Psyllid ID: psy17810

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--
Protein Sequence
MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKGIPHNLQEGQDS
Secondary Structure (PSIPRED)
cccccHHHHHcccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHcHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHcccc
Coil and Loop (DISEMBL)
mlplpaaitsqLDKASIIRLTISYLKlrdfsghgdppwsrdgpspsksvkgiphnlqegqds
Flexible Loop (DISEMBL)
mlplpaaitsqldkASIIRLTISYLKLRDFSGHGdppwsrdgpspsksvkgiphnlqegqds
Low Complexity Region (SEG)
MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKGIPHNLQEGQDS
Disordered region (IsUnstruct)
***********LDKASIIRLTISYLKLRDF********************************
Disordered Region (DISOPRED)
******AITSQLDKASIIRLTISYLKLRDFSG******************************
Disordered Region (DISEMBL)
MLPLPAAITSQLDKASIIRLTISYLKLRDFSGH*****************GIPHNLQEGQDS
Disordered Region (DISPRO)
MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS***********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKGIPHNLQEGQDS
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	62	2.2.26 [Sep-21-2011]
Q24119	1022	Protein trachealess OS=Dr	yes	N/A	0.661	0.040	0.951	8e-17
Q9QZQ0	925	Neuronal PAS domain-conta	yes	N/A	0.822	0.055	0.754	6e-16
Q8IXF0	933	Neuronal PAS domain-conta	yes	N/A	0.838	0.055	0.740	2e-15
Q99742	590	Neuronal PAS domain-conta	no	N/A	0.725	0.076	0.577	4e-09
P97459	594	Neuronal PAS domain-conta	no	N/A	0.612	0.063	0.657	5e-09
Q61079	657	Single-minded homolog 2 O	no	N/A	0.903	0.085	0.580	5e-07
Q14190	667	Single-minded homolog 2 O	no	N/A	0.677	0.062	0.666	7e-07
P05709	697	Protein single-minded OS=	no	N/A	0.451	0.040	0.857	1e-06
P81133	766	Single-minded homolog 1 O	no	N/A	0.451	0.036	0.857	1e-06
A2T6X9	766	Single-minded homolog 1 O	no	N/A	0.451	0.036	0.857	1e-06

>sp|Q24119|TRH_DROME Protein trachealess OS=Drosophila melanogaster GN=trh PE=1 SV=4

 Score = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 39/41 (95%), Positives = 41/41 (100%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRD 41
           MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPW+R+
Sbjct: 112 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWTRE 152

Transcription factor, master regulator of tracheal cell fates in the embryo, necessary for the development of the salivary gland duct and the posterior spiracles. It may induce a general fate of branched tubular structures of epithelial origin. Heterodimers of tgo/trh are involved in the control of breathless expression.
Drosophila melanogaster (taxid: 7227)

>sp|Q9QZQ0|NPAS3_MOUSE Neuronal PAS domain-containing protein 3 OS=Mus musculus GN=Npas3 PE=2 SV=1

 Score = 82.8 bits (203), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 40/53 (75%), Positives = 46/53 (86%), Gaps = 2/53 (3%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKG 51
           +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVKG
Sbjct: 84  LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKG 136

May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness.

Mus musculus (taxid: 10090)

>sp|Q8IXF0|NPAS3_HUMAN Neuronal PAS domain-containing protein 3 OS=Homo sapiens GN=NPAS3 PE=2 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/54 (74%), Positives = 46/54 (85%), Gaps = 2/54 (3%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGI 52
           +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK I
Sbjct: 77  LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKVI 130

May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness.

Homo sapiens (taxid: 9606)

>sp|Q99742|NPAS1_HUMAN Neuronal PAS domain-containing protein 1 OS=Homo sapiens GN=NPAS1 PE=2 SV=2

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 26/45 (57%), Positives = 34/45 (75%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSP 45
           +LPLP AI+SQLDKASI+RL+++YL+LR F+  G PPW      P
Sbjct: 71  LLPLPGAISSQLDKASIVRLSVTYLRLRRFAALGAPPWGLRAAGP 115

May control regulatory pathways relevant to schizophrenia and to psychotic illness. May play a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level.

Homo sapiens (taxid: 9606)

>sp|P97459|NPAS1_MOUSE Neuronal PAS domain-containing protein 1 OS=Mus musculus GN=Npas1 PE=1 SV=1

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 25/38 (65%), Positives = 33/38 (86%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPW 38
           +LPLP AI+SQLDKASI+RL+++YL+LR F+  G PPW
Sbjct: 71  LLPLPGAISSQLDKASIVRLSVTYLRLRRFAALGAPPW 108

May control regulatory pathways relevant to schizophrenia and to psychotic illness. May play a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level.

Mus musculus (taxid: 10090)

>sp|Q61079|SIM2_MOUSE Single-minded homolog 2 OS=Mus musculus GN=Sim2 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 36/62 (58%), Positives = 41/62 (66%), Gaps = 6/62 (9%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLRDF--SGHGDPPW---SRDGPSPSKSVKGIPHN 55
          +LPLP+AITSQLDKASIIRLT SYLK+R     G GD  W   SR GP  S + +   H 
Sbjct: 26 LLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGD-AWGQPSRTGPLDSVAKELGSHL 84

Query: 56 LQ 57
          LQ
Sbjct: 85 LQ 86

Transcription factor that may be a master gene of CNS development in cooperation with Arnt. It may have pleiotropic effects in the tissues expressed during development.

Mus musculus (taxid: 10090)

>sp|Q14190|SIM2_HUMAN Single-minded homolog 2 OS=Homo sapiens GN=SIM2 PE=1 SV=2

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 32/48 (66%), Positives = 35/48 (72%), Gaps = 6/48 (12%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLRDF--SGHGDPPW---SRDGP 43
          +LPLP+AITSQLDKASIIRLT SYLK+R     G GD  W   SR GP
Sbjct: 26 LLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGD-AWGQPSRAGP 72

Transcription factor that may be a master gene of CNS development in cooperation with Arnt. It may have pleiotropic effects in the tissues expressed during development.

Homo sapiens (taxid: 9606)

>sp|P05709|SIM_DROME Protein single-minded OS=Drosophila melanogaster GN=sim PE=1 SV=3

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLR 28
          +LPLPAAITSQLDKAS+IRLT SYLK+R
Sbjct: 50 LLPLPAAITSQLDKASVIRLTTSYLKMR 77

Transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord. Required to correctly specify the formation of the central brain complex, which controls walking behavior. Also required for correct patterning of the embryonic genital disk and anal pad anlage.

Drosophila melanogaster (taxid: 7227)

>sp|P81133|SIM1_HUMAN Single-minded homolog 1 OS=Homo sapiens GN=SIM1 PE=2 SV=2

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLR 28
          +LPLP+AITSQLDKASIIRLT SYLK+R
Sbjct: 26 LLPLPSAITSQLDKASIIRLTTSYLKMR 53

Transcriptional factor that may have pleiotropic effects during embryogenesis and in the adult.

Homo sapiens (taxid: 9606)

>sp|A2T6X9|SIM1_PANTR Single-minded homolog 1 OS=Pan troglodytes GN=SIM1 PE=3 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLR 28
          +LPLP+AITSQLDKASIIRLT SYLK+R
Sbjct: 26 LLPLPSAITSQLDKASIIRLTTSYLKMR 53

Transcriptional factor that may have pleiotropic effects during embryogenesis and in the adult.

Pan troglodytes (taxid: 9598)

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	62
307182730	965	Protein trachealess [Camponotus floridan	0.822	0.052	0.960	2e-20
307202142	927	Protein trachealess [Harpegnathos saltat	0.822	0.055	0.941	1e-19
270015606	851	trachealess [Tribolium castaneum]	0.822	0.059	0.901	3e-19
189241974	820	PREDICTED: similar to Bm trachealess [Tr	0.822	0.062	0.901	4e-19
350424337	907	PREDICTED: protein trachealess-like isof	0.822	0.056	0.901	5e-19
340722623	907	PREDICTED: protein trachealess-like isof	0.822	0.056	0.901	5e-19
350424334	935	PREDICTED: protein trachealess-like isof	0.822	0.054	0.901	5e-19
340722621	990	PREDICTED: protein trachealess-like isof	0.822	0.051	0.901	6e-19
332027679	953	Protein trachealess [Acromyrmex echinati	0.822	0.053	0.942	6e-19
345485710	681	PREDICTED: protein trachealess-like [Nas	0.806	0.073	0.94	7e-19

>gi|307182730|gb|EFN69854.1| Protein trachealess [Camponotus floridanus]

 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/51 (96%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLRDFS HGDPPWSRDGP PSKSVKG
Sbjct: 111 MLPLPAAITSQLDKASIIRLTISYLKLRDFSSHGDPPWSRDGPPPSKSVKG 161

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307202142|gb|EFN81642.1| Protein trachealess [Harpegnathos saltator]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/51 (94%), Positives = 48/51 (94%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLRDFS HGDPPWSRDGP P KSVKG
Sbjct: 80  MLPLPAAITSQLDKASIIRLTISYLKLRDFSSHGDPPWSRDGPPPIKSVKG 130

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015606|gb|EFA12054.1| trachealess [Tribolium castaneum]

 Score = 99.0 bits (245), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGP P+K++K 
Sbjct: 116 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPPPNKTLKA 166

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189241974|ref|XP_967112.2| PREDICTED: similar to Bm trachealess [Tribolium castaneum]

 Score = 99.0 bits (245), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGP P+K++K 
Sbjct: 87  MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPPPNKTLKA 137

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350424337|ref|XP_003493762.1| PREDICTED: protein trachealess-like isoform 2 [Bombus impatiens]

 Score = 98.6 bits (244), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLR+FSGHGDPPW+RDGP P+KS KG
Sbjct: 80  MLPLPAAITSQLDKASIIRLTISYLKLREFSGHGDPPWNRDGPPPNKSGKG 130

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722623|ref|XP_003399703.1| PREDICTED: protein trachealess-like isoform 2 [Bombus terrestris]

 Score = 98.6 bits (244), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLR+FSGHGDPPW+RDGP P+KS KG
Sbjct: 80  MLPLPAAITSQLDKASIIRLTISYLKLREFSGHGDPPWNRDGPPPNKSGKG 130

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350424334|ref|XP_003493761.1| PREDICTED: protein trachealess-like isoform 1 [Bombus impatiens]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLR+FSGHGDPPW+RDGP P+KS KG
Sbjct: 108 MLPLPAAITSQLDKASIIRLTISYLKLREFSGHGDPPWNRDGPPPNKSGKG 158

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722621|ref|XP_003399702.1| PREDICTED: protein trachealess-like isoform 1 [Bombus terrestris]

 Score = 98.2 bits (243), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLR+FSGHGDPPW+RDGP P+KS KG
Sbjct: 163 MLPLPAAITSQLDKASIIRLTISYLKLREFSGHGDPPWNRDGPPPNKSGKG 213

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027679|gb|EGI67747.1| Protein trachealess [Acromyrmex echinatior]

 Score = 97.8 bits (242), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/52 (94%), Positives = 49/52 (94%), Gaps = 1/52 (1%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRD-GPSPSKSVKG 51
           MLPLPAAITSQLDKASIIRLTISYLKLRDFS HGDPPWSRD GP PSKSVKG
Sbjct: 78  MLPLPAAITSQLDKASIIRLTISYLKLRDFSSHGDPPWSRDGGPPPSKSVKG 129

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345485710|ref|XP_001606407.2| PREDICTED: protein trachealess-like [Nasonia vitripennis]

 Score = 97.8 bits (242), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 47/50 (94%), Positives = 48/50 (96%)

Query: 1   MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVK 50
           MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRD P P+KSVK
Sbjct: 120 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDTPPPNKSVK 169

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

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	62
FB|FBgn0262139	1022	trh "trachealess" [Drosophila	0.758	0.045	0.893	1.6e-16
UNIPROTKB|I3LMD4	205	NPAS3 "Uncharacterized protein	0.838	0.253	0.740	4.7e-16
UNIPROTKB|F1NJ70	82	F1NJ70 "Uncharacterized protei	0.806	0.609	0.75	6e-16
MGI|MGI:1351610	925	Npas3 "neuronal PAS domain pro	0.822	0.055	0.754	2.7e-15
UNIPROTKB|F8VR32	938	NPAS3 "Neuronal PAS domain-con	0.822	0.054	0.754	2.8e-15
UNIPROTKB|F8VS42	906	NPAS3 "Neuronal PAS domain-con	0.838	0.057	0.740	9e-15
UNIPROTKB|F6VP83	913	NPAS3 "Uncharacterized protein	0.838	0.056	0.740	9.1e-15
UNIPROTKB|F7HC48	932	NPAS3 "Uncharacterized protein	0.838	0.055	0.740	9.4e-15
UNIPROTKB|Q8IXF0	933	NPAS3 "Neuronal PAS domain-con	0.838	0.055	0.740	9.4e-15
ZFIN|ZDB-GENE-060503-934	770	npas3b "neuronal PAS domain pr	0.903	0.072	0.620	4.3e-12

FB|FBgn0262139 trh "trachealess" [Drosophila melanogaster (taxid:7227)]

 Score = 217 (81.4 bits), Expect = 1.6e-16, P = 1.6e-16
 Identities = 42/47 (89%), Positives = 44/47 (93%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSK 47
             MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPW+R+  S SK
Sbjct:   112 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWTREASSSSK 158

GO:0072175 "epithelial tube formation" evidence=IMP

GO:0005634 "nucleus" evidence=ISS;NAS;IDA;TAS

GO:0000981 "sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=ISS

GO:0007424 "open tracheal system development" evidence=NAS;IMP;TAS

GO:0007431 "salivary gland development" evidence=NAS;IMP

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

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

GO:0046982 "protein heterodimerization activity" evidence=TAS;IPI

GO:0035277 "spiracle morphogenesis, open tracheal system" evidence=IMP

GO:0007443 "Malpighian tubule morphogenesis" evidence=IMP

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=NAS;TAS;IPI

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=NAS

GO:0007425 "epithelial cell fate determination, open tracheal system" evidence=IMP;TAS

GO:0007435 "salivary gland morphogenesis" evidence=IMP;TAS

GO:0004871 "signal transducer activity" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0048813 "dendrite morphogenesis" evidence=IMP

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

GO:0046331 "lateral inhibition" evidence=IMP

UNIPROTKB|I3LMD4 NPAS3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 40/54 (74%), Positives = 46/54 (85%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGI 52
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK I
Sbjct:   113 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKVI 166

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F1NJ70 F1NJ70 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 39/52 (75%), Positives = 45/52 (86%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVK 50
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK
Sbjct:    31 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVK 82

GO:0046983 "protein dimerization activity" evidence=IEA

MGI|MGI:1351610 Npas3 "neuronal PAS domain protein 3" [Mus musculus (taxid:10090)]

 Score = 205 (77.2 bits), Expect = 2.7e-15, P = 2.7e-15
 Identities = 40/53 (75%), Positives = 46/53 (86%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKG 51
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVKG
Sbjct:    84 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKG 136

GO:0003677 "DNA binding" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007165 "signal transduction" evidence=IEA

GO:0007610 "behavior" evidence=IMP

GO:0007626 "locomotory behavior" evidence=IMP

GO:0035176 "social behavior" evidence=IMP

GO:0042711 "maternal behavior" evidence=IMP

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F8VR32 NPAS3 "Neuronal PAS domain-containing protein 3" [Homo sapiens (taxid:9606)]

 Score = 205 (77.2 bits), Expect = 2.8e-15, P = 2.8e-15
 Identities = 40/53 (75%), Positives = 46/53 (86%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKG 51
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVKG
Sbjct:    84 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKG 136

GO:0004871 "signal transducer activity" evidence=IEA

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:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F8VS42 NPAS3 "Neuronal PAS domain-containing protein 3" [Homo sapiens (taxid:9606)]

 Score = 200 (75.5 bits), Expect = 9.0e-15, P = 9.0e-15
 Identities = 40/54 (74%), Positives = 46/54 (85%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGI 52
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK I
Sbjct:    54 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKVI 107

GO:0004871 "signal transducer activity" evidence=IEA

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:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F6VP83 NPAS3 "Uncharacterized protein" [Macaca mulatta (taxid:9544)]

 Score = 200 (75.5 bits), Expect = 9.1e-15, P = 9.1e-15
 Identities = 40/54 (74%), Positives = 46/54 (85%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGI 52
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK I
Sbjct:    61 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKVI 114

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

UNIPROTKB|F7HC48 NPAS3 "Uncharacterized protein" [Callithrix jacchus (taxid:9483)]

 Score = 200 (75.5 bits), Expect = 9.4e-15, P = 9.4e-15
 Identities = 40/54 (74%), Positives = 46/54 (85%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGI 52
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK I
Sbjct:    77 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKVI 130

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

UNIPROTKB|Q8IXF0 NPAS3 "Neuronal PAS domain-containing protein 3" [Homo sapiens (taxid:9606)]

 Score = 200 (75.5 bits), Expect = 9.4e-15, P = 9.4e-15
 Identities = 40/54 (74%), Positives = 46/54 (85%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGI 52
             +LPLPAAITSQLDKASIIRLTISYLK+RDF+  GDPPW+   +GP P+ SVK I
Sbjct:    77 LLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEGPPPNTSVKVI 130

GO:0004871 "signal transducer activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0007626 "locomotory behavior" evidence=IEA

GO:0035176 "social behavior" evidence=IEA

GO:0042711 "maternal behavior" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

ZFIN|ZDB-GENE-060503-934 npas3b "neuronal PAS domain protein 3b" [Danio rerio (taxid:7955)]

 Score = 174 (66.3 bits), Expect = 4.3e-12, P = 4.3e-12
 Identities = 36/58 (62%), Positives = 42/58 (72%)

Query:     1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS--RDGPSPSKSVKGIPHNL 56
             MLPLP AITSQLDKASIIRLTISYL +R F+  GDPPWS   +G +    V+   H+L
Sbjct:    62 MLPLPGAITSQLDKASIIRLTISYLHMRHFASQGDPPWSPLMEGENNCSKVRRTSHSL 119

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8IXF0	NPAS3_HUMAN	No assigned EC number	0.7407	0.8387	0.0557	yes	N/A
Q9QZQ0	NPAS3_MOUSE	No assigned EC number	0.7547	0.8225	0.0551	yes	N/A
Q24119	TRH_DROME	No assigned EC number	0.9512	0.6612	0.0401	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	62
KOG3558|consensus	768		99.54
KOG3559|consensus	598		99.32
KOG3560|consensus	712		99.23
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	95.25
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	95.07
smart00353	53	HLH helix loop helix domain.	94.94

>KOG3558|consensus

Probab=99.54  E-value=2.6e-15  Score=121.52  Aligned_cols=56  Identities=59%  Similarity=0.895  Sum_probs=43.0

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCCCCCCCCCCCCCCCcccCcccccc
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKGIPHNLQ   57 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~~~w~~~~~~~~~t~~lgshlLQ   57 (62)
                      +||||++|++||||||||||||||||||+|+.+++++ ...++.++.-.-.+.|.||
T Consensus        71 ~lPlp~aisshLDkaSimRLtISyLRlrk~a~~g~~p-~~e~~~~~~e~~l~~~iLq  126 (768)
T KOG3558|consen   71 LLPLPAAISSHLDKASIMRLTISYLRLRKFAGAGDPP-RAEGEPENLEQHLGDHILQ  126 (768)
T ss_pred             hCCCcchhhhhhhhHHHHHHHHHHHHHHHHhhcCCcc-cccCCCcchhhhhhhhHHh
Confidence            5999999999999999999999999999999999765 2233333322235566665

>KOG3559|consensus

Probab=99.32  E-value=5.6e-13  Score=105.05  Aligned_cols=58  Identities=50%  Similarity=0.651  Sum_probs=49.6

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCCC-CCCCCC---CCCCCCcccCccccccc
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGD-PPWSRD---GPSPSKSVKGIPHNLQE   58 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~-~~w~~~---~~~~~~t~~lgshlLQe   58 (62)
                      +||||.+|++|||||||+|||.||||||.+|+.|+ ..|+..   .+-......+|+|+||+
T Consensus        26 lLPLa~AItsQlDKasiiRLtTsYlKmr~vFPeGLGeawg~~S~a~~~~g~~~elgshlLqt   87 (598)
T KOG3559|consen   26 LLPLASAITSQLDKASIIRLTTSYLKMRNVFPEGLGEAWGASSRADPLDGVDKELGSHLLQT   87 (598)
T ss_pred             hccchhhhhhccchhhhhhHHHHHHHHHHhcccccchhccCCCccccccchHHHHHHhHHHh
Confidence            69999999999999999999999999999998876 688753   34445566888999986

>KOG3560|consensus

Probab=99.23  E-value=4.4e-12  Score=101.97  Aligned_cols=60  Identities=35%  Similarity=0.492  Sum_probs=46.1

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCCCCCC--CCCCCCCCCcc-c-Cc-ccccccCC
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPW--SRDGPSPSKSV-K-GI-PHNLQEGQ   60 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~~~w--~~~~~~~~~t~-~-lg-shlLQeg~   60 (62)
                      |||||.+|+++|||.||+||++||||.|+||+......  ...+..+++.. . .+ +..|+||.
T Consensus        50 LLPfpqdiisKLDkLSVLRLSVSyLr~KSfFqvvl~~s~~~~~gg~~s~~a~~~yr~gl~llege  114 (712)
T KOG3560|consen   50 LLPFPQDIISKLDKLSVLRLSVSYLRVKSFFQVVLHQSSRQPAGGPPSPHASCPYRNGLALLEGE  114 (712)
T ss_pred             hcCCCHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHhcCccccCCCCCCccccchhhccccccchH
Confidence            69999999999999999999999999999998765433  23455555422 2 33 66788874

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

Probab=95.25  E-value=0.0099  Score=32.83  Aligned_cols=26  Identities=42%  Similarity=0.648  Sum_probs=20.3

Q ss_pred             CCCCc-hHHhhccchhhhhHhhHHHHH
Q psy17810          1 MLPLP-AAITSQLDKASIIRLTISYLK   26 (62)
Q Consensus         1 lLPlp-~~v~s~LDKaSImRLtisyLr   26 (62)
                      +||.. ......+||++|+..++.|++
T Consensus        26 llp~~~~~~~~k~~K~~iL~~ai~yI~   52 (55)
T PF00010_consen   26 LLPSCSAGSSRKLSKASILQKAIDYIK   52 (55)
T ss_dssp             CCSSHHCCTTSSSSHHHHHHHHHHHHH
T ss_pred             hccchhccccccCCHHHHHHHHHHHHH
Confidence            35663 135678999999999999986

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....

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

Probab=95.07  E-value=0.013  Score=31.97  Aligned_cols=26  Identities=35%  Similarity=0.542  Sum_probs=20.6

Q ss_pred             CCCchHHhhccchhhhhHhhHHHHHHH
Q psy17810          2 LPLPAAITSQLDKASIIRLTISYLKLR   28 (62)
Q Consensus         2 LPlp~~v~s~LDKaSImRLtisyLr~r   28 (62)
                      +|... ...++||++|+..++.|++--
T Consensus        30 lp~~~-~~~k~~k~~iL~~a~~yI~~L   55 (60)
T cd00083          30 LPTLP-PSKKLSKAEILRKAVDYIKSL   55 (60)
T ss_pred             CCCCC-CCCCCCHHHHHHHHHHHHHHH
Confidence            44444 467999999999999998754

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=94.94  E-value=0.015  Score=31.39  Aligned_cols=20  Identities=45%  Similarity=0.693  Sum_probs=17.5

Q ss_pred             HhhccchhhhhHhhHHHHHH
Q psy17810          8 ITSQLDKASIIRLTISYLKL   27 (62)
Q Consensus         8 v~s~LDKaSImRLtisyLr~   27 (62)
                      ...++||++|+..+++|++-
T Consensus        27 ~~~k~~k~~iL~~ai~yi~~   46 (53)
T smart00353       27 NNKKLSKAEILRLAIEYIKS   46 (53)
T ss_pred             CCCCCCHHHHHHHHHHHHHH
Confidence            46789999999999999853

---

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	62
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	2e-13
4f3l_A	361	Mclock, circadian locomoter output cycles protein	3e-10

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

 Score = 61.2 bits (148), Expect = 2e-13
 Identities = 7/39 (17%), Positives = 22/39 (56%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS 39
          ++P   A++ +LDK +++R+ + ++K    + +     +
Sbjct: 38 LVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEAN 76

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

 Score = 52.3 bits (125), Expect = 3e-10
 Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLKLRD-FSGHGDPPWSRDGPSPS 46
          MLP       ++DK+++++ +I +L+     +   D    R    P+
Sbjct: 37 MLP---GNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPT 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	62
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	98.32
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.05
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	97.98
4h10_B	71	Circadian locomoter output cycles protein kaput; B	96.23
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	91.92
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	91.89
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	91.86
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	90.55
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	90.38
4ati_A	118	MITF, microphthalmia-associated transcription fact	87.83
1a0a_A	63	BHLH, protein (phosphate system positive regulator	83.17

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

Probab=98.32  E-value=4.6e-08  Score=58.76  Aligned_cols=38  Identities=18%  Similarity=0.250  Sum_probs=25.3

Q ss_pred             CCCchHHhhccchhhhhHhhHHHHHHHHhhcCCCCCCC
Q psy17810          2 LPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWS   39 (62)
Q Consensus         2 LPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~~~w~   39 (62)
                      +|......+++|||+|++.||.|||...+|..++.+|.
T Consensus        35 vP~~~~~~~KldKasIL~~tV~ylk~l~~~~~~~~~~~   72 (73)
T 4h10_A           35 VPTCNAMSRKLDKLTVLRMAVQHMKTLRGAWLEHHHHH   72 (73)
T ss_dssp             SHHHHTCSSCCCHHHHHHHHHHHHHHHSCC--------
T ss_pred             ccccccccccccHHHHHHHHHHHHHHHhcCcccCCccC
Confidence            44444456899999999999999999999999887663

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

Probab=98.05  E-value=1.6e-06  Score=60.77  Aligned_cols=31  Identities=23%  Similarity=0.491  Sum_probs=26.7

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCC
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHG   34 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~   34 (62)
                      |||   +..++|||+||||+||+|||+++.+...
T Consensus        37 ~~p---~~~~~~dk~~il~~~~~~~~~~~~~~~~   67 (361)
T 4f3l_A           37 MLP---GNARKMDKSTVLQKSIDFLRKHKETTAQ   67 (361)
T ss_dssp             TCC---SSSCCCCHHHHHHHHHHHHHHHHHHHTS
T ss_pred             hCC---CCCCCcCHHHHHHHHHHHHHHHHhhccc
Confidence            466   4578999999999999999999998754

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

Probab=97.98  E-value=1e-06  Score=62.80  Aligned_cols=29  Identities=24%  Similarity=0.514  Sum_probs=26.4

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHHHHH
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLKLRD   29 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr~r~   29 (62)
                      |||.+.++.++|||+||||+||+|||..+
T Consensus        38 l~p~~~~~~~k~dk~~il~~~~~~l~~~~   66 (387)
T 4f3l_B           38 LVPTCNAMSRKLDKLTVLRMAVQHMKTLR   66 (387)
T ss_dssp             HCHHHHHCSSCCCHHHHHHHHHHHHHHHH
T ss_pred             hcCCCCccccccCHHHHHHHHHHHHHHhh
Confidence            57888889999999999999999999766

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

Probab=96.23  E-value=0.0014  Score=39.21  Aligned_cols=22  Identities=18%  Similarity=0.507  Sum_probs=18.6

Q ss_pred             hhccchhhhhHhhHHHHHHHHh
Q psy17810          9 TSQLDKASIIRLTISYLKLRDF   30 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr~r~~   30 (62)
                      ...+||++|++.||.|+|.-+-
T Consensus        38 ~~K~dK~sIL~~aI~yik~Lq~   59 (71)
T 4h10_B           38 ARKMDKSTVLQKSIDFLRKHKE   59 (71)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHHH
Confidence            4689999999999999986543

>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=91.92  E-value=0.075  Score=31.08  Aligned_cols=19  Identities=16%  Similarity=0.385  Sum_probs=16.9

Q ss_pred             hhccchhhhhHhhHHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLKL   27 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr~   27 (62)
                      ...+||++|++.++.|++.
T Consensus        33 ~~k~sK~~iL~~Ai~YI~~   51 (83)
T 1nkp_B           33 GEKASRAQILDKATEYIQY   51 (83)
T ss_dssp             TSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            4689999999999999864

>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=91.89  E-value=0.046  Score=30.67  Aligned_cols=18  Identities=22%  Similarity=0.322  Sum_probs=15.9

Q ss_pred             hccchhhhhHhhHHHHHH
Q psy17810         10 SQLDKASIIRLTISYLKL   27 (62)
Q Consensus        10 s~LDKaSImRLtisyLr~   27 (62)
                      ..+||++|+..|+.|++-
T Consensus        41 ~k~~Ka~IL~~ai~YI~~   58 (65)
T 1an4_A           41 SGQSKGGILSKASDYIQE   58 (65)
T ss_dssp             TCCCTTTTTTTTHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            378999999999999864

>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=91.86  E-value=0.077  Score=30.98  Aligned_cols=18  Identities=17%  Similarity=0.427  Sum_probs=16.3

Q ss_pred             hccchhhhhHhhHHHHHH
Q psy17810         10 SQLDKASIIRLTISYLKL   27 (62)
Q Consensus        10 s~LDKaSImRLtisyLr~   27 (62)
                      ..++|++|++.++.|++.
T Consensus        44 ~k~sK~~iL~~Ai~YI~~   61 (80)
T 1hlo_A           44 EKASRAQILDKATEYIQY   61 (80)
T ss_dssp             SCCCHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHHHH
Confidence            589999999999999864

>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=90.55  E-value=0.11  Score=30.67  Aligned_cols=19  Identities=26%  Similarity=0.754  Sum_probs=16.7

Q ss_pred             hhccchhhhhHhhHHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLKL   27 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr~   27 (62)
                      ...+||++|+.-||.|++-
T Consensus        36 ~~k~~Ka~IL~~Ai~YI~~   54 (82)
T 1am9_A           36 EAKLNKSAVLRKAIDYIRF   54 (82)
T ss_dssp             SCCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3689999999999999863

>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=90.38  E-value=0.18  Score=29.41  Aligned_cols=25  Identities=24%  Similarity=0.325  Sum_probs=19.8

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHHH
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLKL   27 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr~   27 (62)
                      ++|.++  -.+|.|..|+|+++.|++.
T Consensus        37 ~iP~~~--~~KlSKi~tLr~Ai~YI~~   61 (68)
T 1mdy_A           37 STSSNP--NQRLPKVEILRNAIRYIEG   61 (68)
T ss_dssp             TSCSCT--TSCCCHHHHHHHHHHHHHH
T ss_pred             hcCCCC--CCCCCHHHHHHHHHHHHHH
Confidence            356544  3699999999999999864

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

Probab=87.83  E-value=0.21  Score=31.48  Aligned_cols=20  Identities=15%  Similarity=0.481  Sum_probs=16.3

Q ss_pred             HhhccchhhhhHhhHHHHHH
Q psy17810          8 ITSQLDKASIIRLTISYLKL   27 (62)
Q Consensus         8 v~s~LDKaSImRLtisyLr~   27 (62)
                      ...++||++|+.-+|.|++-
T Consensus        59 ~~~k~~Ka~IL~~aieYIk~   78 (118)
T 4ati_A           59 PDMRWNKGTILKASVDYIRK   78 (118)
T ss_dssp             --CCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHH
Confidence            34589999999999999874

>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=83.17  E-value=0.53  Score=26.74  Aligned_cols=17  Identities=18%  Similarity=0.403  Sum_probs=15.5

Q ss_pred             hccchhhhhHhhHHHHH
Q psy17810         10 SQLDKASIIRLTISYLK   26 (62)
Q Consensus        10 s~LDKaSImRLtisyLr   26 (62)
                      +.+.||+|+..++.|++
T Consensus        39 ~k~sKa~iL~~Ai~YIk   55 (63)
T 1a0a_A           39 AAPSKATTVEAACRYIR   55 (63)
T ss_dssp             CCSCTTHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHH
Confidence            57889999999999986

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	62
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	93.78
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	91.98
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	90.35
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	89.13
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	88.55
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	82.79
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	82.65

>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=93.78  E-value=0.0094  Score=32.99  Aligned_cols=24  Identities=25%  Similarity=0.400  Sum_probs=18.7

Q ss_pred             CCCCchHHhhccchhhhhHhhHHHHH
Q psy17810          1 MLPLPAAITSQLDKASIIRLTISYLK   26 (62)
Q Consensus         1 lLPlp~~v~s~LDKaSImRLtisyLr   26 (62)
                      +||-.+  ...+||++|++.+|.|++
T Consensus        37 llP~~~--~~k~sK~~iL~~Ai~YI~   60 (68)
T d1mdya_          37 STSSNP--NQRLPKVEILRNAIRYIE   60 (68)
T ss_dssp             TSCSCT--TSCCCHHHHHHHHHHHHH
T ss_pred             HCCCCC--CCCCCHHHHHHHHHHHHH
Confidence            355433  358999999999999995

>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=91.98  E-value=0.034  Score=31.05  Aligned_cols=18  Identities=17%  Similarity=0.407  Sum_probs=16.3

Q ss_pred             hhccchhhhhHhhHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLK   26 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr   26 (62)
                      ...+||++|++.++.|++
T Consensus        33 ~~k~sK~~iL~~A~~yI~   50 (83)
T d1nkpb_          33 GEKASRAQILDKATEYIQ   50 (83)
T ss_dssp             TSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            358999999999999997

>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=90.35  E-value=0.056  Score=29.06  Aligned_cols=19  Identities=16%  Similarity=0.354  Sum_probs=16.5

Q ss_pred             hhccchhhhhHhhHHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLKL   27 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr~   27 (62)
                      ...+||++|++.++.|++-
T Consensus        38 ~~k~sKa~iL~~Av~yI~~   56 (63)
T d1a0aa_          38 SAAPSKATTVEAACRYIRH   56 (63)
T ss_dssp             CCCSCTTHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHH
Confidence            3679999999999999863

>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=89.13  E-value=0.059  Score=29.77  Aligned_cols=18  Identities=17%  Similarity=0.148  Sum_probs=16.0

Q ss_pred             hhccchhhhhHhhHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLK   26 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr   26 (62)
                      ...++|++|++-++.|++
T Consensus        33 ~~k~sK~~iL~~A~~yI~   50 (79)
T d1nlwa_          33 SSRHTTLSLLTKAKLHIK   50 (79)
T ss_dssp             SCCCTTHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            357999999999999987

>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=88.55  E-value=0.091  Score=29.48  Aligned_cols=18  Identities=17%  Similarity=0.364  Sum_probs=16.1

Q ss_pred             hhccchhhhhHhhHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLK   26 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr   26 (62)
                      ....+|++|++.++.|++
T Consensus        38 ~~k~sK~~iL~~A~~yI~   55 (88)
T d1nkpa_          38 NEKAPKVVILKKATAYIL   55 (88)
T ss_dssp             CTTCCHHHHHHHHHHHHH
T ss_pred             CCccCHHHHHHHHHHHHH
Confidence            357999999999999987

>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=82.79  E-value=0.18  Score=27.03  Aligned_cols=18  Identities=22%  Similarity=0.375  Sum_probs=16.1

Q ss_pred             hhccchhhhhHhhHHHHH
Q psy17810          9 TSQLDKASIIRLTISYLK   26 (62)
Q Consensus         9 ~s~LDKaSImRLtisyLr   26 (62)
                      ..++||++|++-++.|++
T Consensus        40 ~~k~sK~~iL~~av~yI~   57 (65)
T d1an4a_          40 KSGQSKGGILSKASDYIQ   57 (65)
T ss_dssp             TTCCCTTTTTTTTHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            358999999999999985

>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=82.65  E-value=0.29  Score=27.03  Aligned_cols=18  Identities=28%  Similarity=0.798  Sum_probs=16.1

Q ss_pred             hccchhhhhHhhHHHHHH
Q psy17810         10 SQLDKASIIRLTISYLKL   27 (62)
Q Consensus        10 s~LDKaSImRLtisyLr~   27 (62)
                      ..+||++|+.-++.|++-
T Consensus        37 ~k~~K~~iL~~a~~yI~~   54 (80)
T d1am9a_          37 AKLNKSAVLRKAIDYIRF   54 (80)
T ss_dssp             CCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            589999999999999873