Psyllid ID: psy3606

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MSTHQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccccHHccccccEEEc
Coil and Loop (DISEMBL)
msthqleqsfnrnsddtmddtddkddskrksrnlsekKRRDQFNMLINELCTMVstnnrkmdksTVLKSTIAFLKNYNGLYDCLIMIGyftnfkci
Flexible Loop (DISEMBL)
msthqleqsfnrnsddtmddtddkddskrksrnlsekkrrdqfnMLINELCTmvstnnrkmdkSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
Low Complexity Region (SEG)
MSTHQLEQSFnrnsddtmddtddkddskrksrnLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
Disordered region (IsUnstruct)
******************************************FNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKC*
Disordered Region (DISOPRED)
****************************************DQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
Disordered Region (DISEMBL)
*********************************LSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
Disordered Region (DISPRO)
***********************************EKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTHQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNFKCI
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	96	2.2.26 [Sep-21-2011]
O61735	1027	Circadian locomoter outpu	yes	N/A	0.520	0.048	0.8	6e-17
Q8QGQ6	875	Circadian locomoter outpu	yes	N/A	0.802	0.088	0.537	4e-16
Q6YGZ4	851	Circadian locomoter outpu	N/A	N/A	0.802	0.090	0.537	5e-16
Q99743	824	Neuronal PAS domain-conta	yes	N/A	0.614	0.071	0.627	9e-16
P97460	816	Neuronal PAS domain-conta	yes	N/A	0.614	0.072	0.627	1e-15
Q5ZQU2	815	Neuronal PAS domain-conta	no	N/A	0.614	0.072	0.627	2e-15
Q91YB2	865	Circadian locomoter outpu	N/A	N/A	0.645	0.071	0.612	9e-15
Q9WVS9	862	Circadian locomoter outpu	no	N/A	0.645	0.071	0.612	9e-15
O08785	855	Circadian locomoter outpu	no	N/A	0.645	0.072	0.612	9e-15
Q91YB0	865	Circadian locomoter outpu	N/A	N/A	0.645	0.071	0.612	1e-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 = 83.6 bits (205), Expect = 4e-16,   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 = 83.2 bits (204), Expect = 5e-16,   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 = 82.0 bits (201), Expect = 9e-16,   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 = 81.6 bits (200), Expect = 1e-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 = 81.3 bits (199), 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.

Gallus gallus (taxid: 9031)

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

 Score = 79.0 bits (193), Expect = 9e-15,   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|Q9WVS9|CLOCK_RAT Circadian locomoter output cycles protein kaput OS=Rattus norvegicus GN=Clock PE=2 SV=1

 Score = 79.0 bits (193), Expect = 9e-15,   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|O08785|CLOCK_MOUSE Circadian locomoter output cycles protein kaput OS=Mus musculus GN=Clock PE=1 SV=1

 Score = 79.0 bits (193), Expect = 9e-15,   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: 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|Q91YB0|CLOCK_NANGA Circadian locomoter output cycles protein kaput OS=Nannospalax galili GN=Clock PE=1 SV=1

 Score = 78.6 bits (192), Expect = 1e-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	96
444245669	673	clock, partial [Solenopsis invicta]	0.656	0.093	0.796	2e-20
305682538	522	CLOCK [Thermobia domestica]	0.541	0.099	0.903	3e-18
443497931	594	CLOCK [Gryllus bimaculatus]	0.541	0.087	0.884	3e-18
357614851	602	clock [Danaus plexippus]	0.541	0.086	0.846	5e-18
158294626	1030	AGAP005711-PA [Anopheles gambiae str. PE	0.541	0.050	0.826	8e-18
321468989	869	hypothetical protein DAPPUDRAFT_346996 [	0.677	0.074	0.696	1e-17
242017615	660	Circadian locomoter output cycles protei	0.541	0.078	0.865	2e-17
339283906	411	clock [Spodoptera exigua]	0.541	0.126	0.846	2e-17
312385502	1105	hypothetical protein AND_00709 [Anophele	0.541	0.047	0.826	2e-17
405962835	466	Circadian locomoter output cycles protei	0.583	0.120	0.785	3e-17

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

 Score =  102 bits (255), Expect = 2e-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 = 95.9 bits (237), Expect = 3e-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 = 95.5 bits (236), 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|357614851|gb|EHJ69324.1| clock [Danaus plexippus]

 Score = 95.1 bits (235), Expect = 5e-18,   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|158294626|ref|XP_315720.4| AGAP005711-PA [Anopheles gambiae str. PEST] gi|157015652|gb|EAA11642.4| AGAP005711-PA [Anopheles gambiae str. PEST]

 Score = 94.4 bits (233), Expect = 8e-18,   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|321468989|gb|EFX79971.1| hypothetical protein DAPPUDRAFT_346996 [Daphnia pulex]

 Score = 94.0 bits (232), Expect = 1e-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|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 = 93.6 bits (231), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/52 (86%), Positives = 50/52 (96%)

Query: 29 RKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGL 80
          R+SRNLSEKKRRDQFNMLINEL +MVSTNNRKMDKSTVLKSTIAFL+++N L
Sbjct: 13 RRSRNLSEKKRRDQFNMLINELSSMVSTNNRKMDKSTVLKSTIAFLESHNEL 64

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 93.2 bits (230), Expect = 2e-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|312385502|gb|EFR29985.1| hypothetical protein AND_00709 [Anopheles darlingi]

 Score = 93.2 bits (230), Expect = 2e-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: 58  TKRKSRNLSEKKRRDQFNLLVNELSSMVSSNSRKMDKSTVLKSTIAFLKSHN 109

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 92.4 bits (228), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 44/56 (78%), Positives = 51/56 (91%)

Query: 22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNY 77
          DD   SKR +RNLSEKKRRDQFNML+NELC+MVST+++KMDKSTVLKSTIA+LK Y
Sbjct: 27 DDGKSSKRVNRNLSEKKRRDQFNMLVNELCSMVSTSSKKMDKSTVLKSTIAYLKTY 82

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

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	96
FB|FBgn0023076	1027	Clk "Clock" [Drosophila melano	0.510	0.047	0.734	9.6e-14
UNIPROTKB|H7C0J4	107	NPAS2 "Neuronal PAS domain-con	0.468	0.420	0.644	1.2e-10
UNIPROTKB|H7C0Z2	208	NPAS2 "Neuronal PAS domain-con	0.458	0.211	0.636	5.2e-10
UNIPROTKB|H7BZA3	258	NPAS2 "Neuronal PAS domain-con	0.458	0.170	0.636	9.9e-10
UNIPROTKB|C9JK03	182	CLOCK "Circadian locomoter out	0.447	0.236	0.651	2.9e-09
UNIPROTKB|J9P4Q7	668	NPAS2 "Uncharacterized protein	0.458	0.065	0.636	7.4e-09
UNIPROTKB|F6QL92	794	NPAS2 "Uncharacterized protein	0.458	0.055	0.636	9.3e-09
UNIPROTKB|F1STF9	796	NPAS2 "Uncharacterized protein	0.458	0.055	0.636	9.4e-09
UNIPROTKB|F1P5G3	815	NPAS2 "Neuronal PAS domain-con	0.458	0.053	0.636	9.7e-09
UNIPROTKB|Q5ZQU2	815	NPAS2 "Neuronal PAS domain-con	0.458	0.053	0.636	9.7e-09

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

 Score = 184 (69.8 bits), Expect = 9.6e-14, Sum P(2) = 9.6e-14
 Identities = 36/49 (73%), Positives = 43/49 (87%)

Query:    34 LSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYD 82
             LSEKKRRDQFN L+N+L  ++ST++RKMDKSTVLKSTIAFLKN+N   D
Sbjct:    22 LSEKKRRDQFNSLVNDLSALISTSSRKMDKSTVLKSTIAFLKNHNEATD 70

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

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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	0.8020	0.088	yes	N/A
Q99743	NPAS2_HUMAN	No assigned EC number	0.6271	0.6145	0.0716	yes	N/A
P97460	NPAS2_MOUSE	No assigned EC number	0.6271	0.6145	0.0723	yes	N/A
O61735	CLOCK_DROME	No assigned EC number	0.8	0.5208	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	96
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-08
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	7e-07
smart00353	53	smart00353, HLH, helix loop helix domain	4e-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 = 45.7 bits (109), Expect = 3e-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 = 42.1 bits (100), Expect = 7e-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 = 39.9 bits (94), Expect = 4e-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	96
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.68
KOG1318|consensus	411		99.68
KOG3561|consensus	803		99.67
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.64
KOG4304|consensus	250		99.6
KOG1319|consensus	229		99.51
smart00353	53	HLH helix loop helix domain.	99.51
KOG2588|consensus	953		98.84
KOG2483|consensus	232		98.25
KOG4029|consensus	228		98.2
KOG0561|consensus	373		98.18
KOG3960|consensus	284		97.98
KOG3560|consensus	712		97.77
KOG3910|consensus	632		97.45
PLN03217	93	transcription factor ATBS1; Provisional	97.29
KOG3558|consensus	768		96.97
KOG3559|consensus	598		95.74
KOG4447|consensus	173		95.35
KOG4395|consensus	285		94.7
KOG3898|consensus	254		94.51

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

Probab=99.68  E-value=8.8e-17  Score=96.90  Aligned_cols=51  Identities=29%  Similarity=0.601  Sum_probs=48.2

Q ss_pred             HhhhhchHHHHHHHHHHHHHHHHHhhcCCC----CCCCCHHHHHHHHHHHHHHhh
Q psy3606          28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN----NRKMDKSTVLKSTIAFLKNYN   78 (96)
Q Consensus        28 ~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~----~~KldK~~IL~~tI~yLk~L~   78 (96)
                      +|..|+.+||+||+.||..|.+|+.+||.+    ..|++|++||+.||+||+.||
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 ....

>KOG1318|consensus

Probab=99.68  E-value=4.3e-17  Score=133.31  Aligned_cols=68  Identities=25%  Similarity=0.408  Sum_probs=60.9

Q ss_pred             CccCCCChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        16 d~~~~~~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      +.+.....++++||.+||+||||||++||.||+||+.|||.|   ..+++|++||+.+++||+.|++...+
T Consensus       221 ~~~~~~~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~  291 (411)
T KOG1318|consen  221 KTDATALERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR  291 (411)
T ss_pred             CcccchhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence            455556788899999999999999999999999999999997   46899999999999999999986654

>KOG3561|consensus

Probab=99.67  E-value=7.1e-17  Score=140.26  Aligned_cols=79  Identities=39%  Similarity=0.492  Sum_probs=68.4

Q ss_pred             CccCCCChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCC---CCCCHHHHHHHHHHHHHHhhhh--hhhhccCCcc
Q psy3606          16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGL--YDCLIMIGYF   90 (96)
Q Consensus        16 d~~~~~~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~---~KldK~~IL~~tI~yLk~L~~~--~~~~~~~~~~   90 (96)
                      +++.+.+.+++.+|++|+.+||||||++|.+|+||++|||.|.   +|+||.+||++||+|||.+++.  ..+..+.+|.
T Consensus         8 ~d~~~~d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~~~~~~~~~~d~K   87 (803)
T KOG3561|consen    8 SDDAESDSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQESENSSIDQDYK   87 (803)
T ss_pred             CCcccccchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhhhccccccccccc
Confidence            3444556666777999999999999999999999999999986   9999999999999999999996  5667777888


Q ss_pred             cccc
Q psy3606          91 TNFK   94 (96)
Q Consensus        91 ~~f~   94 (96)
                      ++|.
T Consensus        88 pSfl   91 (803)
T KOG3561|consen   88 PSFL   91 (803)
T ss_pred             cccc
Confidence            7773

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

Probab=99.64  E-value=8.4e-16  Score=92.52  Aligned_cols=55  Identities=29%  Similarity=0.618  Sum_probs=51.5

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGL   80 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~   80 (96)
                      ..++..|+..||+||++||..|.+|+.+||..  ..+++|++||+.||+||+.|+..
T Consensus         2 ~~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~   58 (60)
T cd00083           2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL   58 (60)
T ss_pred             cHHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999997  58999999999999999999875

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=99.60  E-value=9.4e-16  Score=118.43  Aligned_cols=65  Identities=22%  Similarity=0.391  Sum_probs=56.7

Q ss_pred             ccCCCChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC-------CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          17 TMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-------NRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        17 ~~~~~~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-------~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      .+.+.......++.++.++|||||++||.+|++|+.|||..       ..|++|++||++||+||+.|+...
T Consensus        21 ~~~~~~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~   92 (250)
T KOG4304|consen   21 SDERSSKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ   92 (250)
T ss_pred             CCCcchhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence            34455666678889999999999999999999999999973       379999999999999999999753

>KOG1319|consensus

Probab=99.51  E-value=1.8e-14  Score=109.20  Aligned_cols=73  Identities=29%  Similarity=0.435  Sum_probs=64.6

Q ss_pred             hhhcCCCCCccCCCChhh------hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC------CCCCCHHHHHHHHHHHHH
Q psy3606           8 QSFNRNSDDTMDDTDDKD------DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN------NRKMDKSTVLKSTIAFLK   75 (96)
Q Consensus         8 ~~~~~n~~d~~~~~~~k~------~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~------~~KldK~~IL~~tI~yLk   75 (96)
                      ++|.||+||++++.+...      +++|..|...|++|||.||..+..|+.|||.|      ..|+.|+.||++||+||.
T Consensus        36 ssSApNtdd~ds~~hS~a~k~syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~  115 (229)
T KOG1319|consen   36 ASSAPNTDDEDSDYHSEAYKESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQ  115 (229)
T ss_pred             CCCCCCCCcccccchhHHHHhhHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHH
Confidence            478999999999975433      56799999999999999999999999999986      249999999999999999


Q ss_pred             Hhhhh
Q psy3606          76 NYNGL   80 (96)
Q Consensus        76 ~L~~~   80 (96)
                      +|++.
T Consensus       116 ~L~~~  120 (229)
T KOG1319|consen  116 FLHKE  120 (229)
T ss_pred             HHHHH
Confidence            99864

>smart00353 HLH helix loop helix domain

Probab=99.51  E-value=7.5e-14  Score=82.76  Aligned_cols=49  Identities=29%  Similarity=0.523  Sum_probs=45.2

Q ss_pred             chHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          33 NLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        33 ~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      +..||+||++||..|.+|+.+||.+  ..+++|++||..||+||+.|++..
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  689999999999999999999864

>KOG2588|consensus

Probab=98.84  E-value=1.5e-09  Score=96.15  Aligned_cols=60  Identities=32%  Similarity=0.478  Sum_probs=55.3

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhhhc
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLI   85 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~~KldK~~IL~~tI~yLk~L~~~~~~~~   85 (96)
                      +.+|.+||.||||.|-.||+.|.||+.+||+...|+.|..+|+.|++||+.+++.++.+.
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            477999999999999999999999999999988999999999999999999998765433

>KOG2483|consensus

Probab=98.25  E-value=2e-06  Score=66.35  Aligned_cols=57  Identities=19%  Similarity=0.244  Sum_probs=48.5

Q ss_pred             hhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCCCCC--CHHHHHHHHHHHHHHhhhhh
Q psy3606          25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKM--DKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        25 ~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~~Kl--dK~~IL~~tI~yLk~L~~~~   81 (96)
                      ....|..||+.||+||+.|-.++..|+.+||.....-  +-++||.+|+.||+.|+...
T Consensus        56 ~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~  114 (232)
T KOG2483|consen   56 AASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS  114 (232)
T ss_pred             CCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence            3567899999999999999999999999999853322  25899999999999998654

>KOG4029|consensus

Probab=98.20  E-value=1.2e-06  Score=65.92  Aligned_cols=58  Identities=22%  Similarity=0.426  Sum_probs=51.3

Q ss_pred             hhHHhhhhchHHHHHHHHHHHHHHHHHhhcCC--C-CCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3606          25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVST--N-NRKMDKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        25 ~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~--~-~~KldK~~IL~~tI~yLk~L~~~~~   82 (96)
                      ....+..+|..||.|=..+|.++.+|+.+||.  . +.|++|..+|+.||.||+.|....+
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~  166 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLA  166 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhc
Confidence            34566778888999999999999999999997  4 7899999999999999999998653

>KOG0561|consensus

Probab=98.18  E-value=3.4e-06  Score=68.14  Aligned_cols=61  Identities=20%  Similarity=0.383  Sum_probs=51.9

Q ss_pred             ChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3606          22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        22 ~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-~~KldK~~IL~~tI~yLk~L~~~~~   82 (96)
                      ++..+.||+--|-.||||-.-||..|.-|++|+|-. ..|++|+.||+.|.+||-.|.+.-.
T Consensus        54 D~erRmRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt  115 (373)
T KOG0561|consen   54 DPERRMRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKT  115 (373)
T ss_pred             CHHHHHHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccc
Confidence            344456777777789999999999999999999974 4699999999999999999987543

>KOG3960|consensus

Probab=97.98  E-value=2.2e-05  Score=61.94  Aligned_cols=54  Identities=24%  Similarity=0.452  Sum_probs=46.8

Q ss_pred             HhhhhchHHHHHHHHHHHHHHHHHhh-cCCCCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          28 KRKSRNLSEKKRRDQFNMLINELCTM-VSTNNRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        28 ~r~~h~~~EKrRRd~IN~~i~eL~~L-vP~~~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      ||+.-.+.||||=.++|+.|+.|+.= .+.+++++-|..||+.||+||..||.+.
T Consensus       118 RRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL  172 (284)
T KOG3960|consen  118 RRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALL  172 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHH
Confidence            45667788999999999999999864 4556899999999999999999999754

>KOG3560|consensus

Probab=97.77  E-value=1.9e-05  Score=67.92  Aligned_cols=42  Identities=26%  Similarity=0.514  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHh
Q psy3606          36 EKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNY   77 (96)
Q Consensus        36 EKrRRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L   77 (96)
                      -||.||++|.-++-|++|+|-.   ..|+||.+||+.+|.||+.-
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~K   77 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRVK   77 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHHH
Confidence            6899999999999999999974   58999999999999999854

>KOG3910|consensus

Probab=97.45  E-value=0.00015  Score=61.93  Aligned_cols=60  Identities=17%  Similarity=0.292  Sum_probs=52.2

Q ss_pred             ChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCC---CCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        22 ~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~---~~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      .++++.||...|+.||-|=--||+.|+||.+|.--   .+.-..|..||.+||..|-.|+|++
T Consensus       520 aeREkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQV  582 (632)
T KOG3910|consen  520 AEREKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQV  582 (632)
T ss_pred             hhHHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHH
Confidence            46667889999999999999999999999999764   3455789999999999999998864

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.29  E-value=0.00052  Score=46.57  Aligned_cols=44  Identities=27%  Similarity=0.392  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHhhcCCC-----CCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3606          39 RRDQFNMLINELCTMVSTN-----NRKMDKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        39 RRd~IN~~i~eL~~LvP~~-----~~KldK~~IL~~tI~yLk~L~~~~~   82 (96)
                      --|.||+.+..|+.|+|..     ..+..-+-||+.|+.|||.|+..+.
T Consensus        18 sddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvD   66 (93)
T PLN03217         18 SEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVD   66 (93)
T ss_pred             CHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHH
Confidence            3489999999999999983     4688899999999999999997553

>KOG3558|consensus

Probab=96.97  E-value=0.00095  Score=58.69  Aligned_cols=54  Identities=19%  Similarity=0.345  Sum_probs=45.4

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNG   79 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L~~   79 (96)
                      +.||+.-.-+.|-||-+-|.-|-||+.+||-.   ...+||++|++.||.|||.-+-
T Consensus        44 ~~rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk~  100 (768)
T KOG3558|consen   44 ELRKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRKF  100 (768)
T ss_pred             HHHhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHHH
Confidence            44555556678889999999999999999953   5789999999999999996654

>KOG3559|consensus

Probab=95.74  E-value=0.011  Score=50.03  Aligned_cols=44  Identities=25%  Similarity=0.473  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhh
Q psy3606          35 SEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYN   78 (96)
Q Consensus        35 ~EKrRRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L~   78 (96)
                      ..|.||++-|.-|-||+.++|-.   .+.+||++|++.|..|||...
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~   54 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN   54 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence            46789999999999999999963   456999999999999999654

>KOG4447|consensus

Probab=95.35  E-value=0.012  Score=43.82  Aligned_cols=55  Identities=20%  Similarity=0.315  Sum_probs=50.1

Q ss_pred             HHhhhhchHHHHHHHHHHHHHHHHHhhcCC-CCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          27 SKRKSRNLSEKKRRDQFNMLINELCTMVST-NNRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        27 ~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~-~~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      ..+.-||+-|++|=..+|+.|+.|+.++|. +..|++|..-|+.|..||-.|-+..
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            467889999999999999999999999998 4689999999999999999887754

>KOG4395|consensus

Probab=94.70  E-value=0.077  Score=42.27  Aligned_cols=56  Identities=20%  Similarity=0.350  Sum_probs=50.0

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      ..+|..-|..|+||-.-+|..|+.|...||..  ..|++|-..|++|--||--|-+..
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            46677888999999999999999999999984  689999999999999999887654

>KOG3898|consensus

Probab=94.51  E-value=0.027  Score=43.72  Aligned_cols=55  Identities=16%  Similarity=0.300  Sum_probs=48.5

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLKNYNGL   80 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~--~~~KldK~~IL~~tI~yLk~L~~~   80 (96)
                      ..+|..-|.-||+|---+|+.++.|+.+||.  ...|+.|...|+.|-.||-.|.+.
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            4566677788999999999999999999994  368999999999999999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
4h10_B	71	Intermolecular Recognition Revealed By The Complex		2e-10
4f3l_A	361	Crystal Structure Of The Heterodimeric Clock:bmal1		5e-10
4h10_A	73	Intermolecular Recognition Revealed By The Complex		3e-05
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		7e-05

>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 = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 37/50 (74%)
Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCL 84
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +  +   L
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWL 64

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 28/43 (65%), Positives = 35/43 (81%)
Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNY 77
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKH 61

>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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGLY 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 = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTN 92
          EK+RRD+ N  I+EL ++V T N   RK+DK TVL+  +  +K   G  +      Y   
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPT 80
Query: 93 F 93
          F
Sbjct: 81 F 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
4f3l_A	361	Mclock, circadian locomoter output cycles protein	6e-18
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	2e-14
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-08
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	9e-08
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	3e-07
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	4e-07
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	1e-06

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

 Score = 75.8 bits (186), Expect = 6e-18
 Identities = 37/59 (62%), Positives = 45/59 (76%)

Query: 22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGL 80
          DDKD +KR SRN SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +   
Sbjct: 6  DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET 64

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

 Score = 65.8 bits (160), Expect = 2e-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 FLKNYNGL 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 = 45.4 bits (108), Expect = 4e-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 = 44.3 bits (105), Expect = 9e-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 = 42.7 bits (101), Expect = 3e-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 = 43.1 bits (102), Expect = 4e-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 = 41.6 bits (98), Expect = 1e-06
 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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.86
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.78
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.78
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.77
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.77
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.74
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.68
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.67
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.66
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.65
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.62
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.55
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.52
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.43
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.4
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.28
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.07
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.66

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

Probab=99.86  E-value=4e-22  Score=128.18  Aligned_cols=62  Identities=60%  Similarity=0.811  Sum_probs=56.5

Q ss_pred             ChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        22 ~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      +.++.++|.+|+++||+||++||.+|.+|++|||++..|+||++||++||+||+.|++..+-
T Consensus         2 d~k~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~   63 (71)
T 4h10_B            2 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAW   63 (71)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhH
Confidence            45678999999999999999999999999999998888999999999999999999987643

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

Probab=99.78  E-value=6.3e-20  Score=118.09  Aligned_cols=58  Identities=36%  Similarity=0.595  Sum_probs=53.1

Q ss_pred             hhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhhh
Q psy3606          23 DKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNGL   80 (96)
Q Consensus        23 ~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L~~~   80 (96)
                      .+..++|.+|+++||+||++||..|.+|+.|||.|   ..|+||++||++||+||+.|+..
T Consensus         4 ~k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~~   64 (73)
T 4h10_A            4 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   64 (73)
T ss_dssp             -CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhcC
Confidence            35578899999999999999999999999999985   47999999999999999999874

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

Probab=99.78  E-value=2.5e-19  Score=116.51  Aligned_cols=61  Identities=30%  Similarity=0.375  Sum_probs=56.6

Q ss_pred             hhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhhh
Q psy3606          24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCL   84 (96)
Q Consensus        24 k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~~KldK~~IL~~tI~yLk~L~~~~~~~   84 (96)
                      +...+|.+|+.+||+||++||..|.+|+.|||++..|++|++||++||+||+.|+.....+
T Consensus         2 k~~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L   62 (82)
T 1am9_A            2 SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL   62 (82)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999998899999999999999999999876554

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

Probab=99.77  E-value=3e-19  Score=123.24  Aligned_cols=71  Identities=23%  Similarity=0.378  Sum_probs=49.3

Q ss_pred             CCccCCCChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhhhhhhhc
Q psy3606          15 DDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNGLYDCLI   85 (96)
Q Consensus        15 ~d~~~~~~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L~~~~~~~~   85 (96)
                      .|.+.....+...+|.+|+.+||+||++||.+|.+|+.|||++   ..|++|++||++||+||+.|++....+.
T Consensus        14 t~~~~~~~~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~   87 (118)
T 4ati_A           14 TESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAK   87 (118)
T ss_dssp             -----------------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444456778889999999999999999999999999999986   4689999999999999999998776554

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

Probab=99.77  E-value=1.7e-19  Score=112.92  Aligned_cols=54  Identities=19%  Similarity=0.405  Sum_probs=50.1

Q ss_pred             HhhhhchHHHHHHHHHHHHHHHHHhhcCCC------CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN------NRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        28 ~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~------~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      +|.+|+++||+||++||.+|.+|++|||++      ..+++|++||++||+||+.|++..
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999999999999974      479999999999999999999854

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

Probab=99.74  E-value=2.2e-19  Score=111.62  Aligned_cols=57  Identities=19%  Similarity=0.385  Sum_probs=51.9

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCC-----CCCCHHHHHHHHHHHHHHhhhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTNN-----RKMDKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~-----~KldK~~IL~~tI~yLk~L~~~~~   82 (96)
                      ..+|.+|+.+||+||++||..|.+|+.|||++.     .|++|++||++||+||+.|++.+.
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999864     389999999999999999998653

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

Probab=99.68  E-value=3.1e-17  Score=128.07  Aligned_cols=76  Identities=30%  Similarity=0.493  Sum_probs=56.0

Q ss_pred             cCCCChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCC---CCCCCCHHHHHHHHHHHHHHhhhhhhhhccCCccccc
Q psy3606          18 MDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTNF   93 (96)
Q Consensus        18 ~~~~~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~---~~~KldK~~IL~~tI~yLk~L~~~~~~~~~~~~~~~f   93 (96)
                      +++...|.+.+|.+|+.+|||||++||..|.+|+.|||.   ...|+||++||++||+|||.|++......+.++.++|
T Consensus         3 ~~~~~~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~~~~~~~~~~~~~~   81 (387)
T 4f3l_B            3 YAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPTF   81 (387)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC------CCSSCTT
T ss_pred             cccccchhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcccccccccccCccc
Confidence            345678889999999999999999999999999999996   3589999999999999999999766555555555544

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

Probab=99.67  E-value=5.5e-17  Score=125.03  Aligned_cols=64  Identities=58%  Similarity=0.768  Sum_probs=45.1

Q ss_pred             CCCChhhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3606          19 DDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        19 ~~~~~k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~~KldK~~IL~~tI~yLk~L~~~~~   82 (96)
                      .+...+++.+|.+|+++||+||++||..|.+|++|||...+|+||++||++||+|||.++...+
T Consensus         3 ~~~~~~~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~~   66 (361)
T 4f3l_A            3 VEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTA   66 (361)
T ss_dssp             ----------------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccccccchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhcc
Confidence            4556778899999999999999999999999999999777899999999999999999987643

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

Probab=99.66  E-value=1.5e-16  Score=102.45  Aligned_cols=61  Identities=21%  Similarity=0.312  Sum_probs=55.0

Q ss_pred             hhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhhhh
Q psy3606          24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGLYDCL   84 (96)
Q Consensus        24 k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-~~KldK~~IL~~tI~yLk~L~~~~~~~   84 (96)
                      ....+|.+|+.+||+||+.||.+|.+|+.+||.+ ..|++|++||+.||+||+.|++....+
T Consensus         8 ~~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L   69 (80)
T 1hlo_A            8 SDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH   69 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999985 469999999999999999999876544

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

Probab=99.65  E-value=1.6e-16  Score=102.62  Aligned_cols=56  Identities=21%  Similarity=0.322  Sum_probs=51.5

Q ss_pred             HhhhhchHHHHHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        28 ~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      +|.+|+.+||+||+.||.+|.+|+.+||++ ..|++|++||.+||+||+.|++....
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~   58 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHT   58 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999984 57999999999999999999976543

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

Probab=99.62  E-value=7.2e-16  Score=101.61  Aligned_cols=58  Identities=22%  Similarity=0.329  Sum_probs=53.1

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      ..+|.+||.+||+||+.||.+|..|+.+||..  ..|++|++||..||+||+.|+.....
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~   63 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQK   63 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999984  47999999999999999999987654

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

Probab=99.55  E-value=4.5e-15  Score=95.88  Aligned_cols=57  Identities=25%  Similarity=0.320  Sum_probs=46.0

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCC--CCCCC-CHHHHHHHHHHHHHHhhhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKM-DKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~--~~~Kl-dK~~IL~~tI~yLk~L~~~~~   82 (96)
                      ..+|.+||.+||+||+.||.+|.+|+.+||.  ...|. +|++||+.||+||+.|++...
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~   62 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVR   62 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999995  23455 899999999999999998764

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

Probab=99.52  E-value=1.5e-14  Score=93.92  Aligned_cols=55  Identities=18%  Similarity=0.260  Sum_probs=50.6

Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          29 RKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        29 r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      |..||.+||+||+.||.+|..|+.+||..  ..|++|++||.+|++||+.|++....
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~   58 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRK   58 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            68899999999999999999999999974  47999999999999999999987654

>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B*

Probab=99.43  E-value=3.8e-13  Score=85.31  Aligned_cols=56  Identities=23%  Similarity=0.485  Sum_probs=51.5

Q ss_pred             hhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhh
Q psy3606          25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGL   80 (96)
Q Consensus        25 ~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-~~KldK~~IL~~tI~yLk~L~~~   80 (96)
                      ...+|..||..||+|+..||..|..|+.+||.. +.|++|..||+.||+||..|++.
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~   65 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQAL   65 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHT
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            356788999999999999999999999999974 57999999999999999999985

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

Probab=99.40  E-value=7.1e-13  Score=82.08  Aligned_cols=55  Identities=20%  Similarity=0.331  Sum_probs=50.4

Q ss_pred             HHhhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        27 ~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      ++|..||..||+|+..||..|..|+.+||..  ..|++|..||+.|++||..|++..
T Consensus         1 ~rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L   57 (60)
T 2ql2_B            1 SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL   57 (60)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHH
Confidence            3678899999999999999999999999973  689999999999999999999854

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

Probab=99.28  E-value=4.9e-12  Score=83.37  Aligned_cols=48  Identities=21%  Similarity=0.308  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhhhhhhhcc
Q psy3606          39 RRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNGLYDCLIM   86 (96)
Q Consensus        39 RRd~IN~~i~eL~~LvP~~---~~KldK~~IL~~tI~yLk~L~~~~~~~~~   86 (96)
                      -|+.||.+|.||..|||++   ..|++|++||+.||+||+.|++.++++.+
T Consensus         3 ~R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e   53 (83)
T 4ath_A            3 MRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD   53 (83)
T ss_dssp             CHHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             chhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999974   46999999999999999999987765443

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

Probab=99.07  E-value=3.9e-11  Score=76.56  Aligned_cols=50  Identities=12%  Similarity=0.192  Sum_probs=44.9

Q ss_pred             hhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhh
Q psy3606          31 SRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGL   80 (96)
Q Consensus        31 ~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~   80 (96)
                      .-+.-||+|+..||..|..|+.+||..  +.|++|..||+.||+||..|+.+
T Consensus        17 ~a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~a   68 (68)
T 2lfh_A           17 PAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVV   68 (68)
T ss_dssp             CCBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHcC
Confidence            455779999999999999999999973  68999999999999999999863

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

Probab=98.66  E-value=7.5e-08  Score=64.89  Aligned_cols=48  Identities=19%  Similarity=0.261  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          36 EKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        36 EKrRRd~IN~~i~eL~~LvP~--~~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      |+.|-..+|..|..|+.+||.  ...|++|..+|+.||+||..|++....
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            566778999999999999997  368999999999999999999986543

---

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	96
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-08
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	4e-08
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	5e-08
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	9e-07
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-06
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	7e-06
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-05

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

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

 Score = 44.9 bits (106), Expect = 2e-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

>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 = 44.1 bits (104), Expect = 4e-08
 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 = 43.6 bits (103), Expect = 5e-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 = 40.2 bits (94), Expect = 9e-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 = 40.3 bits (94), Expect = 2e-06
 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 = 37.9 bits (88), Expect = 7e-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 = 38.0 bits (88), Expect = 1e-05
 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

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	96
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.73
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.69
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.68
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.65
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.36

>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=1.5e-18  Score=110.39  Aligned_cols=60  Identities=30%  Similarity=0.381  Sum_probs=55.4

Q ss_pred             hhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhhh
Q psy3606          25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCL   84 (96)
Q Consensus        25 ~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~~~KldK~~IL~~tI~yLk~L~~~~~~~   84 (96)
                      .+.+|.+|+.+||+||++||..|.+|+.|||++..|++|++||..||+||+.|+..+..+
T Consensus         3 ~~~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L   62 (80)
T d1am9a_           3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL   62 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            467889999999999999999999999999998889999999999999999999876543

>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=99.73  E-value=1e-18  Score=107.04  Aligned_cols=54  Identities=19%  Similarity=0.386  Sum_probs=50.0

Q ss_pred             HhhhhchHHHHHHHHHHHHHHHHHhhcCC------CCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          28 KRKSRNLSEKKRRDQFNMLINELCTMVST------NNRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        28 ~r~~h~~~EKrRRd~IN~~i~eL~~LvP~------~~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      +|.+|+++||+||++||.+|.+|+.|||+      ...|++|++||+.||+||+.|++..
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            57899999999999999999999999995      3689999999999999999998754

>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=99.69  E-value=1.6e-18  Score=106.78  Aligned_cols=57  Identities=19%  Similarity=0.384  Sum_probs=51.8

Q ss_pred             hHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC-----CCCCCHHHHHHHHHHHHHHhhhhhh
Q psy3606          26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-----NRKMDKSTVLKSTIAFLKNYNGLYD   82 (96)
Q Consensus        26 ~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-----~~KldK~~IL~~tI~yLk~L~~~~~   82 (96)
                      +.+|.+|+.+||+||+.||.+|.+|+.|||.+     ..|++|++||++||+||+.|++.++
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            45688999999999999999999999999973     4699999999999999999998654

>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=99.68  E-value=3.9e-17  Score=101.48  Aligned_cols=58  Identities=22%  Similarity=0.469  Sum_probs=52.4

Q ss_pred             hhhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3606          24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGLY   81 (96)
Q Consensus        24 k~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-~~KldK~~IL~~tI~yLk~L~~~~   81 (96)
                      ....+|..|+..||+||+.||.+|.+|+.|||++ ..|++|++||+.||+||+.|++..
T Consensus         8 ~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l   66 (68)
T d1mdya_           8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            3456789999999999999999999999999986 478999999999999999999753

>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=99.66  E-value=7.1e-17  Score=102.66  Aligned_cols=56  Identities=21%  Similarity=0.322  Sum_probs=51.1

Q ss_pred             HhhhhchHHHHHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        28 ~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~-~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      +|.+|+.+||+||++||..|.+|+++||++ ..|++|++||+.||+||+.|++....
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~   58 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHT   58 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999974 57999999999999999999876543

>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=99.65  E-value=9.1e-17  Score=101.33  Aligned_cols=55  Identities=18%  Similarity=0.260  Sum_probs=50.3

Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          29 RKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        29 r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      |..|+.+||+||+.||.+|.+|+++||++  ..|++|++||..||+||+.|+.....
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  46899999999999999999986544

>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=99.65  E-value=1.3e-16  Score=102.36  Aligned_cols=59  Identities=22%  Similarity=0.307  Sum_probs=53.2

Q ss_pred             hhHHhhhhchHHHHHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhhhh
Q psy3606          25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGLYDC   83 (96)
Q Consensus        25 ~~~~r~~h~~~EKrRRd~IN~~i~eL~~LvP~~--~~KldK~~IL~~tI~yLk~L~~~~~~   83 (96)
                      ...+|.+|+.+||+||+.||.+|.+|+++||++  ..|++|++||..||+||+.|+.....
T Consensus         3 ~~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~   63 (88)
T d1nkpa_           3 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQK   63 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHH
Confidence            357889999999999999999999999999974  46899999999999999999986543

>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=99.36  E-value=7.2e-14  Score=84.75  Aligned_cols=45  Identities=33%  Similarity=0.409  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhhh
Q psy3606          40 RDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCL   84 (96)
Q Consensus        40 Rd~IN~~i~eL~~LvP~~~~KldK~~IL~~tI~yLk~L~~~~~~~   84 (96)
                      |++||+.|.+|+.+||++..|++|++||..||+||+.|+..+..+
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L   45 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKL   45 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999998889999999999999999999877554