSSINDKIIELKDLVV--GTEAKLNKSAVLRKAIDYIRFLQHSNQ 60

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

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

 Score = 31.2 bits (71), Expect = 0.004
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 61 EAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
           + N    EL+ L+     D K+ K  +LR AI YI YL
Sbjct: 2  SSINDKIIELKDLVM--GTDAKMHKSGVLRKAIDYIKYL 38

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	105
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.79
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.66
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.65
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.53
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.97

>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=99.79  E-value=2.1e-19  Score=111.81  Aligned_cols=61  Identities=38%  Similarity=0.555  Sum_probs=55.5

Q ss_pred             hcHHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          44 ATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        44 ~~~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      ....+|..||.+||.|+..||.+|+.|+.+||+. +++++||++||+.||+||.+|+++|++
T Consensus         8 ~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~-~~~k~sK~~iL~~Ai~YI~~Lq~~l~e   68 (68)
T d1mdya_           8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD   68 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSC-TTSCCCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCCHHHHHHHHHHHHHHHHHHhhC
Confidence            3456788999999999999999999999999985 456999999999999999999999975

>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=99.67  E-value=5.8e-17  Score=102.47  Aligned_cols=56  Identities=21%  Similarity=0.309  Sum_probs=52.4

Q ss_pred             hHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          49 RTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        49 R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      |..||..||.|+..||++|+.|+.+||+.+...|+||++||..|++||..|+..+.
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            78899999999999999999999999988778899999999999999999997653

>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=99.66  E-value=8.3e-17  Score=103.59  Aligned_cols=57  Identities=30%  Similarity=0.422  Sum_probs=53.1

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      +|..||..||.|+..||++|+.|+.+||..+.+.|+||++||..||+||..|+..+.
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~   62 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ   62 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHH
Confidence            578899999999999999999999999988788999999999999999999997653

>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=99.65  E-value=4e-17  Score=99.76  Aligned_cols=58  Identities=28%  Similarity=0.288  Sum_probs=52.4

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCC----CCCCCCCCHHHHHHHHHHHHHHHHHhhcC
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPT----LPPDKKLSKIEILRLAICYIAYLNNVLET  105 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~----~~~~~klSKi~~Lr~Ai~YI~~L~~~L~~  105 (105)
                      +|..||..||.|+..||.+|+.|+.+||.    ...+.|++|++||..|++||.+|++.+.|
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v~T   63 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST   63 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSCC
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhhcC
Confidence            36789999999999999999999999994    24678999999999999999999987764

>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=99.62  E-value=5e-16  Score=98.91  Aligned_cols=55  Identities=33%  Similarity=0.488  Sum_probs=50.4

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      +|..||.+||.|+..||++|+.|+.+||.. ++.++||++||+.|++||..|+..+
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~-~~~k~sK~~iL~~A~~yI~~L~~~~   56 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKN   56 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGG-TTSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            578899999999999999999999999964 5679999999999999999998754

>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=99.55  E-value=6.8e-15  Score=93.21  Aligned_cols=56  Identities=34%  Similarity=0.427  Sum_probs=50.6

Q ss_pred             HHHhHHhhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhh
Q psy8078          46 QKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL  103 (105)
Q Consensus        46 ~~~R~~an~rER~R~~~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L  103 (105)
                      ..+|..||..||.|+..||++|+.|+.+||.  ...+++|++||..|++||..|+..+
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~--~~~k~~K~~iL~~a~~yI~~L~~~~   59 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSN   59 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--SSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3467889999999999999999999999995  4569999999999999999999765

>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=99.53  E-value=8.4e-16  Score=94.24  Aligned_cols=55  Identities=31%  Similarity=0.318  Sum_probs=49.6

Q ss_pred             HhHHhhHHHHHHHHHHHHHHHHHHhhCCCCC---CCCCCCHHHHHHHHHHHHHHHHHh
Q psy8078          48 YRTAHATRERVRVEAFNSAFGELRKLLPTLP---PDKKLSKIEILRLAICYIAYLNNV  102 (105)
Q Consensus        48 ~R~~an~rER~R~~~in~af~~LR~~vP~~~---~~~klSKi~~Lr~Ai~YI~~L~~~  102 (105)
                      +|..||..||.|+..||.+|+.|+.+||...   .+.++||++||..|++||..|++.
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            4677999999999999999999999999743   457999999999999999999863

>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=98.97  E-value=1.4e-10  Score=69.71  Aligned_cols=41  Identities=39%  Similarity=0.527  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy8078          62 AFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE  104 (105)
Q Consensus        62 ~in~af~~LR~~vP~~~~~~klSKi~~Lr~Ai~YI~~L~~~L~  104 (105)
                      .||+.|..|+++||+  .+.|++|++||..||+||..|+....
T Consensus         3 ~in~~f~~L~~lvP~--~~~K~~Ka~iL~~Ai~YI~~Lq~~~~   43 (61)
T d1uklc_           3 SINDKIIELKDLVMG--TDAKMHKSGVLRKAIDYIKYLQQVNH   43 (61)
T ss_dssp             CHHHHHHHHHHHHSC--SSCCCCTTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCC--CCCcccHHHHHHHHHHHHHHHHHHHH
Confidence            599999999999995  34699999999999999999998653