Psyllid ID: psy2848

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80------
Protein Sequence
LPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMDPS
Secondary Structure (PSIPRED)
cccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEcccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEEccccccccccccccHHHHHccccccEEEccc
Coil and Loop (DISEMBL)
LPIIRVVKRRNTANKKERRRTQSINNAFSDLREcipniletddiisiddfkadlsnhsshrknksqydspseissnqssqyvmdps
Flexible Loop (DISEMBL)
lpiirvvkrrntankkerrrtqsinnafsdlrECIPNILETDDIISIDDFKADLSNHSshrknksqydspseissnqssqyvmdps
Low Complexity Region (SEG)
LPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRKNKSQYDspseissnqssQYVMDPS
Disordered region (IsUnstruct)
**************************AFSDLRECIPNILETDDIISIDDF************************************
Disordered Region (DISOPRED)
*************************NAFSDLRECIPNILETDDIISIDDFK***********************************
Disordered Region (DISEMBL)
LPIIRVVKRRN********RTQSINNAFSDLRECIPNILETDDIISIDDFKADLS*******************************
Disordered Region (DISPRO)
LPIIRVVKRRNT*NKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSN******************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
LPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMDPS
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	86	2.2.26 [Sep-21-2011]
P57102	208	Heart- and neural crest d	yes	N/A	0.395	0.163	0.794	4e-10
Q90690	216	Heart- and neural crest d	yes	N/A	0.372	0.148	0.812	6e-10
P61295	217	Heart- and neural crest d	yes	N/A	0.372	0.147	0.812	7e-10
Q61039	217	Heart- and neural crest d	yes	N/A	0.372	0.147	0.812	7e-10
P61296	217	Heart- and neural crest d	yes	N/A	0.372	0.147	0.812	7e-10
P57101	210	Heart- and neural crest d	N/A	N/A	0.395	0.161	0.764	5e-09
P97832	216	Heart- and neural crest d	no	N/A	0.790	0.314	0.351	4e-08
Q64279	216	Heart- and neural crest d	no	N/A	0.825	0.328	0.350	5e-08
Q28555	204	Heart- and neural crest d	N/A	N/A	0.395	0.166	0.617	1e-07
Q0VCE2	218	Heart- and neural crest d	no	N/A	0.395	0.155	0.617	2e-07

>sp|P57102|HAND2_DANRE Heart- and neural crest derivatives-expressed protein 2 OS=Danio rerio GN=hand2 PE=2 SV=1

 Score = 63.5 bits (153), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query: 5   RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct: 87  RTVKRRPTANRKERRRTQSINSAFAELRECIPNV 120

Essential for myocardial and pectoral fin differentiation, patterning and morphogenesis.
Danio rerio (taxid: 7955)

>sp|Q90690|HAND2_CHICK Heart- and neural crest derivatives-expressed protein 2 OS=Gallus gallus GN=HAND2 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 26/32 (81%), Positives = 31/32 (96%)

Query: 7   VKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct: 97  VKRRGTANRKERRRTQSINSAFAELRECIPNV 128

Essential for cardiac morphogenesis. Binds DNA on E-box consensus sequence 5'-CANNTG-3' (By similarity). Plays an important role in limb development, particularly in the establishment of anterior-posterior polarization of the limb bud.

Gallus gallus (taxid: 9031)

>sp|P61295|HAND2_RAT Heart- and neural crest derivatives-expressed protein 2 OS=Rattus norvegicus GN=Hand2 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 26/32 (81%), Positives = 31/32 (96%)

Query: 7   VKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct: 98  VKRRGTANRKERRRTQSINSAFAELRECIPNV 129

Essential for cardiac morphogenesis, particularly for the formation of the right ventricle and of the aortic arch arteries. Required for vascular development and regulation of angiogenesis, possibly through a VEGF signaling pathway. Plays also an important role in limb development, particularly in the establishment of anterior-posterior polarization, acting as an upstream regulator of sonic hedgehog (SHH) induction in the limb bud. Is involved in the development of branchial arches, which give rise to unique structures in the head and neck. Binds DNA on E-box consensus sequence 5'-CANNTG-3'.

Rattus norvegicus (taxid: 10116)

>sp|Q61039|HAND2_MOUSE Heart- and neural crest derivatives-expressed protein 2 OS=Mus musculus GN=Hand2 PE=1 SV=3

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 26/32 (81%), Positives = 31/32 (96%)

Query: 7   VKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct: 98  VKRRGTANRKERRRTQSINSAFAELRECIPNV 129

Essential for cardiac morphogenesis, particularly for the formation of the right ventricle and of the aortic arch arteries. Required for vascular development and regulation of angiogenesis, possibly through a VEGF signaling pathway. Plays also an important role in limb development, particularly in the establishment of anterior-posterior polarization, acting as an upstream regulator of sonic hedgehog (SHH) induction in the limb bud. Is involved in the development of branchial arches, which give rise to unique structures in the head and neck. Binds DNA on E-box consensus sequence 5'-CANNTG-3'.

Mus musculus (taxid: 10090)

>sp|P61296|HAND2_HUMAN Heart- and neural crest derivatives-expressed protein 2 OS=Homo sapiens GN=HAND2 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 26/32 (81%), Positives = 31/32 (96%)

Query: 7   VKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct: 98  VKRRGTANRKERRRTQSINSAFAELRECIPNV 129

Essential for cardiac morphogenesis, particularly for the formation of the right ventricle and of the aortic arch arteries. Required for vascular development and regulation of angiogenesis, possibly through a VEGF signaling pathway. Plays also an important role in limb development, particularly in the establishment of anterior-posterior polarization, acting as an upstream regulator of sonic hedgehog (SHH) induction in the limb bud. Is involved in the development of branchial arches, which give rise to unique structures in the head and neck. Binds DNA on E-box consensus sequence 5'-CANNTG-3'.

Homo sapiens (taxid: 9606)

>sp|P57101|HAND2_XENLA Heart- and neural crest derivatives-expressed protein 2 OS=Xenopus laevis GN=hand2 PE=2 SV=1

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/34 (76%), Positives = 31/34 (91%)

Query: 5   RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           R VKRR TAN+KERRRT SIN+AF++LRECIPN+
Sbjct: 89  RPVKRRGTANRKERRRTISINSAFAELRECIPNV 122

Essential for cardiac morphogenesis and for the development of branchial arches. Binds DNA on E-box consensus sequence 5'-CANNTG-3'.

Xenopus laevis (taxid: 8355)

>sp|P97832|HAND1_RAT Heart- and neural crest derivatives-expressed protein 1 OS=Rattus norvegicus GN=Hand1 PE=2 SV=2

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 49/94 (52%), Gaps = 26/94 (27%)

Query: 5   RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI-------------LETDDIISIDD-- 49
           R+ +R+ +  KKERRRT+SIN+AF++LRECIPN+             L T  I  + D  
Sbjct: 91  RLPRRKGSGPKKERRRTESINSAFAELRECIPNVPADTKLSKIKTLRLATSYIAYLMDVL 150

Query: 50  -----------FKADLSNHSSHRKNKSQYDSPSE 72
                      FKA+L      R++K + +SP +
Sbjct: 151 AKDAQAGDPEAFKAELKKTDGGRESKRKRESPQQ 184

Transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. In the adult, could be required for ongoing expression of cardiac-specific genes. Binds the DNA sequence 5'-NRTCTG-3' (non-canonical E-box).

Rattus norvegicus (taxid: 10116)

>sp|Q64279|HAND1_MOUSE Heart- and neural crest derivatives-expressed protein 1 OS=Mus musculus GN=Hand1 PE=1 SV=1

 Score = 56.2 bits (134), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 49/97 (50%), Gaps = 26/97 (26%)

Query: 5   RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI-------------LETDDIISIDD-- 49
           R+ KR+ +  KKERRRT+SIN+AF++LRECIPN+             L T  I  + D  
Sbjct: 91  RLPKRKGSGPKKERRRTESINSAFAELRECIPNVPADTKLSKIKTLRLATSYIAYLMDVL 150

Query: 50  -----------FKADLSNHSSHRKNKSQYDSPSEISS 75
                      FKA+L      R++K + + P +  S
Sbjct: 151 AKDAQAGDPEAFKAELKKTDGGRESKRKRELPQQPES 187

Transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. In the adult, could be required for ongoing expression of cardiac-specific genes. Binds the DNA sequence 5'-NRTCTG-3' (non-canonical E-box).

Mus musculus (taxid: 10090)

>sp|Q28555|HAND1_SHEEP Heart- and neural crest derivatives-expressed protein 1 OS=Ovis aries GN=HAND1 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/34 (61%), Positives = 30/34 (88%)

Query: 5   RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           R+ +R+ +  KKERRRT+SIN+AF++LRECIPN+
Sbjct: 97  RLGRRKGSGPKKERRRTESINSAFAELRECIPNV 130

Transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. In the adult, could be required for ongoing expression of cardiac-specific genes. Binds the DNA sequence 5'-NRTCTG-3' (non-canonical E-box).

Ovis aries (taxid: 9940)

>sp|Q0VCE2|HAND1_BOVIN Heart- and neural crest derivatives-expressed protein 1 OS=Bos taurus GN=HAND1 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/34 (61%), Positives = 30/34 (88%)

Query: 5   RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           R+ +R+ +  KKERRRT+SIN+AF++LRECIPN+
Sbjct: 94  RLGRRKGSGPKKERRRTESINSAFAELRECIPNV 127

Transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. In the adult, could be required for ongoing expression of cardiac-specific genes. Binds the DNA sequence 5'-NRTCTG-3' (non-canonical E-box).

Bos taurus (taxid: 9913)

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	86
242005999	156	dhand, putative [Pediculus humanus corpo	0.418	0.230	0.888	2e-11
91076044	172	PREDICTED: similar to heart and neural c	0.441	0.220	0.789	3e-11
357616233	260	putative heart and neural crest derivati	0.418	0.138	0.833	2e-10
357622264	274	putative heart and neural crest derivati	0.418	0.131	0.833	2e-10
193632021	445	PREDICTED: hypothetical protein LOC10016	0.581	0.112	0.513	1e-09
321473851	119	hypothetical protein DAPPUDRAFT_7671 [Da	0.558	0.403	0.666	2e-09
350397475	285	PREDICTED: hypothetical protein LOC10074	0.360	0.108	0.903	3e-09
340715290	285	PREDICTED: hypothetical protein LOC10064	0.360	0.108	0.903	3e-09
380019878	284	PREDICTED: uncharacterized protein LOC10	0.360	0.109	0.903	3e-09
328782232	285	PREDICTED: hypothetical protein LOC10057	0.360	0.108	0.903	4e-09

>gi|242005999|ref|XP_002423846.1| dhand, putative [Pediculus humanus corporis] gi|212507068|gb|EEB11108.1| dhand, putative [Pediculus humanus corporis]

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/36 (88%), Positives = 36/36 (100%)

Query: 3  IIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
          I+RVVKRRNTANKKERRRTQSINNAF+DLR+CIPN+
Sbjct: 8  IVRVVKRRNTANKKERRRTQSINNAFADLRDCIPNV 43

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91076044|ref|XP_972310.1| PREDICTED: similar to heart and neural crest derivatives expressed transcript 2 [Tribolium castaneum] gi|270014677|gb|EFA11125.1| hypothetical protein TcasGA2_TC004726 [Tribolium castaneum]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/38 (78%), Positives = 36/38 (94%)

Query: 1  LPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
          +P +RVVKRR TANKKERRRTQSINNA++DLR+CIPN+
Sbjct: 38 VPFVRVVKRRTTANKKERRRTQSINNAYADLRDCIPNV 75

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357616233|gb|EHJ70086.1| putative heart and neural crest derivatives expressed transcript 2 [Danaus plexippus]

 Score = 69.7 bits (169), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/36 (83%), Positives = 33/36 (91%)

Query: 3   IIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
            +RVVKRR TANKKERRRTQSIN AF+DLRECIPN+
Sbjct: 112 FVRVVKRRTTANKKERRRTQSINTAFTDLRECIPNV 147

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357622264|gb|EHJ73816.1| putative heart and neural crest derivatives expressed transcript 2 [Danaus plexippus]

 Score = 69.3 bits (168), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/36 (83%), Positives = 33/36 (91%)

Query: 3   IIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
            +RVVKRR TANKKERRRTQSIN AF+DLRECIPN+
Sbjct: 133 FVRVVKRRTTANKKERRRTQSINTAFTDLRECIPNV 168

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193632021|ref|XP_001945320.1| PREDICTED: hypothetical protein LOC100168554 [Acyrthosiphon pisum]

 Score = 67.0 bits (162), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/76 (51%), Positives = 44/76 (57%), Gaps = 26/76 (34%)

Query: 11  NTANKKERRRTQSINNAFSDLRECIPN-------------------------ILETDDII 45
           NTANKKERRRTQSINNAFSDLR+CIPN                         +L++DD  
Sbjct: 309 NTANKKERRRTQSINNAFSDLRDCIPNVPSDTKLSKIKTLRLATSYIGYLMTVLDSDD-P 367

Query: 46  SIDDFKADLSNHSSHR 61
             D FKADLS H+S R
Sbjct: 368 DTDGFKADLSAHTSKR 383

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321473851|gb|EFX84817.1| hypothetical protein DAPPUDRAFT_7671 [Daphnia pulex]

 Score = 66.2 bits (160), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/48 (66%), Positives = 36/48 (75%)

Query: 5  RVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKA 52
          RVVKRRNTANKKERRRT SINNAFS+LR+CIPN+     +  I    A
Sbjct: 1  RVVKRRNTANKKERRRTMSINNAFSELRDCIPNVPADTKLSKIKTLPA 48

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350397475|ref|XP_003484889.1| PREDICTED: hypothetical protein LOC100740604 [Bombus impatiens]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/31 (90%), Positives = 31/31 (100%)

Query: 8   KRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           KRRNTANKKERRRTQSINNAF+DLR+CIPN+
Sbjct: 156 KRRNTANKKERRRTQSINNAFADLRDCIPNV 186

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715290|ref|XP_003396149.1| PREDICTED: hypothetical protein LOC100643078 [Bombus terrestris]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/31 (90%), Positives = 31/31 (100%)

Query: 8   KRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           KRRNTANKKERRRTQSINNAF+DLR+CIPN+
Sbjct: 156 KRRNTANKKERRRTQSINNAFADLRDCIPNV 186

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019878|ref|XP_003693828.1| PREDICTED: uncharacterized protein LOC100865984 [Apis florea]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/31 (90%), Positives = 31/31 (100%)

Query: 8   KRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           KRRNTANKKERRRTQSINNAF+DLR+CIPN+
Sbjct: 156 KRRNTANKKERRRTQSINNAFADLRDCIPNV 186

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782232|ref|XP_003250109.1| PREDICTED: hypothetical protein LOC100576222 [Apis mellifera]

 Score = 65.5 bits (158), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/31 (90%), Positives = 31/31 (100%)

Query: 8   KRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           KRRNTANKKERRRTQSINNAF+DLR+CIPN+
Sbjct: 157 KRRNTANKKERRRTQSINNAFADLRDCIPNV 187

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	86
FB|FBgn0032209	174	Hand "Hand" [Drosophila melano	0.476	0.235	0.761	9.4e-11
UNIPROTKB|E1C225	216	E1C225 "Uncharacterized protei	0.395	0.157	0.794	3.2e-10
UNIPROTKB|F1NPU0	214	F1NPU0 "Uncharacterized protei	0.395	0.158	0.794	3.2e-10
UNIPROTKB|F1P1U1	173	F1P1U1 "Uncharacterized protei	0.395	0.196	0.794	3.2e-10
UNIPROTKB|Q90690	216	HAND2 "Heart- and neural crest	0.395	0.157	0.794	3.2e-10
UNIPROTKB|F1MLT3	191	LOC781874 "Uncharacterized pro	0.395	0.178	0.794	3.2e-10
UNIPROTKB|F1PX30	222	HAND2 "Uncharacterized protein	0.395	0.153	0.794	3.2e-10
UNIPROTKB|P61296	217	HAND2 "Heart- and neural crest	0.395	0.156	0.794	3.2e-10
UNIPROTKB|F1RJ02	176	HAND2 "Uncharacterized protein	0.395	0.193	0.794	3.2e-10
MGI|MGI:103580	217	Hand2 "heart and neural crest	0.395	0.156	0.794	3.2e-10

FB|FBgn0032209 Hand "Hand" [Drosophila melanogaster (taxid:7227)]

 Score = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIIS 46
             R+VK+RNTANKKERRRTQSINNAFS LRE IPN+  TD  +S
Sbjct:    55 RIVKKRNTANKKERRRTQSINNAFSYLREKIPNV-PTDTKLS 95

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

GO:0005634 "nucleus" evidence=IC;IDA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0035050 "embryonic heart tube development" evidence=IMP

GO:0007508 "larval heart development" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IDA

GO:0030097 "hemopoiesis" evidence=IMP

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IDA

UNIPROTKB|E1C225 E1C225 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    95 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 128

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

GO:0048935 "peripheral nervous system neuron development" evidence=IEA

GO:0060021 "palate development" evidence=IEA

GO:0060536 "cartilage morphogenesis" evidence=IEA

GO:0060982 "coronary artery morphogenesis" evidence=IEA

GO:0061032 "visceral serous pericardium development" evidence=IEA

GO:0061325 "cell proliferation involved in outflow tract morphogenesis" evidence=IEA

GO:0070888 "E-box binding" evidence=IEA

GO:2000679 "positive regulation of transcription regulatory region DNA binding" evidence=IEA

GO:2000763 "positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process" evidence=IEA

GO:2000764 "positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001947 "heart looping" evidence=IEA

GO:0001967 "suckling behavior" evidence=IEA

GO:0003219 "cardiac right ventricle formation" evidence=IEA

GO:0003253 "cardiac neural crest cell migration involved in outflow tract morphogenesis" evidence=IEA

GO:0003266 "regulation of secondary heart field cardioblast proliferation" evidence=IEA

GO:0003680 "AT DNA binding" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0007512 "adult heart development" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0010463 "mesenchymal cell proliferation" evidence=IEA

GO:0010667 "negative regulation of cardiac muscle cell apoptotic process" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0042733 "embryonic digit morphogenesis" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0043392 "negative regulation of DNA binding" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043586 "tongue development" evidence=IEA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IEA

UNIPROTKB|F1NPU0 F1NPU0 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    93 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 126

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F1P1U1 F1P1U1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    50 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 83

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|Q90690 HAND2 "Heart- and neural crest derivatives-expressed protein 2" [Gallus gallus (taxid:9031)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    95 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 128

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:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1MLT3 LOC781874 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    70 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 103

GO:2000764 "positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis" evidence=IEA

GO:2000763 "positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process" evidence=IEA

GO:2000679 "positive regulation of transcription regulatory region DNA binding" evidence=IEA

GO:0070888 "E-box binding" evidence=IEA

GO:0061325 "cell proliferation involved in outflow tract morphogenesis" evidence=IEA

GO:0061032 "visceral serous pericardium development" evidence=IEA

GO:0060982 "coronary artery morphogenesis" evidence=IEA

GO:0060536 "cartilage morphogenesis" evidence=IEA

GO:0060021 "palate development" evidence=IEA

GO:0048935 "peripheral nervous system neuron development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IEA

GO:0043586 "tongue development" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043392 "negative regulation of DNA binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0042733 "embryonic digit morphogenesis" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0010667 "negative regulation of cardiac muscle cell apoptotic process" evidence=IEA

GO:0010463 "mesenchymal cell proliferation" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007512 "adult heart development" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0003680 "AT DNA binding" evidence=IEA

GO:0003266 "regulation of secondary heart field cardioblast proliferation" evidence=IEA

GO:0003253 "cardiac neural crest cell migration involved in outflow tract morphogenesis" evidence=IEA

GO:0003219 "cardiac right ventricle formation" evidence=IEA

GO:0001967 "suckling behavior" evidence=IEA

GO:0001947 "heart looping" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

UNIPROTKB|F1PX30 HAND2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:   101 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 134

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|P61296 HAND2 "Heart- and neural crest derivatives-expressed protein 2" [Homo sapiens (taxid:9606)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    96 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 129

GO:0001525 "angiogenesis" evidence=IEA

GO:0001967 "suckling behavior" evidence=IEA

GO:0003219 "cardiac right ventricle formation" evidence=IEA

GO:0003253 "cardiac neural crest cell migration involved in outflow tract morphogenesis" evidence=IEA

GO:0010463 "mesenchymal cell proliferation" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0042733 "embryonic digit morphogenesis" evidence=IEA

GO:0043392 "negative regulation of DNA binding" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043586 "tongue development" evidence=IEA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IEA

GO:0048935 "peripheral nervous system neuron development" evidence=IEA

GO:0060021 "palate development" evidence=IEA

GO:0060536 "cartilage morphogenesis" evidence=IEA

GO:0060982 "coronary artery morphogenesis" evidence=IEA

GO:0061032 "visceral serous pericardium development" evidence=IEA

GO:0061325 "cell proliferation involved in outflow tract morphogenesis" evidence=IEA

GO:0003680 "AT DNA binding" evidence=IDA

GO:0007507 "heart development" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0070888 "E-box binding" evidence=ISS;IDA

GO:0043234 "protein complex" evidence=IDA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IDA

GO:0000790 "nuclear chromatin" evidence=IDA

GO:2000679 "positive regulation of transcription regulatory region DNA binding" evidence=IDA

GO:0003357 "noradrenergic neuron differentiation" evidence=NAS

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

GO:0061309 "cardiac neural crest cell development involved in outflow tract morphogenesis" evidence=ISS

GO:0048538 "thymus development" evidence=ISS

GO:0010667 "negative regulation of cardiac muscle cell apoptotic process" evidence=ISS

GO:0003266 "regulation of secondary heart field cardioblast proliferation" evidence=ISS

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0008134 "transcription factor binding" evidence=ISS

GO:0033613 "activating transcription factor binding" evidence=ISS

GO:0001947 "heart looping" evidence=ISS

GO:0005667 "transcription factor complex" evidence=ISS

GO:0044212 "transcription regulatory region DNA binding" evidence=ISS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0042803 "protein homodimerization activity" evidence=ISS

GO:0001701 "in utero embryonic development" evidence=ISS

GO:0003007 "heart morphogenesis" evidence=ISS

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

GO:0006915 "apoptotic process" evidence=ISS

GO:0014032 "neural crest cell development" evidence=ISS

GO:0007512 "adult heart development" evidence=IEP

GO:2000763 "positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process" evidence=ISS

GO:2000764 "positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis" evidence=ISS

UNIPROTKB|F1RJ02 HAND2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    55 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 88

GO:2000764 "positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis" evidence=IEA

GO:2000763 "positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process" evidence=IEA

GO:2000679 "positive regulation of transcription regulatory region DNA binding" evidence=IEA

GO:0070888 "E-box binding" evidence=IEA

GO:0061325 "cell proliferation involved in outflow tract morphogenesis" evidence=IEA

GO:0061032 "visceral serous pericardium development" evidence=IEA

GO:0060982 "coronary artery morphogenesis" evidence=IEA

GO:0060536 "cartilage morphogenesis" evidence=IEA

GO:0060021 "palate development" evidence=IEA

GO:0048935 "peripheral nervous system neuron development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IEA

GO:0043586 "tongue development" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043392 "negative regulation of DNA binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0042733 "embryonic digit morphogenesis" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0010667 "negative regulation of cardiac muscle cell apoptotic process" evidence=IEA

GO:0010463 "mesenchymal cell proliferation" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007512 "adult heart development" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0003680 "AT DNA binding" evidence=IEA

GO:0003266 "regulation of secondary heart field cardioblast proliferation" evidence=IEA

GO:0003253 "cardiac neural crest cell migration involved in outflow tract morphogenesis" evidence=IEA

GO:0003219 "cardiac right ventricle formation" evidence=IEA

GO:0001967 "suckling behavior" evidence=IEA

GO:0001947 "heart looping" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

MGI|MGI:103580 Hand2 "heart and neural crest derivatives expressed transcript 2" [Mus musculus (taxid:10090)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/34 (79%), Positives = 32/34 (94%)

Query:     5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
             R VKRR TAN+KERRRTQSIN+AF++LRECIPN+
Sbjct:    96 RPVKRRGTANRKERRRTQSINSAFAELRECIPNV 129

GO:0000790 "nuclear chromatin" evidence=ISO

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=ISO

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=ISO

GO:0001525 "angiogenesis" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IMP

GO:0001947 "heart looping" evidence=IMP

GO:0001967 "suckling behavior" evidence=IMP

GO:0003007 "heart morphogenesis" evidence=IMP

GO:0003219 "cardiac right ventricle formation" evidence=IMP

GO:0003253 "cardiac neural crest cell migration involved in outflow tract morphogenesis" evidence=IMP

GO:0003266 "regulation of secondary heart field cardioblast proliferation" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0003680 "AT DNA binding" evidence=ISO

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005667 "transcription factor complex" evidence=IDA

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

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

GO:0006915 "apoptotic process" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007507 "heart development" evidence=IGI

GO:0007512 "adult heart development" evidence=IMP

GO:0008134 "transcription factor binding" evidence=ISO;IPI

GO:0010463 "mesenchymal cell proliferation" evidence=IMP

GO:0010667 "negative regulation of cardiac muscle cell apoptotic process" evidence=IMP

GO:0014032 "neural crest cell development" evidence=IMP

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0030154 "cell differentiation" evidence=IEA

GO:0033613 "activating transcription factor binding" evidence=ISO

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IGI

GO:0042733 "embryonic digit morphogenesis" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0043234 "protein complex" evidence=ISO

GO:0043392 "negative regulation of DNA binding" evidence=IDA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0043565 "sequence-specific DNA binding" evidence=IGI

GO:0043586 "tongue development" evidence=IMP

GO:0044212 "transcription regulatory region DNA binding" evidence=IDA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IMP;IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IGI;IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IGI;ISO;IDA

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IDA

GO:0048538 "thymus development" evidence=IMP

GO:0048935 "peripheral nervous system neuron development" evidence=IDA

GO:0060021 "palate development" evidence=IMP

GO:0060485 "mesenchyme development" evidence=IGI

GO:0060536 "cartilage morphogenesis" evidence=IGI

GO:0060982 "coronary artery morphogenesis" evidence=IMP

GO:0061032 "visceral serous pericardium development" evidence=IMP

GO:0061309 "cardiac neural crest cell development involved in outflow tract morphogenesis" evidence=IMP

GO:0061325 "cell proliferation involved in outflow tract morphogenesis" evidence=IMP

GO:0061371 "determination of heart left/right asymmetry" evidence=IMP

GO:0070888 "E-box binding" evidence=ISO;IDA

GO:2000679 "positive regulation of transcription regulatory region DNA binding" evidence=ISO

GO:2000763 "positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process" evidence=IMP

GO:2000764 "positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	86
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	5e-07
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-05

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

 Score = 42.1 bits (100), Expect = 5e-07
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 9  RRNTANKKERRRTQSINNAFSDLRECIPN 37
          RR   N++ERRR   IN+AF +LRE +P 
Sbjct: 1  RRKAHNERERRRRDRINDAFEELRELLPT 29

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 = 37.2 bits (87), Expect = 5e-05
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 7  VKRRNTANKKERRRTQSINNAFSDLRECIPN 37
            RR   N +ERRR + IN+AF +LR  +P 
Sbjct: 2  KSRREAHNLRERRRRERINDAFDELRSLLPT 32

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	86
KOG4029|consensus	228		99.75
KOG3898|consensus	254		99.65
KOG4395|consensus	285		99.37
KOG4447|consensus	173		99.32
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.3
KOG3960|consensus	284		99.28
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.14
smart00353	53	HLH helix loop helix domain.	99.12
KOG0561|consensus	373		99.05
KOG3910|consensus	632		98.69
KOG4447|consensus	173		97.34
KOG1319|consensus	229		97.12
KOG1318|consensus	411		95.83
KOG2483|consensus	232		93.91
KOG3561|consensus	803		93.81
KOG4304|consensus	250		92.87
KOG2588|consensus	953		92.07

>KOG4029|consensus

Probab=99.75  E-value=6.3e-19  Score=130.03  Aligned_cols=63  Identities=24%  Similarity=0.374  Sum_probs=56.5

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCC-CCCCCHHHHHHHHhhhhhhhhhccCCCC
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILE-TDDIISIDDFKADLSNHSSHRKNKSQYD   68 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~-~~KLSKietLrlAi~~~~~~~~~~~~~~   68 (86)
                      ...+|.++|+|||.||++||.||++||.+||+.|. ++|||||||||+||.||.....-.....
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~  169 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE  169 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence            45789999999999999999999999999999999 9999999999999999977666554443

>KOG3898|consensus

Probab=99.65  E-value=5e-17  Score=123.41  Aligned_cols=56  Identities=29%  Similarity=0.442  Sum_probs=51.7

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ...+|.++|+|||.|||+||+||+.||++||+++.+.|||||||||+|-.||....
T Consensus        69 ~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als  124 (254)
T KOG3898|consen   69 LTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALS  124 (254)
T ss_pred             hhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhc
Confidence            46789999999999999999999999999999999999999999999988885544

>KOG4395|consensus

Probab=99.37  E-value=5.1e-13  Score=103.74  Aligned_cols=52  Identities=27%  Similarity=0.390  Sum_probs=49.0

Q ss_pred             hHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhh
Q psy2848           7 VKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHS   58 (86)
Q Consensus         7 ~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~   58 (86)
                      ..+|.+||+|||+||++||.|||+||..+|..-+++||||.+||..|-.||.
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~  223 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYIL  223 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHh
Confidence            3678999999999999999999999999999999999999999999988883

>KOG4447|consensus

Probab=99.32  E-value=1.3e-12  Score=95.64  Aligned_cols=55  Identities=35%  Similarity=0.454  Sum_probs=50.3

Q ss_pred             HHHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhh
Q psy2848           4 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSS   59 (86)
Q Consensus         4 ~~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~   59 (86)
                      .....+|.-||-|||+|.++||.||..||+.||+.|.| |||||.||++|-.|++-
T Consensus        73 dE~q~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsd-klSkiqtLklA~ryidf  127 (173)
T KOG4447|consen   73 DELQKQRVMANVRERQRTQSLNEAFAALRKIIPTLPSD-KLSKIQTLKLAARYIDF  127 (173)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCcc-ccccccchhhcccCCch
Confidence            34567999999999999999999999999999999986 99999999999988854

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

Probab=99.30  E-value=9.7e-12  Score=73.65  Aligned_cols=52  Identities=27%  Similarity=0.465  Sum_probs=47.2

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCCC--CCCCCCCHHHHHHHHhhhhhhh
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPNI--LETDDIISIDDFKADLSNHSSH   60 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~~--p~~~KLSKietLrlAi~~~~~~   60 (86)
                      +|...|.+||.|...||.+|+.|+.+||..  ....|++|+++|..||.||...
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~L   54 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQL   54 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHh
Confidence            578899999999999999999999999985  3678999999999999998654

; 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 ....

>KOG3960|consensus

Probab=99.28  E-value=7.1e-12  Score=97.37  Aligned_cols=53  Identities=23%  Similarity=0.392  Sum_probs=48.4

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhh
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSS   59 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~   59 (86)
                      .+.||.+|.-|||+|.+.||+||+.|+.+--..|+ ++|.|+||||.||.||..
T Consensus       115 svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPN-QRLPKVEILRsAI~YIE~  167 (284)
T KOG3960|consen  115 SVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPN-QRLPKVEILRSAIRYIER  167 (284)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc-ccccHHHHHHHHHHHHHH
Confidence            46899999999999999999999999998877775 799999999999999944

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

Probab=99.14  E-value=2.4e-10  Score=67.37  Aligned_cols=55  Identities=27%  Similarity=0.498  Sum_probs=50.1

Q ss_pred             HHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           8 KRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         8 ~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      .+|...|..||.|...+|.+|+.|+.+||..+...|++|+.+|..||.|+...+.
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~   57 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQE   57 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            4677899999999999999999999999988778999999999999999977543

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=99.12  E-value=2.1e-10  Score=66.70  Aligned_cols=49  Identities=27%  Similarity=0.495  Sum_probs=44.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848          14 NKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus        14 N~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      |..||.|...+|.+|+.|+..||......+++|+.+|..||.|+....+
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~   49 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQE   49 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999987778999999999999999976544

>KOG0561|consensus

Probab=99.05  E-value=2.5e-10  Score=91.03  Aligned_cols=64  Identities=27%  Similarity=0.332  Sum_probs=54.6

Q ss_pred             hHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhhccCCCCCCc
Q psy2848           7 VKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRKNKSQYDSPS   71 (86)
Q Consensus         7 ~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~~~~~~~~~s   71 (86)
                      .-||.-||..||+||++||.+|..||.+||..- ..||||.++|.....||.+..+.|-....++
T Consensus        58 RmRReIANsNERRRMQSINAGFqsLr~LlPr~e-GEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn  121 (373)
T KOG0561|consen   58 RMRREIANSNERRRMQSINAGFQSLRALLPRKE-GEKLSKAAILQQTADYIHQLEGHKTELLPQN  121 (373)
T ss_pred             HHHHHhhcchHHHHHHhhhHHHHHHHHhcCccc-chhhHHHHHHHHHHHHHHHHHhccccccccc
Confidence            367889999999999999999999999999875 4699999999999999988766665544433

>KOG3910|consensus

Probab=98.69  E-value=1.6e-08  Score=84.94  Aligned_cols=55  Identities=27%  Similarity=0.367  Sum_probs=50.6

Q ss_pred             hHHHhHHHhHHhHHHHHHHHHHHHHHHHH-HhhCCCCCCCCCCCHHHHHHHHhhhh
Q psy2848           3 IIRVVKRRNTANKKERRRTQSINNAFSDL-RECIPNILETDDIISIDDFKADLSNH   57 (86)
Q Consensus         3 ~~~~~~rR~~aN~RER~R~~~lN~AF~~L-R~~IP~~p~~~KLSKietLrlAi~~~   57 (86)
                      ..|..+||.+.|+|||-|+++||+||.+| |.|--+.-++|--+|+-||..|+.-|
T Consensus       520 aeREkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVI  575 (632)
T KOG3910|consen  520 AEREKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVI  575 (632)
T ss_pred             hhHHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHH
Confidence            45789999999999999999999999999 88888877899999999999998777

>KOG4447|consensus

Probab=97.34  E-value=0.00011  Score=54.29  Aligned_cols=53  Identities=15%  Similarity=0.166  Sum_probs=44.7

Q ss_pred             hHHHhHHhHH-HHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhh
Q psy2848           7 VKRRNTANKK-ERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSH   60 (86)
Q Consensus         7 ~~rR~~aN~R-ER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~   60 (86)
                      +.++..+|.| ||.|...+|.||+.|++++|..|++ +.+++.|||.+-.++.+.
T Consensus        19 ~~~~~~~r~~~e~~R~~~ls~~s~l~g~l~pgspa~-gk~~~ktlr~~~~~~~~~   72 (173)
T KOG4447|consen   19 VSEEECDRQRKERGRKRRLSDASTLLGKLEPGSPAD-GKRGKKTLRIGTDSIQSL   72 (173)
T ss_pred             hhhhhhhhhHHHHhHHhhhhhhhhhccccCCCCCCc-ccccccccccCCCchhhH
Confidence            3566677777 9999999999999999999999976 778999999987776543

>KOG1319|consensus

Probab=97.12  E-value=0.00059  Score=52.04  Aligned_cols=55  Identities=16%  Similarity=0.311  Sum_probs=44.0

Q ss_pred             HhHHhHHHHHHHHHHHHHHHHHHhhCCCC-CCC---CCCCHHHHHHHHhhhhhhhhhcc
Q psy2848          10 RNTANKKERRRTQSINNAFSDLRECIPNI-LET---DDIISIDDFKADLSNHSSHRKNK   64 (86)
Q Consensus        10 R~~aN~RER~R~~~lN~AF~~LR~~IP~~-p~~---~KLSKietLrlAi~~~~~~~~~~   64 (86)
                      |.+...=||+|-..||.+|+.|..+||.. |++   .||||..+|--+|.|+......+
T Consensus        63 r~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k  121 (229)
T KOG1319|consen   63 RRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEK  121 (229)
T ss_pred             HHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445559999999999999999999963 333   69999999999999996654333

>KOG1318|consensus

Probab=95.83  E-value=0.022  Score=46.98  Aligned_cols=57  Identities=26%  Similarity=0.307  Sum_probs=49.3

Q ss_pred             HHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCC-CCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI-LETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         5 ~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~-p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      +..++|.-.|+=||+|-.+||...-+|-..||.. -.+-|+.|--+|..+..||.+.+
T Consensus       229 rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lq  286 (411)
T KOG1318|consen  229 RDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQ  286 (411)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHH
Confidence            4566777889999999999999999999999964 45689999999999999996653

>KOG2483|consensus

Probab=93.91  E-value=0.15  Score=39.15  Aligned_cols=50  Identities=18%  Similarity=0.355  Sum_probs=42.1

Q ss_pred             HHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhh
Q psy2848           8 KRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNH   57 (86)
Q Consensus         8 ~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~   57 (86)
                      ..|..-|+=||+|-..|=.-|+.|+..||..+..++=.-+.+|+-|+.+|
T Consensus        58 ~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i  107 (232)
T KOG2483|consen   58 SSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHI  107 (232)
T ss_pred             cchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHH
Confidence            45788899999999999999999999999987665554677777777776

>KOG3561|consensus

Probab=93.81  E-value=0.17  Score=44.84  Aligned_cols=59  Identities=15%  Similarity=0.263  Sum_probs=50.7

Q ss_pred             HHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHhhhhhhhhhc
Q psy2848           5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNIL-ETDDIISIDDFKADLSNHSSHRKN   63 (86)
Q Consensus         5 ~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p-~~~KLSKietLrlAi~~~~~~~~~   63 (86)
                      +....|..+|.=|++|-..+|.-.++|=..||..- -.+|+=|..+||.||..+...++-
T Consensus        16 k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   16 KDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             hhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            34456888999999999999999999999999743 469999999999999998776553

>KOG4304|consensus

Probab=92.87  E-value=0.081  Score=40.69  Aligned_cols=50  Identities=18%  Similarity=0.383  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCC-----CCCCCHHHHHHHHhhhhhhhhhcc
Q psy2848          15 KKERRRTQSINNAFSDLRECIPNILE-----TDDIISIDDFKADLSNHSSHRKNK   64 (86)
Q Consensus        15 ~RER~R~~~lN~AF~~LR~~IP~~p~-----~~KLSKietLrlAi~~~~~~~~~~   64 (86)
                      -=||+|-.-||.-+++|+.+||..-.     ..||-|.|+|-+++.++...+.-.
T Consensus        38 l~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~   92 (250)
T KOG4304|consen   38 LLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ   92 (250)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence            34888999999999999999996332     279999999999999987765444

>KOG2588|consensus

Probab=92.07  E-value=0.12  Score=46.51  Aligned_cols=58  Identities=21%  Similarity=0.370  Sum_probs=48.8

Q ss_pred             chHHHh---HHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           2 PIIRVV---KRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         2 ~~~~~~---~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ||.++.   .+|.+.|.=|++=--+||+-..+||..||..+  -|+.|-++||-||+++...+
T Consensus       266 Pi~rl~~G~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~--aKl~kSavLr~ai~~i~dl~  326 (953)
T KOG2588|consen  266 PIKRLLPGGEKRTAHNIIEKRYRSSINDKIIELKDLVPGTE--AKLNKSAVLRKAIDYIEDLQ  326 (953)
T ss_pred             chhhcCCCCcccchhhHHHHHhhcchhHHHHHHHHhcCccH--hhhhhhhhHHHHHHHHHHhh
Confidence            454443   46999999999988899999999999999664  59999999999999995543

---

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	86
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	8e-10
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	7e-08
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	2e-04

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

 Score = 48.8 bits (117), Expect = 8e-10
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 9  RRNTANKKERRRTQSINNAFSDLRECIPNI 38
          RR  AN +ER R   +N A  +LR+ +P  
Sbjct: 2  RRMKANARERNRMHGLNAALDNLRKVVPCY 31

>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 = 43.9 bits (104), Expect = 7e-08
 Identities = 11/33 (33%), Positives = 14/33 (42%)

Query: 4  IRVVKRRNTANKKERRRTQSINNAFSDLRECIP 36
               RR  A  +ERRR   +N AF  L+    
Sbjct: 7  TTNADRRKAATMRERRRLSKVNEAFETLKRSTS 39

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

 Score = 35.6 bits (82), Expect = 2e-04
 Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)

Query: 7  VKRRNTANKKERRRTQSINNAFSDL-RECIPNI 38
            +R   N  ER+R + IN AF +L R C  ++
Sbjct: 3  ADKRAHHNALERKRRRDINEAFRELGRMCQMHL 35

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	86
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.88
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.85
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.83
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	99.77
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.59
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.47
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.43
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.41
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.3
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.04
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.01
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	98.86
4h10_B	71	Circadian locomoter output cycles protein kaput; B	98.77
1a0a_A	63	BHLH, protein (phosphate system positive regulator	98.7
4ati_A	118	MITF, microphthalmia-associated transcription fact	98.65
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.16
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	97.72
4ath_A	83	MITF, microphthalmia-associated transcription fact	95.97
3muj_A	138	Transcription factor COE3; immunoglobulin like fol	87.71

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

Probab=99.88  E-value=4.9e-23  Score=126.79  Aligned_cols=54  Identities=26%  Similarity=0.419  Sum_probs=51.0

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      +|.++|+|||.||+.||.||+.||.+||+.|.++|||||+||++||.||...++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~   55 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSE   55 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999999999999999999999999977553

>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=99.85  E-value=2.1e-21  Score=122.23  Aligned_cols=56  Identities=20%  Similarity=0.338  Sum_probs=51.4

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      ...+|.++|+|||.||+.||.||+.||.+||..| ++|||||+||+.||.||...+.
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~-~~KlSKi~tLr~Ai~YI~~L~~   64 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQA   64 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCT-TSCCCHHHHHHHHHHHHHHHHH
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999876 7899999999999999977543

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

Probab=99.83  E-value=5.8e-22  Score=125.92  Aligned_cols=51  Identities=14%  Similarity=0.255  Sum_probs=47.9

Q ss_pred             hHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848          11 NTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus        11 ~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ..||+|||.||++||.||+.||.+||+.|.++|||||||||+||.||...+
T Consensus        16 ~~a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq   66 (68)
T 2lfh_A           16 GPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQ   66 (68)
T ss_dssp             CCCBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999999999999997654

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

Probab=99.77  E-value=2.4e-19  Score=120.25  Aligned_cols=56  Identities=14%  Similarity=0.229  Sum_probs=45.6

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhhcc
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRKNK   64 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~~~   64 (86)
                      |+..+..+||.||++||.||+.||.+||+.|.++|||||||||+||.||...+.-.
T Consensus        25 R~k~~~~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L   80 (97)
T 4aya_A           25 RSKTPVDDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIAL   80 (97)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcccccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHH
Confidence            33344567799999999999999999999999999999999999999997655444

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

Probab=99.59  E-value=5.1e-16  Score=99.24  Aligned_cols=58  Identities=17%  Similarity=0.232  Sum_probs=46.7

Q ss_pred             hHHHhHHhHHHHHHHHHHHHHHHHHHhhCC-CCCCCCCCCHHHHHHHHhhhhhhhhhcc
Q psy2848           7 VKRRNTANKKERRRTQSINNAFSDLRECIP-NILETDDIISIDDFKADLSNHSSHRKNK   64 (86)
Q Consensus         7 ~~rR~~aN~RER~R~~~lN~AF~~LR~~IP-~~p~~~KLSKietLrlAi~~~~~~~~~~   64 (86)
                      ..+|..+|++||+|+..||.+|+.||.+|| ..+.++.+||++||+.||.||...+...
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l   61 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQV   61 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999 4677777899999999999997765544

>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=99.47  E-value=7.2e-14  Score=88.55  Aligned_cols=57  Identities=19%  Similarity=0.310  Sum_probs=50.6

Q ss_pred             HHHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           4 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         4 ~~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      .....+|..+|.+||+|+..||.+|+.||.+||..+. .|+||++||+.||.||...+
T Consensus         7 ~~~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~-~k~sK~~iL~~Ai~YI~~L~   63 (80)
T 1hlo_A            7 ESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQG-EKASRAQILDKATEYIQYMR   63 (80)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTT-SCCCHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCC-CCccHHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999998764 58999999999999996654

>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=99.43  E-value=2.2e-13  Score=88.44  Aligned_cols=56  Identities=23%  Similarity=0.292  Sum_probs=51.5

Q ss_pred             hHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           7 VKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         7 ~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      ..+|...|..||+|...||.+|+.||.+||..+...|+||+.||+.||.||...+.
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~   59 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQA   59 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999998888999999999999999966543

>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=99.41  E-value=3.2e-13  Score=85.78  Aligned_cols=52  Identities=21%  Similarity=0.371  Sum_probs=47.5

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      +|..+|.+||+|+..||.+|+.||.+||..+ +.|+||++||+.||.||...+
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~-~~k~sK~~iL~~Ai~YI~~L~   53 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYMR   53 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHH
Confidence            6889999999999999999999999999876 468999999999999996654

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

Probab=99.30  E-value=5.3e-12  Score=80.91  Aligned_cols=53  Identities=13%  Similarity=0.182  Sum_probs=49.1

Q ss_pred             HhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848          10 RNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus        10 R~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      |...|..||.|...||.+|+.||.+||..+.+.|+||+.||+.|+.||...+.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~   54 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLED   54 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            67889999999999999999999999999889999999999999999966543

>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=99.04  E-value=6.3e-11  Score=72.13  Aligned_cols=56  Identities=27%  Similarity=0.267  Sum_probs=48.7

Q ss_pred             HHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCC---CCCCHHHHHHHHhhhhhhhhhc
Q psy2848           8 KRRNTANKKERRRTQSINNAFSDLRECIPNILET---DDIISIDDFKADLSNHSSHRKN   63 (86)
Q Consensus         8 ~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~---~KLSKietLrlAi~~~~~~~~~   63 (86)
                      .+|...|..||.|...||.+|+.|+.+||.....   .|++|..+|..||.|+...++.
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~   62 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHH
Confidence            3577889999999999999999999999976543   5899999999999999876543

>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=99.01  E-value=6.7e-10  Score=70.85  Aligned_cols=54  Identities=15%  Similarity=0.204  Sum_probs=48.2

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ...+|...|..||+|...||.+|..|+.+||.  .+.|++|..+|..||.||...+
T Consensus         3 ~~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~--~~~k~~Ka~IL~~Ai~YI~~Lq   56 (82)
T 1am9_A            3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQ   56 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--SSCCCCHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHhhhhHHHHHHHHHHHHHHHHHHhccC--CCCCCCHHHHHHHHHHHHHHHH
Confidence            35678899999999999999999999999996  3689999999999999996543

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

Probab=98.86  E-value=2.7e-09  Score=67.54  Aligned_cols=58  Identities=16%  Similarity=0.305  Sum_probs=50.2

Q ss_pred             HHHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCC-CCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           4 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNI-LETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         4 ~~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~-p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ++...+|...+.-||+|-..||..|++|+.+||.. ....|+.|+++|+.||.|+...+
T Consensus         4 ~k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~   62 (73)
T 4h10_A            4 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR   62 (73)
T ss_dssp             -CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHh
Confidence            35567888999999999999999999999999953 34689999999999999997654

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

Probab=98.77  E-value=1.7e-08  Score=63.81  Aligned_cols=56  Identities=16%  Similarity=0.274  Sum_probs=49.1

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhhc
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRKN   63 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~~   63 (86)
                      ...+|...|.-||+|-..||..|.+|+.+||.  .+.|+.|..+|..||.|+...++.
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~--~~~K~dK~sIL~~aI~yik~Lq~~   60 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPG--NARKMDKSTVLQKSIDFLRKHKEI   60 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSS--CCSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCC--CCCCCcHHHHHHHHHHHHHHHHHh
Confidence            35678889999999999999999999999993  457999999999999999776543

>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=98.70  E-value=5.7e-09  Score=64.10  Aligned_cols=54  Identities=15%  Similarity=0.183  Sum_probs=45.6

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCCCC----CCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPNIL----ETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p----~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      +|...+.=||.|...||.+|++|+.+||...    +..++||.+||-.||.|+...+.
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~   59 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQ   59 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHT
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHH
Confidence            3556677899999999999999999999642    25799999999999999987654

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

Probab=98.65  E-value=4.6e-08  Score=66.18  Aligned_cols=56  Identities=21%  Similarity=0.201  Sum_probs=42.2

Q ss_pred             HHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHhhhhhhh
Q psy2848           5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNIL-ETDDIISIDDFKADLSNHSSH   60 (86)
Q Consensus         5 ~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p-~~~KLSKietLrlAi~~~~~~   60 (86)
                      +...+|...|.-||+|-..||..|..|+.+||... .+.|++|..+|..||.|+...
T Consensus        23 k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~L   79 (118)
T 4ati_A           23 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKL   79 (118)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHH
Confidence            34456778899999999999999999999999753 478999999999999999654

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

Probab=98.16  E-value=2.3e-06  Score=64.30  Aligned_cols=55  Identities=16%  Similarity=0.267  Sum_probs=41.0

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      ...+|...|.-||+|-..+|..|.+|+.+||  ....||.|..+|++||.|+...+.
T Consensus         9 ~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p--~~~~~~dk~~il~~~~~~~~~~~~   63 (361)
T 4f3l_A            9 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLP--GNARKMDKSTVLQKSIDFLRKHKE   63 (361)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHTCC--SSSCCCCHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhHHHHHHHHHHHHHHHHHHHhCC--CCCCCcCHHHHHHHHHHHHHHHHh
Confidence            3456788899999999999999999999999  456899999999999999976554

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

Probab=97.72  E-value=3.3e-05  Score=58.79  Aligned_cols=59  Identities=15%  Similarity=0.283  Sum_probs=49.1

Q ss_pred             HHHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCC-CCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           4 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNIL-ETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         4 ~~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p-~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      .|...+|...|.-||+|-..+|..|.+|+.+||... ...||.|..+|++||.|+...++
T Consensus         8 ~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B            8 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             chhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            355667888899999999999999999999999633 45899999999999999976653

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

Probab=95.97  E-value=0.015  Score=37.67  Aligned_cols=38  Identities=18%  Similarity=0.093  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHhhCCCC-CCCCCCCHHHHHHHHhhhhhhh
Q psy2848          23 SINNAFSDLRECIPNI-LETDDIISIDDFKADLSNHSSH   60 (86)
Q Consensus        23 ~lN~AF~~LR~~IP~~-p~~~KLSKietLrlAi~~~~~~   60 (86)
                      +||..+.+|...||.. ..+-|++|-.+|+.|+.||...
T Consensus         6 nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~L   44 (83)
T 4ath_A            6 NINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKL   44 (83)
T ss_dssp             HHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHH
T ss_pred             hHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHH
Confidence            6999999999999963 3578999999999999999554

>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=87.71  E-value=0.85  Score=31.83  Aligned_cols=34  Identities=18%  Similarity=0.205  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhhCCCCCCC-CCCCHHHHHHHHhhh
Q psy2848          23 SINNAFSDLRECIPNILET-DDIISIDDFKADLSN   56 (86)
Q Consensus        23 ~lN~AF~~LR~~IP~~p~~-~KLSKietLrlAi~~   56 (86)
                      .|+-+|++|.+.||..|.| .+|.|--+|+-|..-
T Consensus        95 tId~gfqrl~k~~pr~pgdpe~lpk~~~lkraa~l  129 (138)
T 3muj_A           95 TIDYGFQRLQKVIPRHPGDPERLPKEVLLKRAADL  129 (138)
T ss_dssp             CHHHHHHHHHHHSCCCTTCCSSCCHHHHHHHHHHH
T ss_pred             ccccchhhhccccCCCCCChhhhhHHHHHHHHHHH
Confidence            4788999999999999876 899999999987654

---

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	86
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	9e-06
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	7e-05
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-04
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-04
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	0.001
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	0.002

>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 = 37.5 bits (87), Expect = 9e-06
 Identities = 11/33 (33%), Positives = 15/33 (45%)

Query: 5  RVVKRRNTANKKERRRTQSINNAFSDLRECIPN 37
              RR  A  +ERRR   +N AF  L+    +
Sbjct: 8  TNADRRKAATMRERRRLSKVNEAFETLKRSTSS 40

>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 = 35.2 bits (81), Expect = 7e-05
 Identities = 7/38 (18%), Positives = 16/38 (42%)

Query: 9  RRNTANKKERRRTQSINNAFSDLRECIPNILETDDIIS 46
          +R +    E+ R   +  A  +L   IP   +  ++ +
Sbjct: 2  KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSA 39

>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 = 35.3 bits (81), Expect = 1e-04
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 5  RVVKRRNTANKKERRRTQSINNAFSDLRECIPNI 38
           +  +R T N  ER+R   +  +F  LR+ IP +
Sbjct: 2  HMNVKRRTHNVLERQRRNELKRSFFALRDQIPEL 35

>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 = 34.4 bits (79), Expect = 1e-04
 Identities = 14/35 (40%), Positives = 17/35 (48%)

Query: 8  KRRNTANKKERRRTQSINNAFSDLRECIPNILETD 42
          KRR   N+ ERRR   INN    L + IP+     
Sbjct: 4  KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMES 38

>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 = 32.1 bits (73), Expect = 0.001
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 9  RRNTANKKERRRTQSINNAFSDLRECIP 36
          +R   N  ER+R   I ++F  LR+ +P
Sbjct: 2  KRAHHNALERKRRDHIKDSFHSLRDSVP 29

>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 = 31.4 bits (71), Expect = 0.002
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 10 RNTANKKERRRTQSINNAFSDLRECIPNILETD 42
          R+T N+ E+ R   +  +   L+  +P   ++ 
Sbjct: 2  RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSS 34

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	86
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.52
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.37
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.32
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.26
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.13
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.03
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.09

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

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

Probab=99.52  E-value=1.8e-14  Score=88.11  Aligned_cols=56  Identities=20%  Similarity=0.341  Sum_probs=50.5

Q ss_pred             HhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhhh
Q psy2848           6 VVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHRK   62 (86)
Q Consensus         6 ~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~~   62 (86)
                      ...+|..+|.+||.|...||.+|+.|+.+||..+. +|+||++||+.||.||...+.
T Consensus         9 ~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~-~k~sK~~iL~~Ai~YI~~Lq~   64 (68)
T d1mdya_           9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPN-QRLPKVEILRNAIRYIEGLQA   64 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTT-SCCCHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999998765 599999999999999976543

>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=99.37  E-value=4.7e-13  Score=84.14  Aligned_cols=57  Identities=23%  Similarity=0.302  Sum_probs=51.5

Q ss_pred             HHhHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           5 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         5 ~~~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ..-.+|...|.+||.|...||.+|+.|+.+||..+...|+||+++|..||.||...+
T Consensus         2 ~~~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~   58 (88)
T d1nkpa_           2 HMNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ   58 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHH
Confidence            345688899999999999999999999999998888899999999999999996543

>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=99.35  E-value=9.7e-13  Score=81.22  Aligned_cols=52  Identities=13%  Similarity=0.182  Sum_probs=48.4

Q ss_pred             HhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848          10 RNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus        10 R~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      |...|..||.|...||.+|+.|+.+||..+...|+||+++|..||.||...+
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~   53 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLE   53 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            7788999999999999999999999999888889999999999999997654

>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=99.32  E-value=1.1e-12  Score=81.59  Aligned_cols=51  Identities=20%  Similarity=0.347  Sum_probs=46.6

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhh
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSH   60 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~   60 (86)
                      +|...|.+||.|...||.+|+.|+.+||..+ +.|+||+++|+.||.||...
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~-~~k~sK~~iL~~A~~yI~~L   52 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYM   52 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGT-TSCCCHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CCCCCHHHHHHHHHHHHHHH
Confidence            7889999999999999999999999999765 46999999999999999654

>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=99.26  E-value=2.2e-12  Score=77.30  Aligned_cols=55  Identities=16%  Similarity=0.194  Sum_probs=48.7

Q ss_pred             HHhHHhHHHHHHHHHHHHHHHHHHhhCCC----CCCCCCCCHHHHHHHHhhhhhhhhhc
Q psy2848           9 RRNTANKKERRRTQSINNAFSDLRECIPN----ILETDDIISIDDFKADLSNHSSHRKN   63 (86)
Q Consensus         9 rR~~aN~RER~R~~~lN~AF~~LR~~IP~----~p~~~KLSKietLrlAi~~~~~~~~~   63 (86)
                      +|...|..||+|...||.+|+.|+.+||.    ...+.|+||.++|..||.||...++.
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~   60 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQN   60 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTC
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Confidence            57889999999999999999999999995    23468999999999999999876554

>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=99.13  E-value=6.4e-12  Score=75.59  Aligned_cols=56  Identities=27%  Similarity=0.279  Sum_probs=49.0

Q ss_pred             HHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCC---CCCCCCHHHHHHHHhhhhhhhhhc
Q psy2848           8 KRRNTANKKERRRTQSINNAFSDLRECIPNIL---ETDDIISIDDFKADLSNHSSHRKN   63 (86)
Q Consensus         8 ~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p---~~~KLSKietLrlAi~~~~~~~~~   63 (86)
                      .+|...|..||+|...||.+|+.|+.+||...   .+.|+||+++|..|+.||...++.
T Consensus         4 ~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            35778999999999999999999999999743   457999999999999999876543

>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=99.03  E-value=2.9e-10  Score=70.33  Aligned_cols=53  Identities=15%  Similarity=0.221  Sum_probs=47.2

Q ss_pred             hHHHhHHhHHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848           7 VKRRNTANKKERRRTQSINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus         7 ~~rR~~aN~RER~R~~~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      ..+|...|..||.|...||.+|+.|+.+||.  ...|+||.++|..||.||....
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~--~~~k~~K~~iL~~a~~yI~~L~   56 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQ   56 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--SSCCCCHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CCCCCCHHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999995  3569999999999999996543

>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=98.09  E-value=8.7e-07  Score=52.07  Aligned_cols=37  Identities=11%  Similarity=0.179  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHhhCCCCCCCCCCCHHHHHHHHhhhhhhhh
Q psy2848          23 SINNAFSDLRECIPNILETDDIISIDDFKADLSNHSSHR   61 (86)
Q Consensus        23 ~lN~AF~~LR~~IP~~p~~~KLSKietLrlAi~~~~~~~   61 (86)
                      .||..|..||.+||..  ..|++|+++|..||.||...+
T Consensus         3 ~in~~f~~L~~lvP~~--~~K~~Ka~iL~~Ai~YI~~Lq   39 (61)
T d1uklc_           3 SINDKIIELKDLVMGT--DAKMHKSGVLRKAIDYIKYLQ   39 (61)
T ss_dssp             CHHHHHHHHHHHHSCS--SCCCCTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCCC--CCcccHHHHHHHHHHHHHHHH
Confidence            4899999999999953  469999999999999996543