Psyllid ID: psy3607

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----
Protein Sequence
MSTHQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSAYA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccEEcccccHHHHHHcc
Coil and Loop (DISEMBL)
msthqleqsfnrnsddtmddtddkddskrksrnlsekKRRDQFNMLINELCTMVstnnrkmdksTVLKSTIAFLKNyngtyyfgcSLNFFLSAYA
Flexible Loop (DISEMBL)
msthqleqsfnrnsddtmddtddkddskrksrnlsekkrrdqfnMLINELCTmvstnnrkmdkSTVLKSTIAFLKNYNGTYYFGCSLNFFLSAYA
Low Complexity Region (SEG)
MSTHQLEQSFnrnsddtmddtddkddskrksrnLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSAYA
Disordered region (IsUnstruct)
******************************************FNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSA**
Disordered Region (DISOPRED)
****************************************DQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN******C***FFLSAYA
Disordered Region (DISEMBL)
*********************************LSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSAYA
Disordered Region (DISPRO)
***********************************EKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSAYA
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTHQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSAYA
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	95	2.2.26 [Sep-21-2011]
O61735	1027	Circadian locomoter outpu	yes	N/A	0.526	0.048	0.8	6e-17
Q8QGQ6	875	Circadian locomoter outpu	yes	N/A	0.810	0.088	0.537	1e-15
Q6YGZ4	851	Circadian locomoter outpu	N/A	N/A	0.810	0.090	0.537	2e-15
Q99743	824	Neuronal PAS domain-conta	yes	N/A	0.621	0.071	0.627	2e-15
P97460	816	Neuronal PAS domain-conta	yes	N/A	0.621	0.072	0.627	3e-15
Q5ZQU2	815	Neuronal PAS domain-conta	no	N/A	0.621	0.072	0.627	5e-15
O08785	855	Circadian locomoter outpu	no	N/A	0.684	0.076	0.6	1e-14
Q9WVS9	862	Circadian locomoter outpu	no	N/A	0.652	0.071	0.612	2e-14
Q91YB2	865	Circadian locomoter outpu	N/A	N/A	0.652	0.071	0.612	3e-14
Q91YB0	865	Circadian locomoter outpu	N/A	N/A	0.652	0.071	0.612	3e-14

>sp|O61735|CLOCK_DROME Circadian locomoter output cycles protein kaput OS=Drosophila melanogaster GN=Clk PE=2 SV=3

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 40/50 (80%), Positives = 47/50 (94%)

Query: 29 RKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          RKSRNLSEKKRRDQFN L+N+L  ++ST++RKMDKSTVLKSTIAFLKN+N
Sbjct: 17 RKSRNLSEKKRRDQFNSLVNDLSALISTSSRKMDKSTVLKSTIAFLKNHN 66

Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours. Oscillates in antiphase to the cycling observed for period (PER) and timeless (TIM). According to PubMed:9742131, reaches peak abundance within several hours of the dark-light transition at ZT0 (zeitgeber 0), whereas PubMed:9616122 describes bimodal oscillating expression with maximum at ZT5 and ZT23. Clock-cycle heterodimers activate cycling transcription of PER and TIM by binding to the E-box (3'-CACGTG-5') present in their promoters. Once induced, Period and Timeless block Clock's ability to transactivate their promoters.
Drosophila melanogaster (taxid: 7227)

>sp|Q8QGQ6|CLOCK_CHICK Circadian locomoter output cycles protein kaput OS=Gallus gallus GN=CLOCK PE=1 SV=2

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/80 (53%), Positives = 56/80 (70%), Gaps = 3/80 (3%)

Query: 1  MSTHQLEQSFNRNSDDTMD---DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN 57
          +STH++    +RN     D   + DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N
Sbjct: 5  ISTHKMSSIADRNDGSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGN 64

Query: 58 NRKMDKSTVLKSTIAFLKNY 77
           RKMDKSTVL+ +I FL+ +
Sbjct: 65 ARKMDKSTVLQKSIDFLRKH 84

BMAL1/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. May play a role in DNA damage response (DDR) signaling during the S phase.

Gallus gallus (taxid: 9031)

>sp|Q6YGZ4|CLOCK_TYTAL Circadian locomoter output cycles protein kaput OS=Tyto alba GN=CLOCK PE=2 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/80 (53%), Positives = 56/80 (70%), Gaps = 3/80 (3%)

Query: 1  MSTHQLEQSFNRNSDDTMD---DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN 57
          +STH++    +RN     D   + DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N
Sbjct: 5  ISTHKMSSIADRNDGSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGN 64

Query: 58 NRKMDKSTVLKSTIAFLKNY 77
           RKMDKSTVL+ +I FL+ +
Sbjct: 65 ARKMDKSTVLQKSIDFLRKH 84

BMAL1/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. May play a role in DNA damage response (DDR) signaling during the S phase.

Tyto alba (taxid: 56313)

>sp|Q99743|NPAS2_HUMAN Neuronal PAS domain-containing protein 2 OS=Homo sapiens GN=NPAS2 PE=2 SV=3

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 37/59 (62%), Positives = 46/59 (77%)

Query: 20 DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          D D+KD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct: 2  DEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 60

BMAL1-NPAS2 heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins.

Homo sapiens (taxid: 9606)

>sp|P97460|NPAS2_MOUSE Neuronal PAS domain-containing protein 2 OS=Mus musculus GN=Npas2 PE=1 SV=1

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 37/59 (62%), Positives = 46/59 (77%)

Query: 20 DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          D D+KD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct: 2  DEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 60

BMAL1-NPAS2 heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins.

Mus musculus (taxid: 10090)

>sp|Q5ZQU2|NPAS2_CHICK Neuronal PAS domain-containing protein 2 OS=Gallus gallus GN=NPAS2 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 37/59 (62%), Positives = 46/59 (77%)

Query: 20 DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          D D+KD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct: 2  DEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 60

BMAL1-NPAS2 heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins.

Gallus gallus (taxid: 9031)

>sp|O08785|CLOCK_MOUSE Circadian locomoter output cycles protein kaput OS=Mus musculus GN=Clock PE=1 SV=1

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/65 (60%), Positives = 49/65 (75%)

Query: 16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
          D + + DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+
Sbjct: 23 DGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 82

Query: 76 NYNGT 80
           +  T
Sbjct: 83 KHKET 87

ARNTL/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression. Acetylates primarily histones H3 and H4. Acetylates also a non-histone substrate: its own partner, ARNTL. Plays a role in DNA damage response (DDR) signaling during the S phase.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q9WVS9|CLOCK_RAT Circadian locomoter output cycles protein kaput OS=Rattus norvegicus GN=Clock PE=2 SV=1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/62 (61%), Positives = 48/62 (77%)

Query: 16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
          D + + DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+
Sbjct: 23 DGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 82

Query: 76 NY 77
           +
Sbjct: 83 KH 84

ARNTL/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression. Acetylates primarily histones H3 and H4. Acetylates also a non-histone substrate: ARNTL. Plays a role in DNA damage response (DDR) signaling during the S phase.

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q91YB2|CLOCK_SPACA Circadian locomoter output cycles protein kaput OS=Spalax carmeli GN=Clock PE=2 SV=1

 Score = 77.4 bits (189), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/62 (61%), Positives = 48/62 (77%)

Query: 16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
          D + + DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+
Sbjct: 23 DGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 82

Query: 76 NY 77
           +
Sbjct: 83 KH 84

ARNTL/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression. Acetylates primarily histones H3 and H4. Acetylates also a non-histone substrate: ARNTL. Plays a role in DNA damage response (DDR) signaling during the S phase.

Spalax carmeli (taxid: 164324)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q91YB0|CLOCK_NANGA Circadian locomoter output cycles protein kaput OS=Nannospalax galili GN=Clock PE=1 SV=1

 Score = 77.4 bits (189), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/62 (61%), Positives = 48/62 (77%)

Query: 16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
          D + + DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+
Sbjct: 23 DGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 82

Query: 76 NY 77
           +
Sbjct: 83 KH 84

ARNTL/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression. Acetylates primarily histones H3 and H4. Acetylates also a non-histone substrate: ARNTL. Plays a role in DNA damage response (DDR) signaling during the S phase.

Nannospalax galili (taxid: 1026970)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

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	95
444245669	673	clock, partial [Solenopsis invicta]	0.663	0.093	0.796	1e-20
305682538	522	CLOCK [Thermobia domestica]	0.547	0.099	0.903	2e-18
443497931	594	CLOCK [Gryllus bimaculatus]	0.547	0.087	0.884	3e-18
405962835	466	Circadian locomoter output cycles protei	0.621	0.126	0.762	1e-17
339283906	411	clock [Spodoptera exigua]	0.547	0.126	0.846	1e-17
357614851	602	clock [Danaus plexippus]	0.547	0.086	0.846	2e-17
242017615	660	Circadian locomoter output cycles protei	0.526	0.075	0.88	2e-17
321468989	869	hypothetical protein DAPPUDRAFT_346996 [	0.684	0.074	0.696	4e-17
158294626	1030	AGAP005711-PA [Anopheles gambiae str. PE	0.547	0.050	0.826	5e-17
61353791	704	clock [Macrobrachium rosenbergii]	0.515	0.069	0.877	7e-17

>gi|444245669|gb|AGD94516.1| clock, partial [Solenopsis invicta]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 51/64 (79%), Positives = 57/64 (89%), Gaps = 1/64 (1%)

Query: 16 DTMDD-TDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFL 74
          D MDD  D+KDD+KRKSRNLSEKKRRDQFNML+NEL +M+S N RKMDKSTVLKSTI FL
Sbjct: 17 DIMDDNIDEKDDTKRKSRNLSEKKRRDQFNMLVNELGSMISANTRKMDKSTVLKSTILFL 76

Query: 75 KNYN 78
          KN+N
Sbjct: 77 KNHN 80

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|305682538|dbj|BAJ16353.1| CLOCK [Thermobia domestica]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/52 (90%), Positives = 50/52 (96%)

Query: 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          +KRKSRNLSEKKRRDQFNMLINEL +MVST NRKMDKSTVLKSTIAFLKN+N
Sbjct: 16 TKRKSRNLSEKKRRDQFNMLINELSSMVSTTNRKMDKSTVLKSTIAFLKNHN 67

Source: Thermobia domestica

Species: Thermobia domestica

Genus: Thermobia

Family: Lepismatidae

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443497931|dbj|BAM76759.1| CLOCK [Gryllus bimaculatus]

 Score = 95.9 bits (237), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 51/52 (98%)

Query: 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          +KRKSRNLSEKKRRDQFNMLINEL +MVSTN+RKMDKSTVLKSTI+FLKN+N
Sbjct: 27 TKRKSRNLSEKKRRDQFNMLINELSSMVSTNSRKMDKSTVLKSTISFLKNHN 78

Source: Gryllus bimaculatus

Species: Gryllus bimaculatus

Genus: Gryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405962835|gb|EKC28478.1| Circadian locomoter output cycles protein kaput [Crassostrea gigas]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 52/59 (88%)

Query: 22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGT 80
          DD   SKR +RNLSEKKRRDQFNML+NELC+MVST+++KMDKSTVLKSTIA+LK Y  T
Sbjct: 27 DDGKSSKRVNRNLSEKKRRDQFNMLVNELCSMVSTSSKKMDKSTVLKSTIAYLKTYQET 85

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|339283906|gb|AEJ38222.1| clock [Spodoptera exigua]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/52 (84%), Positives = 50/52 (96%)

Query: 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          +KR++RNLSEKKRRDQFNML+NEL  MVSTNNRKMDKSTVLKSTI+FLKN+N
Sbjct: 11 TKRRTRNLSEKKRRDQFNMLVNELSAMVSTNNRKMDKSTVLKSTISFLKNHN 62

Source: Spodoptera exigua

Species: Spodoptera exigua

Genus: Spodoptera

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357614851|gb|EHJ69324.1| clock [Danaus plexippus]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 44/52 (84%), Positives = 51/52 (98%)

Query: 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          +KR++RNLSEKKRRDQFNML+NEL +MVSTNNRKMDKSTVLKSTI+FLKN+N
Sbjct: 11 TKRRTRNLSEKKRRDQFNMLVNELGSMVSTNNRKMDKSTVLKSTISFLKNHN 62

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242017615|ref|XP_002429283.1| Circadian locomoter output cycles protein kaput, putative [Pediculus humanus corporis] gi|212514179|gb|EEB16545.1| Circadian locomoter output cycles protein kaput, putative [Pediculus humanus corporis]

 Score = 92.8 bits (229), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/50 (88%), Positives = 49/50 (98%)

Query: 29 RKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          R+SRNLSEKKRRDQFNMLINEL +MVSTNNRKMDKSTVLKSTIAFL+++N
Sbjct: 13 RRSRNLSEKKRRDQFNMLINELSSMVSTNNRKMDKSTVLKSTIAFLESHN 62

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321468989|gb|EFX79971.1| hypothetical protein DAPPUDRAFT_346996 [Daphnia pulex]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 46/66 (69%), Positives = 56/66 (84%), Gaps = 1/66 (1%)

Query: 14 SDDTMDD-TDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIA 72
          SDD ++D  D+K   KRKSRNLSEKKRRDQFN+LINELC+MV T  RKMDKST+LKS I+
Sbjct: 28 SDDGLEDEVDEKGVIKRKSRNLSEKKRRDQFNILINELCSMVCTGKRKMDKSTILKSAIS 87

Query: 73 FLKNYN 78
          F++N+N
Sbjct: 88 FIRNHN 93

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158294626|ref|XP_315720.4| AGAP005711-PA [Anopheles gambiae str. PEST] gi|157015652|gb|EAA11642.4| AGAP005711-PA [Anopheles gambiae str. PEST]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 43/52 (82%), Positives = 51/52 (98%)

Query: 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
          +KRKSRNLSEKKRRDQFN+L+NEL +MVS+N+RKMDKSTVLKSTIAFLK++N
Sbjct: 11 TKRKSRNLSEKKRRDQFNLLVNELSSMVSSNSRKMDKSTVLKSTIAFLKSHN 62

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|61353791|gb|AAX44045.1| clock [Macrobrachium rosenbergii]

 Score = 91.3 bits (225), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 43/49 (87%), Positives = 48/49 (97%)

Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKN 76
          KRKSRNLSEKKRRDQFN+LINEL +MV++NNRKMDKSTVLK+TIAFLKN
Sbjct: 12 KRKSRNLSEKKRRDQFNLLINELSSMVASNNRKMDKSTVLKATIAFLKN 60

Source: Macrobrachium rosenbergii

Species: Macrobrachium rosenbergii

Genus: Macrobrachium

Family: Palaemonidae

Order: Decapoda

Class: Malacostraca

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	95
FB|FBgn0023076	1027	Clk "Clock" [Drosophila melano	0.473	0.043	0.777	7e-13
UNIPROTKB|H7C0J4	107	NPAS2 "Neuronal PAS domain-con	0.473	0.420	0.644	1.2e-10
UNIPROTKB|H7C0Z2	208	NPAS2 "Neuronal PAS domain-con	0.463	0.211	0.636	5.2e-10
UNIPROTKB|H7BZA3	258	NPAS2 "Neuronal PAS domain-con	0.463	0.170	0.636	9.9e-10
UNIPROTKB|C9JK03	182	CLOCK "Circadian locomoter out	0.452	0.236	0.651	2.9e-09
UNIPROTKB|J9P4Q7	668	NPAS2 "Uncharacterized protein	0.463	0.065	0.636	7.4e-09
UNIPROTKB|F6QL92	794	NPAS2 "Uncharacterized protein	0.463	0.055	0.636	9.3e-09
UNIPROTKB|F1STF9	796	NPAS2 "Uncharacterized protein	0.463	0.055	0.636	9.4e-09
UNIPROTKB|F1P5G3	815	NPAS2 "Neuronal PAS domain-con	0.463	0.053	0.636	9.7e-09
UNIPROTKB|Q5ZQU2	815	NPAS2 "Neuronal PAS domain-con	0.463	0.053	0.636	9.7e-09

FB|FBgn0023076 Clk "Clock" [Drosophila melanogaster (taxid:7227)]

 Score = 183 (69.5 bits), Expect = 7.0e-13, P = 7.0e-13
 Identities = 35/45 (77%), Positives = 42/45 (93%)

Query:    34 LSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             LSEKKRRDQFN L+N+L  ++ST++RKMDKSTVLKSTIAFLKN+N
Sbjct:    22 LSEKKRRDQFNSLVNDLSALISTSSRKMDKSTVLKSTIAFLKNHN 66

GO:0003677 "DNA binding" evidence=IDA;NAS

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

GO:0007623 "circadian rhythm" evidence=NAS;IMP;TAS

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

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

GO:0008134 "transcription factor binding" evidence=IPI

GO:0005634 "nucleus" evidence=NAS

GO:0048148 "behavioral response to cocaine" evidence=NAS;TAS

GO:0045475 "locomotor rhythm" evidence=IMP;NAS;TAS

GO:0008062 "eclosion rhythm" evidence=NAS;TAS

GO:0045187 "regulation of circadian sleep/wake cycle, sleep" evidence=IMP

GO:0007622 "rhythmic behavior" evidence=TAS

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

GO:0007165 "signal transduction" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=NAS

GO:0032922 "circadian regulation of gene expression" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|H7C0J4 NPAS2 "Neuronal PAS domain-containing protein 2" [Homo sapiens (taxid:9606)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 29/45 (64%), Positives = 36/45 (80%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNG 79
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +NG
Sbjct:     1 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNG 45

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|H7C0Z2 NPAS2 "Neuronal PAS domain-containing protein 2" [Homo sapiens (taxid:9606)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:    83 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 126

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|H7BZA3 NPAS2 "Neuronal PAS domain-containing protein 2" [Homo sapiens (taxid:9606)]

 Score = 143 (55.4 bits), Expect = 9.9e-10, P = 9.9e-10
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:     7 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 50

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|C9JK03 CLOCK "Circadian locomoter output cycles protein kaput" [Homo sapiens (taxid:9606)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 28/43 (65%), Positives = 35/43 (81%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNY 77
             SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +
Sbjct:    42 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKH 84

GO:0004871 "signal transducer activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000982 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0001190 "RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0032922 "circadian regulation of gene expression" evidence=IEA

UNIPROTKB|J9P4Q7 NPAS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 143 (55.4 bits), Expect = 7.4e-09, P = 7.4e-09
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:     7 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 50

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

GO:0003677 "DNA binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

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

UNIPROTKB|F6QL92 NPAS2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 143 (55.4 bits), Expect = 9.3e-09, P = 9.3e-09
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:     7 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 50

GO:0051879 "Hsp90 protein binding" evidence=IEA

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

GO:0045475 "locomotor rhythm" evidence=IEA

GO:0042745 "circadian sleep/wake cycle" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

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

UNIPROTKB|F1STF9 NPAS2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 143 (55.4 bits), Expect = 9.4e-09, P = 9.4e-09
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:    17 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 60

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

GO:0003677 "DNA binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

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

UNIPROTKB|F1P5G3 NPAS2 "Neuronal PAS domain-containing protein 2" [Gallus gallus (taxid:9031)]

 Score = 143 (55.4 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:    17 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 60

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|Q5ZQU2 NPAS2 "Neuronal PAS domain-containing protein 2" [Gallus gallus (taxid:9031)]

 Score = 143 (55.4 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 28/44 (63%), Positives = 35/44 (79%)

Query:    35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYN 78
             SEKKRRDQFN+LI EL +M+  N RKMDK+TVL+  I FL+ +N
Sbjct:    17 SEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHN 60

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0048511 "rhythmic process" 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)
Q8QGQ6	CLOCK_CHICK	No assigned EC number	0.5375	0.8105	0.088	yes	N/A
Q99743	NPAS2_HUMAN	No assigned EC number	0.6271	0.6210	0.0716	yes	N/A
P97460	NPAS2_MOUSE	No assigned EC number	0.6271	0.6210	0.0723	yes	N/A
O61735	CLOCK_DROME	No assigned EC number	0.8	0.5263	0.0486	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	95
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	1e-08
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	3e-07
smart00353	53	smart00353, HLH, helix loop helix domain	1e-06

>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 = 46.8 bits (112), Expect = 1e-08
 Identities = 15/54 (27%), Positives = 36/54 (66%), Gaps = 2/54 (3%)

Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKN 76
            S+R++ NL E++RR++ N   +EL +++ T   ++K+ K+ +L+  + ++K+
Sbjct: 1  RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKS 54

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

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

 Score = 42.8 bits (102), Expect = 3e-07
 Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
          +RK+ N  E++RRD+ N    EL  ++ +  N+K+ K+ +L+  I ++K
Sbjct: 1  RRKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIK 49

Length = 52

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

 Score = 41.1 bits (97), Expect = 1e-06
 Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 2/45 (4%)

Query: 33 NLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLK 75
          N  E++RR + N   +EL +++ T   N+K+ K+ +L+  I ++K
Sbjct: 1  NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIK 45

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	95
KOG1318|consensus	411		99.73
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.7
KOG3561|consensus	803		99.66
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.65
KOG4304|consensus	250		99.55
smart00353	53	HLH helix loop helix domain.	99.53
KOG1319|consensus	229		99.39
KOG2588|consensus	953		98.73
KOG0561|consensus	373		98.49
KOG2483|consensus	232		98.45
KOG4029|consensus	228		98.16
KOG3960|consensus	284		98.05
KOG3560|consensus	712		97.53
KOG3910|consensus	632		97.37
KOG3558|consensus	768		97.29
PLN03217	93	transcription factor ATBS1; Provisional	97.27
KOG4447|consensus	173		95.65
KOG3559|consensus	598		95.5
KOG3898|consensus	254		95.4
KOG4395|consensus	285		94.46

>KOG1318|consensus

Probab=99.73  E-value=3.5e-18  Score=139.47  Aligned_cols=71  Identities=25%  Similarity=0.380  Sum_probs=63.3

Q ss_pred             CCcCCCCCchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607          15 DDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNGTYYFGC   85 (95)
Q Consensus        15 ~d~~~~~~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~L~~~~~~~~   85 (95)
                      .+.+-....++++||++||++|||||++||+||.+|+.|||.|   ..+++|++||+.+++||+.|++...+..
T Consensus       220 ~~~~~~~~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~  293 (411)
T KOG1318|consen  220 PKTDATALERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR  293 (411)
T ss_pred             CCcccchhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence            3555557789999999999999999999999999999999997   5799999999999999999998776544

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

Probab=99.70  E-value=3.6e-17  Score=98.47  Aligned_cols=51  Identities=29%  Similarity=0.601  Sum_probs=48.2

Q ss_pred             hhhhcchHHHhHHHHHHHHHHHHHhhcCCC----CCCCCHHHHHHHHHHHHHHhh
Q psy3607          28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN----NRKMDKSTVLKSTIAFLKNYN   78 (95)
Q Consensus        28 ~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~----~~K~dK~sIL~~aI~ylk~L~   78 (95)
                      +|..|+..||+||+.||.+|.+|+.+||.+    ..|++|++||+.||+||+.||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            578999999999999999999999999986    589999999999999999986

; 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 ....

>KOG3561|consensus

Probab=99.66  E-value=1.5e-16  Score=138.14  Aligned_cols=70  Identities=40%  Similarity=0.491  Sum_probs=62.5

Q ss_pred             CcCCCCCchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCC---CCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607          16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGTYYFGC   85 (95)
Q Consensus        16 d~~~~~~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~---~K~dK~sIL~~aI~ylk~L~~~~~~~~   85 (95)
                      +++.+.+.+++.+|++||.+||||||++|.+|.||++|||.|.   +|+||++||++||++||.+++.+...+
T Consensus         8 ~d~~~~d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~~~~~~   80 (803)
T KOG3561|consen    8 SDDAESDSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQESENS   80 (803)
T ss_pred             CCcccccchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhhhcccc
Confidence            4555677888888999999999999999999999999999986   999999999999999999998754444

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

Probab=99.65  E-value=4.2e-16  Score=93.67  Aligned_cols=56  Identities=27%  Similarity=0.576  Sum_probs=51.7

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGTY   81 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~--~~K~dK~sIL~~aI~ylk~L~~~~   81 (95)
                      ..+|.+|+..||+||++||.+|.+|+.+||..  ..|++|++||..||+||+.|+...
T Consensus         2 ~~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             cHHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999997  589999999999999999998653

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

>KOG4304|consensus

Probab=99.55  E-value=4.2e-15  Score=114.68  Aligned_cols=64  Identities=22%  Similarity=0.389  Sum_probs=54.9

Q ss_pred             CCCchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-------CCCCCHHHHHHHHHHHHHHhhhhhhc
Q psy3607          20 DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-------NRKMDKSTVLKSTIAFLKNYNGTYYF   83 (95)
Q Consensus        20 ~~~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-------~~K~dK~sIL~~aI~ylk~L~~~~~~   83 (95)
                      +......-+|.+|.++|||||++||.+|++|+.|||+.       ..|++|+.||++||+||++|+.....
T Consensus        24 ~~~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   24 RSSKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             cchhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            44445567788999999999999999999999999973       37999999999999999999965443

>smart00353 HLH helix loop helix domain

Probab=99.53  E-value=3.1e-14  Score=84.29  Aligned_cols=49  Identities=29%  Similarity=0.542  Sum_probs=45.1

Q ss_pred             chHHHhHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607          33 NLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGTY   81 (95)
Q Consensus        33 n~~EKrRRd~iN~~i~eL~~LIP~~--~~K~dK~sIL~~aI~ylk~L~~~~   81 (95)
                      |..||+||++||.+|.+|+.+||.+  ..+++|++||..||+||+.|++..
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~   51 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEEL   51 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999973  689999999999999999998764

>KOG1319|consensus

Probab=99.39  E-value=5.4e-13  Score=101.14  Aligned_cols=72  Identities=29%  Similarity=0.443  Sum_probs=61.9

Q ss_pred             cccCCCCCcCCCCCc------hhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC------CCCCCHHHHHHHHHHHHHH
Q psy3607           9 SFNRNSDDTMDDTDD------KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN------NRKMDKSTVLKSTIAFLKN   76 (95)
Q Consensus         9 ~~~~~~~d~~~~~~~------k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~------~~K~dK~sIL~~aI~ylk~   76 (95)
                      +|.+|.+|++++...      .++.+|+.|...|++|||-||..++.|+.|||.|      +.|+.|+-||.+||+||.+
T Consensus        37 sSApNtdd~ds~~hS~a~k~syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~  116 (229)
T KOG1319|consen   37 SSAPNTDDEDSDYHSEAYKESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQF  116 (229)
T ss_pred             CCCCCCCcccccchhHHHHhhHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHH
Confidence            567888888887443      3456789999999999999999999999999986      3499999999999999999


Q ss_pred             hhhh
Q psy3607          77 YNGT   80 (95)
Q Consensus        77 L~~~   80 (95)
                      |+..
T Consensus       117 L~~~  120 (229)
T KOG1319|consen  117 LHKE  120 (229)
T ss_pred             HHHH
Confidence            9854

>KOG2588|consensus

Probab=98.73  E-value=5.6e-09  Score=92.41  Aligned_cols=60  Identities=30%  Similarity=0.400  Sum_probs=55.0

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGC   85 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~~K~dK~sIL~~aI~ylk~L~~~~~~~~   85 (95)
                      ..+|..||.||||-|..||++|.||+.+||+...|+.|..+|+.||+||+.+++....+.
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk  333 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLK  333 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccc
Confidence            367899999999999999999999999999988999999999999999999997665554

>KOG0561|consensus

Probab=98.49  E-value=2.1e-07  Score=75.01  Aligned_cols=67  Identities=19%  Similarity=0.311  Sum_probs=57.9

Q ss_pred             CchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhhcccchh
Q psy3607          22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGTYYFGCSLN   88 (95)
Q Consensus        22 ~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~~~~~~~~~~   88 (95)
                      ++..+-+|+--|-.||||-.-||..|.-|+.|||-. ..|+.|+.||+.|.+||.+|.+...++...|
T Consensus        54 D~erRmRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn  121 (373)
T KOG0561|consen   54 DPERRMRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQN  121 (373)
T ss_pred             CHHHHHHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccccccc
Confidence            345567778888899999999999999999999963 5899999999999999999998877765443

>KOG2483|consensus

Probab=98.45  E-value=3.4e-07  Score=70.53  Aligned_cols=56  Identities=20%  Similarity=0.261  Sum_probs=47.6

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCCCCCC--HHHHHHHHHHHHHHhhhhh
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMD--KSTVLKSTIAFLKNYNGTY   81 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~~K~d--K~sIL~~aI~ylk~L~~~~   81 (95)
                      ...|..||..||+||+.|-.+|..|+.+||.......  -++||++|+.||+.|+...
T Consensus        57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~  114 (232)
T KOG2483|consen   57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS  114 (232)
T ss_pred             CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence            4577899999999999999999999999997432222  5899999999999998543

>KOG4029|consensus

Probab=98.16  E-value=1.7e-06  Score=65.07  Aligned_cols=56  Identities=21%  Similarity=0.411  Sum_probs=49.5

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC--C-CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--N-NRKMDKSTVLKSTIAFLKNYNGTY   81 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~--~-~~K~dK~sIL~~aI~ylk~L~~~~   81 (95)
                      ...+..+|..||.|=..+|.+|.+|+.+||.  . ..|+.|+.+|+.||.||+.|.+.-
T Consensus       107 ~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL  165 (228)
T KOG4029|consen  107 SAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLL  165 (228)
T ss_pred             hhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHh
Confidence            4555677888999999999999999999997  3 689999999999999999998653

>KOG3960|consensus

Probab=98.05  E-value=1.2e-05  Score=63.34  Aligned_cols=53  Identities=23%  Similarity=0.434  Sum_probs=44.6

Q ss_pred             hhhhcchHHHhHHHHHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHhhhh
Q psy3607          28 KRKSRNLSEKKRRDQFNMLINELCTMVS-TNNRKMDKSTVLKSTIAFLKNYNGT   80 (95)
Q Consensus        28 ~r~~hn~~EKrRRd~iN~~i~eL~~LIP-~~~~K~dK~sIL~~aI~ylk~L~~~   80 (95)
                      ||+.-.+-||||=-++|+.|..|+.=-- ..++++-|+.||+.||+||..||..
T Consensus       118 RRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~L  171 (284)
T KOG3960|consen  118 RRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQAL  171 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHH
Confidence            3445567799999999999999986544 4578999999999999999999864

>KOG3560|consensus

Probab=97.53  E-value=7.1e-05  Score=64.47  Aligned_cols=41  Identities=27%  Similarity=0.544  Sum_probs=37.7

Q ss_pred             HHhHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHH
Q psy3607          36 EKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKN   76 (95)
Q Consensus        36 EKrRRd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~   76 (95)
                      -||.||++|.-++-|++|+|-.   ..|+||.+||+.+|.||+-
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~   76 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV   76 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence            6899999999999999999963   5799999999999999984

>KOG3910|consensus

Probab=97.37  E-value=0.00026  Score=60.42  Aligned_cols=59  Identities=17%  Similarity=0.308  Sum_probs=49.6

Q ss_pred             chhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCC---CCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607          23 DKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIAFLKNYNGTY   81 (95)
Q Consensus        23 ~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~---~~~K~dK~sIL~~aI~ylk~L~~~~   81 (95)
                      ++++.||...|..||-|=.-||+.|+||..|.--   ...--.|..||..||.-|-.|++..
T Consensus       521 eREkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQV  582 (632)
T KOG3910|consen  521 EREKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQV  582 (632)
T ss_pred             hHHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHH
Confidence            4566778888999999999999999999999875   2334579999999999999998754

>KOG3558|consensus

Probab=97.29  E-value=0.00032  Score=61.48  Aligned_cols=60  Identities=18%  Similarity=0.309  Sum_probs=49.6

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC---CCCCCCHHHHHHHHHHHHHHhhhhhhcccc
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIAFLKNYNGTYYFGCS   86 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~---~~~K~dK~sIL~~aI~ylk~L~~~~~~~~~   86 (95)
                      +.||+.-..+-|-||-+-|.-|-||+.++|-   ....+||++|++.||.||| |+...+.+|.
T Consensus        44 ~~rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR-lrk~a~~g~~  106 (768)
T KOG3558|consen   44 ELRKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR-LRKFAGAGDP  106 (768)
T ss_pred             HHHhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH-HHHHhhcCCc
Confidence            3456666677899999999999999999994   2578999999999999999 6666666665

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.27  E-value=0.0006  Score=46.27  Aligned_cols=45  Identities=24%  Similarity=0.284  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHhhcCCC-----CCCCCHHHHHHHHHHHHHHhhhhhhcc
Q psy3607          40 RDQFNMLINELCTMVSTN-----NRKMDKSTVLKSTIAFLKNYNGTYYFG   84 (95)
Q Consensus        40 Rd~iN~~i~eL~~LIP~~-----~~K~dK~sIL~~aI~ylk~L~~~~~~~   84 (95)
                      -|.||+.+..|+.|+|..     ..|..-+-||++|+.||+.|+.+...+
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdL   68 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDL   68 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            488999999999999972     457888899999999999999766544

>KOG4447|consensus

Probab=95.65  E-value=0.006  Score=45.37  Aligned_cols=53  Identities=21%  Similarity=0.302  Sum_probs=47.5

Q ss_pred             hhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhh
Q psy3607          27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNG   79 (95)
Q Consensus        27 ~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~   79 (95)
                      ..|.-||.-|++|=..+|+.|..|+.+||.. ..|+.|..-|+.|-.||-.|-+
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~  130 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ  130 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence            4567899999999999999999999999983 5799999999999999987754

>KOG3559|consensus

Probab=95.50  E-value=0.016  Score=49.17  Aligned_cols=44  Identities=25%  Similarity=0.473  Sum_probs=38.4

Q ss_pred             HHHhHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhh
Q psy3607          35 SEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYN   78 (95)
Q Consensus        35 ~EKrRRd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~L~   78 (95)
                      .-|.||++-|.-|-||+.++|-.   ...+||++|++.|-.|||.-+
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~   54 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN   54 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence            46889999999999999999952   356999999999999999654

>KOG3898|consensus

Probab=95.40  E-value=0.011  Score=45.80  Aligned_cols=55  Identities=16%  Similarity=0.289  Sum_probs=47.9

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHhhhh
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLKNYNGT   80 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~--~~~K~dK~sIL~~aI~ylk~L~~~   80 (95)
                      ..+|..-|.-||+|--.+|+.++.|+.+||.  ...|+.|+..|+.|-.||..|.+.
T Consensus        70 ~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   70 TLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            4556667778999999999999999999994  468999999999999999998853

>KOG4395|consensus

Probab=94.46  E-value=0.083  Score=42.07  Aligned_cols=55  Identities=18%  Similarity=0.328  Sum_probs=47.9

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHhhhh
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLKNYNGT   80 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~--~~~K~dK~sIL~~aI~ylk~L~~~   80 (95)
                      ..+|-.-|..||||-.-+|..|+.|+..||.  ...|+.|-.-|++|--||--|-..
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~  228 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCL  228 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHh
Confidence            4556678889999999999999999999997  468999999999999999877543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	95
4f3l_A	361	Crystal Structure Of The Heterodimeric Clock:bmal1		6e-11
4h10_B	71	Intermolecular Recognition Revealed By The Complex		1e-10
4h10_A	73	Intermolecular Recognition Revealed By The Complex		1e-05
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		5e-05

>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 361

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 36/46 (78%)
Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGT 80
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +  T
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET 64

>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex Structure Of Human Clock-bmal1 Basic Helix-loop-helix Domains With E-box Dna Length = 71

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/43 (65%), Positives = 35/43 (81%)
Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNY 77
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKH 57

>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex Structure Of Human Clock-bmal1 Basic Helix-loop-helix Domains With E-box Dna Length = 73

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGTY 81
          EK+RRD+ N  I+EL ++V T N   RK+DK TVL+  +  +K   G +
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGAW 65

>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 387

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 3/48 (6%)
Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGT 80
          EK+RRD+ N  I+EL ++V T N   RK+DK TVL+  +  +K   G 
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	95
4f3l_A	361	Mclock, circadian locomoter output cycles protein	9e-18
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	3e-14
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	2e-08
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	3e-08
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	1e-07
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-07
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	3e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	8e-04

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

 Score = 75.0 bits (184), Expect = 9e-18
 Identities = 37/54 (68%), Positives = 44/54 (81%)

Query: 22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
          DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+
Sbjct: 6  DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59

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

 Score = 65.0 bits (158), Expect = 3e-14
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 18 MDDT--DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIA 72
          M+      +  + R++ +  EK+RRD+ N  I+EL ++V T    +RK+DK TVL+  + 
Sbjct: 1  MEYAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQ 60

Query: 73 FLKNYNGT 80
           +K   G 
Sbjct: 61 HMKTLRGA 68

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 46.2 bits (110), Expect = 2e-08
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 19 DDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
          D   + D  KR   N  E+KRRD      + L   V S    K  ++ +L     +++
Sbjct: 3  DIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 60

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82

 Score = 45.4 bits (108), Expect = 3e-08
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
              KR + N  EK+ R   N  I EL  +V     K++KS VL+  I +++
Sbjct: 2  SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIR 53

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 43.9 bits (104), Expect = 1e-07
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMV-----STNNRKMDKSTVLKSTIAFLK 75
          D+ +R   N  E++RRD+ N  I +L  ++      +      K  +L     +++
Sbjct: 2  DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQ 57

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Length = 88

 Score = 43.9 bits (104), Expect = 1e-07
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLK 75
           + KR++ N+ E++RR++       L   +    NN K  K  +LK   A++ 
Sbjct: 3  MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYIL 55

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Length = 83

 Score = 43.1 bits (102), Expect = 3e-07
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
          KR   N  E+KRRD      + L   V S    K  ++ +L     +++
Sbjct: 2  KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 50

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

 Score = 34.0 bits (78), Expect = 8e-04
 Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 29 RKSRNLSEKKRRDQFNMLINELCTMV--STNNRKMDKSTVLKSTIAFLKN 76
          R + N  EK RR    + + +L  +V    ++ +    ++L      +K 
Sbjct: 2  RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKK 51

---

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	95
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	6e-09
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	8e-09
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-08
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	3e-07
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	4e-07
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	3e-06
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	4e-06
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	0.003

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

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

 Score = 46.5 bits (110), Expect = 6e-09
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
              KR + N  EK+ R   N  I EL  +V     K++KS VL+  I +++
Sbjct: 2  SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIR 53

>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 = 46.0 bits (109), Expect = 8e-09
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
          KR   N  E+KRRD      + L   V S    K  ++ +L     +++
Sbjct: 2  KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 50

>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 = 45.1 bits (107), Expect = 1e-08
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMV-----STNNRKMDKSTVLKSTIAFLK 75
          D+ +R   N  E++RRD+ N  I +L  ++      +      K  +L     +++
Sbjct: 2  DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQ 57

>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 = 41.4 bits (97), Expect = 3e-07
 Identities = 10/54 (18%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV------STNNRKMDKSTVLKSTIAFLK 75
          KR+S   +E+ RR++  + ++EL +++         +    K+T +++   +++
Sbjct: 2  KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIR 55

>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 = 41.8 bits (98), Expect = 4e-07
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 26 DSKRKSRNLSEKKRRDQFNMLINELCTMV--STNNRKMDKSTVLKSTIAFLK 75
          + KR++ N+ E++RR++       L   +    NN K  K  +LK   A++ 
Sbjct: 4  NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYIL 55

>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 = 39.1 bits (91), Expect = 3e-06
 Identities = 11/53 (20%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRK-MDKSTVLKSTIAFLK 75
           +  +RK+  + E++R  + N     L    S+N  + + K  +L++ I +++
Sbjct: 8  TNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIE 60

>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 = 39.1 bits (91), Expect = 4e-06
 Identities = 10/49 (20%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 29 RKSRNLSEKKRRDQFNMLINELCTMV--STNNRKMDKSTVLKSTIAFLK 75
          R + N  EK RR    + + +L  +V    ++ +    ++L      +K
Sbjct: 2  RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIK 50

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

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

 Score = 31.2 bits (71), Expect = 0.003
 Identities = 14/36 (38%), Positives = 19/36 (52%)

Query: 40 RDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
          R   N  I EL  +V   + KM KS VL+  I ++K
Sbjct: 1  RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIK 36

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	95
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.74
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.71
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.69
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.67
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.39

>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=99.75  E-value=5.4e-19  Score=112.29  Aligned_cols=61  Identities=28%  Similarity=0.316  Sum_probs=55.9

Q ss_pred             hhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607          25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGC   85 (95)
Q Consensus        25 ~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~~K~dK~sIL~~aI~ylk~L~~~~~~~~   85 (95)
                      ...+|.+|+.+||+||+.||.+|.+|+.|||++..|++|++||..||+||+.|+.....+.
T Consensus         3 ~~~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~   63 (80)
T d1am9a_           3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK   63 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999988899999999999999999997765543

>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=99.74  E-value=9.1e-19  Score=107.12  Aligned_cols=54  Identities=19%  Similarity=0.408  Sum_probs=49.6

Q ss_pred             hhhhcchHHHhHHHHHHHHHHHHHhhcCC------CCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607          28 KRKSRNLSEKKRRDQFNMLINELCTMVST------NNRKMDKSTVLKSTIAFLKNYNGTY   81 (95)
Q Consensus        28 ~r~~hn~~EKrRRd~iN~~i~eL~~LIP~------~~~K~dK~sIL~~aI~ylk~L~~~~   81 (95)
                      +|..|+.+||+||++||.+|.+|+.|||+      ...|++|++||+.||+||+.|++..
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            67899999999999999999999999995      3579999999999999999998653

>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=99.71  E-value=9.1e-19  Score=107.71  Aligned_cols=57  Identities=19%  Similarity=0.390  Sum_probs=51.7

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-----CCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-----NRKMDKSTVLKSTIAFLKNYNGTYY   82 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-----~~K~dK~sIL~~aI~ylk~L~~~~~   82 (95)
                      +.+|.+|+.+||+||+.||.+|.+|+.+||.+     ..|++|++||.+||+||+.|++...
T Consensus         3 ~~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~~   64 (65)
T d1an4a_           3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhhC
Confidence            46788999999999999999999999999974     4699999999999999999997654

>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=99.69  E-value=2.3e-17  Score=102.47  Aligned_cols=57  Identities=21%  Similarity=0.446  Sum_probs=51.7

Q ss_pred             hhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhh
Q psy3607          24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGT   80 (95)
Q Consensus        24 k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~~   80 (95)
                      ....+|..||..||+||+.||.+|.+|+.+||++ ..|++|++||+.||+||+.|++.
T Consensus         8 ~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~   65 (68)
T d1mdya_           8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQAL   65 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            3456788999999999999999999999999986 47899999999999999999864

>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=99.67  E-value=2.5e-17  Score=104.66  Aligned_cols=55  Identities=22%  Similarity=0.328  Sum_probs=50.5

Q ss_pred             hhhhcchHHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3607          28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGTYY   82 (95)
Q Consensus        28 ~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~~~~   82 (95)
                      +|.+||.+||+||+.||.+|.+|+++||++ +.|++|++||+.||+||+.|++...
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~   57 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNH   57 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999974 5799999999999999999986543

>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=99.67  E-value=3.6e-17  Score=104.88  Aligned_cols=59  Identities=22%  Similarity=0.296  Sum_probs=53.1

Q ss_pred             hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhhhcc
Q psy3607          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGTYYFG   84 (95)
Q Consensus        26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~--~~K~dK~sIL~~aI~ylk~L~~~~~~~   84 (95)
                      ..+|.+||.+||+||+.||.+|.+|+.+||++  ..|++|++||..||+||+.|+.....+
T Consensus         4 ~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l   64 (88)
T d1nkpa_           4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL   64 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            57889999999999999999999999999974  468999999999999999999765443

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.67  E-value=3.9e-17  Score=102.91  Aligned_cols=55  Identities=18%  Similarity=0.270  Sum_probs=50.1

Q ss_pred             hhhcchHHHhHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhhhc
Q psy3607          29 RKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGTYYF   83 (95)
Q Consensus        29 r~~hn~~EKrRRd~iN~~i~eL~~LIP~~--~~K~dK~sIL~~aI~ylk~L~~~~~~   83 (95)
                      |..||.+||+||+.||.+|.+|+++||++  ..|++|++||..||+||+.|+.....
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~   58 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRK   58 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999974  56899999999999999999976544

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

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

Probab=99.39  E-value=3.1e-14  Score=86.33  Aligned_cols=48  Identities=29%  Similarity=0.258  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhcccch
Q psy3607          40 RDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGCSL   87 (95)
Q Consensus        40 Rd~iN~~i~eL~~LIP~~~~K~dK~sIL~~aI~ylk~L~~~~~~~~~~   87 (95)
                      |++||++|.+|+.+||++..|++|++||.+||+||+.|+.....+-.+
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e   48 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE   48 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999998889999999999999999999877665443