Psyllid ID: psy11625

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310----

MKWNKGVKSRLLNHLNSCVSGLQQLTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVVYLSPHNAEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQAEPCSSSILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEVC

ccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHcccEEEccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccc

cccccHHHHHHHHHHHHHHHcHHccccccccccccccccccccccccccccccccccccccEEEccccEEEEcccccccEEEEEEccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHcccccccccHHccccccccEccccccEEEEEcccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHccccccccc

MKWNKGVKSRLLNHLNSCvsglqqltpfslpssttappppvtlppapslledvnnnEASARLQMISSGIqvipsrlptGELALLLsgssglfssppevsssessssdrvSAFSvvehkkpkspppsptsstdgdvvylsphnaevtststtqdnvfkvpslqtkafsskpsyfspytnessllmkvppyhqaepcsssILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKdparhsklekADILEMTVKHLQNVQRQQLsvavasdptVLQKFKSGFGDCAVEINRYIsrldgldtevc

MKWNKGVKSRLLNHLNSCVSGLQQLTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLSGSSGLFSSPPevsssessssDRVSAFSvvehkkpkspppsptsstDGDVVYLSPHNAevtststtqdnvfkVPSLQtkafsskpsyFSPYTNESSLLMKVPPYHQAEPCSSSILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRyisrldgldtevc

MKWNKGVKSRLLNHLNSCVSGLQQltpfslpssttappppvtlppapsllEDVNNNEASARLQMISSGIQVIPSRLPTGElalllsgssglfssppevsssessssdrvsafsvvEHkkpkspppsptsstDGDVVYLSPHNAEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQAEPCSSSILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEVC

***********LNHLNSCVS************************************************IQVI*******ELALL*************************************************************************************************LLMKVPPYHQAEPCSSSILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEA**************DILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDG******

****KGVKSRLLNHLNSCV************************************************************EL*LLLSGSSG*FS*********************************************************************************************************************************RRRARINNCLNELKSLILEAMR***********ADILEMTVKHLQNVQ****************KFKSGFGDCAVEINRYISRLD*******

********SRLLNHLNSCVSGLQQLTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLSGSSG******************************************GDVVYLSPHNAEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQAEPCSSSILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEVC

*KWNKGVKSRLLNHLNSCVSGLQQLTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLSGSSGLFSSPPEVSS*********S*******************************************N*FK*PSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQAEPCSSSILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLD****

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		314	2.2.26 [Sep-21-2011]
Q26263		435	Protein deadpan OS=Drosop	yes	N/A	0.251	0.181	0.78	1e-43
Q90Z12		281	Transcription factor HES-	N/A	N/A	0.245	0.274	0.62	3e-33
Q04666		281	Transcription factor HES-	yes	N/A	0.318	0.355	0.61	4e-33
Q14469		280	Transcription factor HES-	yes	N/A	0.318	0.357	0.61	5e-33
Q3ZBG4		280	Transcription factor HES-	yes	N/A	0.318	0.357	0.61	5e-33
Q6PBD4		281	Transcription factor HES-	yes	N/A	0.238	0.266	0.61	6e-33
P35428		282	Transcription factor HES-	yes	N/A	0.318	0.354	0.61	7e-33
Q90VV1		277	Transcription factor HES-	N/A	N/A	0.318	0.361	0.61	8e-33
Q6IRB2		267	Transcription factor HES-	N/A	N/A	0.318	0.374	0.61	1e-32
Q8AVU4		267	Transcription factor HES-	N/A	N/A	0.318	0.374	0.6	2e-32

>sp\|Q26263\|DPN_DROME Protein deadpan OS=Drosophila melanogaster GN=dpn PE=1 SV=2	Back alignment and function desciption

 Score =  177 bits (448), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 78/100 (78%), Positives = 96/100 (96%)

Query: 214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
           ++NKPIMEKRRRARIN+CLNELKSLILEAM+KDPARH+KLEKADILEMTVKHLQ+VQRQQ
Sbjct: 42  KTNKPIMEKRRRARINHCLNELKSLILEAMKKDPARHTKLEKADILEMTVKHLQSVQRQQ 101

Query: 274 LSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEV 313
           L++A+ SDP+V+QKFK+GF +CA E+NRY+S++DG+DT V
Sbjct: 102 LNMAIQSDPSVVQKFKTGFVECAEEVNRYVSQMDGIDTGV 141

Transcriptional repressor of genes that require a bHLH protein for their transcription. Likely to be involved in the functional rather than the morphological differentiation of neurons. Loss of DPN function results in weak motor activity, lethargic behavior, and death. Implicated in sex determination as Groucho-DPN complex act directly to repress SXL transcription.
Drosophila melanogaster (taxid: 7227)

>sp\|Q90Z12\|HES4A_XENLA Transcription factor HES-4-A OS=Xenopus laevis GN=hes4-a PE=1 SV=2	Back alignment and function description

>sp\|Q04666\|HES1_RAT Transcription factor HES-1 OS=Rattus norvegicus GN=Hes1 PE=1 SV=1	Back alignment and function description

>sp\|Q14469\|HES1_HUMAN Transcription factor HES-1 OS=Homo sapiens GN=HES1 PE=1 SV=1	Back alignment and function description

>sp\|Q3ZBG4\|HES1_BOVIN Transcription factor HES-1 OS=Bos taurus GN=HES1 PE=2 SV=1	Back alignment and function description

>sp\|Q6PBD4\|HES4_XENTR Transcription factor HES-4 OS=Xenopus tropicalis GN=hes4 PE=2 SV=1	Back alignment and function description

>sp\|P35428\|HES1_MOUSE Transcription factor HES-1 OS=Mus musculus GN=Hes1 PE=1 SV=1	Back alignment and function description

>sp\|Q90VV1\|HES4B_XENLA Transcription factor HES-4-B OS=Xenopus laevis GN=hes4-b PE=1 SV=1	Back alignment and function description

>sp\|Q6IRB2\|HES1A_XENLA Transcription factor HES-1-A OS=Xenopus laevis GN=hes1-a PE=1 SV=1	Back alignment and function description

>sp\|Q8AVU4\|HES1B_XENLA Transcription factor HES-1-B OS=Xenopus laevis GN=hes1-b PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		314
195474645		435	GE23198 [Drosophila yakuba] gi\|194175702	0.251	0.181	0.78	5e-42
194863545		435	GG10662 [Drosophila erecta] gi\|190662360	0.251	0.181	0.78	6e-42
195332406		435	GM20707 [Drosophila sechellia] gi\|194124	0.251	0.181	0.78	6e-42
17136808		435	deadpan [Drosophila melanogaster] gi\|173	0.251	0.181	0.78	6e-42
423828		435	helix-loop-helix protein Dpn - fruit fly	0.251	0.181	0.78	7e-42
195551484		435	GD15288 [Drosophila simulans] gi\|1942018	0.251	0.181	0.78	1e-41
195431349		465	GK15770 [Drosophila willistoni] gi\|19415	0.264	0.178	0.77	5e-41
242004766		615	transcription factor hes-1, putative [Pe	0.210	0.107	0.77	6e-41
194753135		441	GF12602 [Drosophila ananassae] gi\|190620	0.277	0.197	0.77	7e-41
195149518		439	GL10878 [Drosophila persimilis] gi\|19410	0.315	0.225	0.77	1e-39

>gi\|195474645\|ref\|XP_002089601.1\| GE23198 [Drosophila yakuba] gi\|194175702\|gb\|EDW89313.1\| GE23198 [Drosophila yakuba]	Back alignment and taxonomy information

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 78/100 (78%), Positives = 96/100 (96%)

Query: 214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
           ++NKPIMEKRRRARIN+CLNELKSLILEAM+KDPARH+KLEKADILEMTVKHLQ+VQRQQ
Sbjct: 42  KTNKPIMEKRRRARINHCLNELKSLILEAMKKDPARHTKLEKADILEMTVKHLQSVQRQQ 101

Query: 274 LSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEV 313
           L++A+ SDP+V+QKFK+GF +CA E+NRY+S++DG+DT V
Sbjct: 102 LNMAIQSDPSVVQKFKTGFVECAEEVNRYVSQMDGIDTGV 141

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|194863545\|ref\|XP_001970493.1\| GG10662 [Drosophila erecta] gi\|190662360\|gb\|EDV59552.1\| GG10662 [Drosophila erecta]	Back alignment and taxonomy information

>gi\|195332406\|ref\|XP_002032889.1\| GM20707 [Drosophila sechellia] gi\|194124859\|gb\|EDW46902.1\| GM20707 [Drosophila sechellia]	Back alignment and taxonomy information

>gi\|17136808\|ref\|NP_476923.1\| deadpan [Drosophila melanogaster] gi\|17380360\|sp\|Q26263.2\|DPN_DROME RecName: Full=Protein deadpan gi\|7304075\|gb\|AAF59113.1\| deadpan [Drosophila melanogaster] gi\|17945810\|gb\|AAL48952.1\| RE34993p [Drosophila melanogaster] gi\|220942546\|gb\|ACL83816.1\| dpn-PA [synthetic construct] gi\|220952694\|gb\|ACL88890.1\| dpn-PA [synthetic construct]	Back alignment and taxonomy information

>gi\|423828\|pir\|\|A46231 helix-loop-helix protein Dpn - fruit fly (Drosophila sp.) gi\|259772\|gb\|AAB24149.1\| Dpn [Drosophila sp.]	Back alignment and taxonomy information

>gi\|195551484\|ref\|XP_002076238.1\| GD15288 [Drosophila simulans] gi\|194201887\|gb\|EDX15463.1\| GD15288 [Drosophila simulans]	Back alignment and taxonomy information

>gi\|195431349\|ref\|XP_002063705.1\| GK15770 [Drosophila willistoni] gi\|194159790\|gb\|EDW74691.1\| GK15770 [Drosophila willistoni]	Back alignment and taxonomy information

>gi\|242004766\|ref\|XP_002423249.1\| transcription factor hes-1, putative [Pediculus humanus corporis] gi\|212506235\|gb\|EEB10511.1\| transcription factor hes-1, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

>gi\|194753135\|ref\|XP_001958873.1\| GF12602 [Drosophila ananassae] gi\|190620171\|gb\|EDV35695.1\| GF12602 [Drosophila ananassae]	Back alignment and taxonomy information

>gi\|195149518\|ref\|XP_002015704.1\| GL10878 [Drosophila persimilis] gi\|194109551\|gb\|EDW31594.1\| GL10878 [Drosophila persimilis]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		314
FB\|FBgn0010109		435	dpn "deadpan" [Drosophila mela	0.318	0.229	0.78	2.3e-39
FB\|FBgn0001168		337	h "hairy" [Drosophila melanoga	0.283	0.264	0.719	2.6e-31
UNIPROTKB\|Q90Z12		281	hes4-a "Transcription factor H	0.318	0.355	0.62	1.4e-30
UNIPROTKB\|G3N2D5		304	HES1 "Transcription factor HES	0.318	0.328	0.61	1.8e-30
UNIPROTKB\|Q3ZBG4		280	HES1 "Transcription factor HES	0.318	0.357	0.61	1.8e-30
UNIPROTKB\|Q14469		280	HES1 "Transcription factor HES	0.318	0.357	0.61	1.8e-30
UNIPROTKB\|I3LM61		280	HES1 "Uncharacterized protein"	0.318	0.357	0.61	1.8e-30
MGI\|MGI:104853		282	Hes1 "hairy and enhancer of sp	0.318	0.354	0.61	1.8e-30
RGD\|62081		281	Hes1 "hairy and enhancer of sp	0.318	0.355	0.61	1.8e-30
ZFIN\|ZDB-GENE-980526-144		334	her6 "hairy-related 6" [Danio	0.318	0.299	0.62	1.8e-30

FB\|FBgn0010109 dpn "deadpan" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 78/100 (78%), Positives = 96/100 (96%)

Query:   214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
             ++NKPIMEKRRRARIN+CLNELKSLILEAM+KDPARH+KLEKADILEMTVKHLQ+VQRQQ
Sbjct:    42 KTNKPIMEKRRRARINHCLNELKSLILEAMKKDPARHTKLEKADILEMTVKHLQSVQRQQ 101

Query:   274 LSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEV 313
             L++A+ SDP+V+QKFK+GF +CA E+NRY+S++DG+DT V
Sbjct:   102 LNMAIQSDPSVVQKFKTGFVECAEEVNRYVSQMDGIDTGV 141

GO:0008345 "larval locomotory behavior" evidence=IMP

GO:0007549 "dosage compensation" evidence=IMP

GO:0008344 "adult locomotory behavior" evidence=IMP

GO:0007540 "sex determination, establishment of X:A ratio" evidence=IGI;NAS;IMP

GO:0005634 "nucleus" evidence=IC;IDA

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS;IDA

GO:0003677 "DNA binding" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=NAS

GO:0007530 "sex determination" evidence=NAS

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0048813 "dendrite morphogenesis" evidence=IMP

GO:0007219 "Notch signaling pathway" evidence=IGI

GO:0002052 "positive regulation of neuroblast proliferation" evidence=IMP

FB\|FBgn0001168 h "hairy" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

UNIPROTKB\|Q90Z12 hes4-a "Transcription factor HES-4-A" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|G3N2D5 HES1 "Transcription factor HES-1" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3ZBG4 HES1 "Transcription factor HES-1" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q14469 HES1 "Transcription factor HES-1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LM61 HES1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

MGI\|MGI:104853 Hes1 "hairy and enhancer of split 1 (Drosophila)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 61/100 (61%), Positives = 88/100 (88%)

Query:   214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
             +S+KPIMEKRRRARIN  L++LK+LIL+A++KD +RHSKLEKADILEMTVKHL+N+QR Q
Sbjct:    36 KSSKPIMEKRRRARINESLSQLKTLILDALKKDSSRHSKLEKADILEMTVKHLRNLQRAQ 95

Query:   274 LSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEV 313
             ++ A+++DP+VL K+++GF +C  E+ R++S  +G++TEV
Sbjct:    96 MTAALSTDPSVLGKYRAGFSECMNEVTRFLSTCEGVNTEV 135

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO;IGI;IMP;IDA

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

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IDA

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

GO:0001889 "liver development" evidence=IMP

GO:0003143 "embryonic heart tube morphogenesis" evidence=IMP

GO:0003151 "outflow tract morphogenesis" evidence=IMP

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

GO:0003281 "ventricular septum development" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005622 "intracellular" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

GO:0006461 "protein complex assembly" evidence=IDA

GO:0007155 "cell adhesion" evidence=IGI

GO:0007219 "Notch signaling pathway" evidence=ISO;NAS;TAS

GO:0007224 "smoothened signaling pathway" evidence=IDA

GO:0007262 "STAT protein import into nucleus" evidence=IDA

GO:0007389 "pattern specification process" evidence=IGI;IMP

GO:0008134 "transcription factor binding" evidence=NAS

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0016477 "cell migration" evidence=IGI

GO:0021537 "telencephalon development" evidence=IGI;IMP

GO:0021555 "midbrain-hindbrain boundary morphogenesis" evidence=IGI

GO:0021557 "oculomotor nerve development" evidence=IGI

GO:0021558 "trochlear nerve development" evidence=IGI

GO:0021575 "hindbrain morphogenesis" evidence=IGI

GO:0021861 "forebrain radial glial cell differentiation" evidence=ISO

GO:0021915 "neural tube development" evidence=IGI

GO:0021983 "pituitary gland development" evidence=IGI;IMP

GO:0021984 "adenohypophysis development" evidence=IMP

GO:0030324 "lung development" evidence=IMP

GO:0030513 "positive regulation of BMP signaling pathway" evidence=IGI

GO:0030901 "midbrain development" evidence=IGI

GO:0031016 "pancreas development" evidence=IMP

GO:0035019 "somatic stem cell maintenance" evidence=IMP

GO:0035909 "aorta morphogenesis" evidence=IMP

GO:0035910 "ascending aorta morphogenesis" evidence=IMP

GO:0042102 "positive regulation of T cell proliferation" evidence=IMP

GO:0042491 "auditory receptor cell differentiation" evidence=IMP

GO:0042517 "positive regulation of tyrosine phosphorylation of Stat3 protein" evidence=IDA

GO:0042668 "auditory receptor cell fate determination" evidence=IMP

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0042826 "histone deacetylase binding" evidence=ISO

GO:0043388 "positive regulation of DNA binding" evidence=IDA

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

GO:0045165 "cell fate commitment" evidence=IMP

GO:0045596 "negative regulation of cell differentiation" evidence=IMP

GO:0045598 "regulation of fat cell differentiation" evidence=IMP

GO:0045608 "negative regulation of auditory receptor cell differentiation" evidence=IMP

GO:0045665 "negative regulation of neuron differentiation" evidence=IGI;IMP

GO:0045747 "positive regulation of Notch signaling pathway" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISO;IMP

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

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

GO:0045977 "positive regulation of mitotic cell cycle, embryonic" evidence=IMP

GO:0046331 "lateral inhibition" evidence=IMP

GO:0046427 "positive regulation of JAK-STAT cascade" evidence=IDA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0048469 "cell maturation" evidence=IGI

GO:0048505 "regulation of timing of cell differentiation" evidence=IMP

GO:0048538 "thymus development" evidence=IMP

GO:0048667 "cell morphogenesis involved in neuron differentiation" evidence=IGI

GO:0048711 "positive regulation of astrocyte differentiation" evidence=IDA

GO:0048715 "negative regulation of oligodendrocyte differentiation" evidence=IDA

GO:0048844 "artery morphogenesis" evidence=IMP

GO:0050767 "regulation of neurogenesis" evidence=IGI

GO:0060037 "pharyngeal system development" evidence=IMP

GO:0060164 "regulation of timing of neuron differentiation" evidence=IGI;IMP

GO:0060253 "negative regulation of glial cell proliferation" evidence=IDA

GO:0060412 "ventricular septum morphogenesis" evidence=IMP

GO:0060716 "labyrinthine layer blood vessel development" evidence=IMP

GO:0061009 "common bile duct development" evidence=IMP

GO:0061106 "negative regulation of stomach neuroendocrine cell differentiation" evidence=IMP

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

GO:0071820 "N-box binding" evidence=IDA

GO:0090102 "cochlea development" evidence=IGI;IMP

GO:0097084 "vascular smooth muscle cell development" evidence=IMP

GO:0097150 "neuronal stem cell maintenance" evidence=ISO;IMP

GO:2000227 "negative regulation of pancreatic A cell differentiation" evidence=IMP

GO:2000737 "negative regulation of stem cell differentiation" evidence=ISO

GO:2000974 "negative regulation of pro-B cell differentiation" evidence=ISO

GO:2000978 "negative regulation of forebrain neuron differentiation" evidence=ISO

GO:2000981 "negative regulation of inner ear receptor cell differentiation" evidence=IMP

RGD\|62081 Hes1 "hairy and enhancer of split 1 (Drosophila)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 61/100 (61%), Positives = 88/100 (88%)

Query:   214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
             +S+KPIMEKRRRARIN  L++LK+LIL+A++KD +RHSKLEKADILEMTVKHL+N+QR Q
Sbjct:    36 KSSKPIMEKRRRARINESLSQLKTLILDALKKDSSRHSKLEKADILEMTVKHLRNLQRAQ 95

Query:   274 LSVAVASDPTVLQKFKSGFGDCAVEINRYISRLDGLDTEV 313
             ++ A+++DP+VL K+++GF +C  E+ R++S  +G++TEV
Sbjct:    96 MTAALSTDPSVLGKYRAGFSECMNEVTRFLSTCEGVNTEV 135

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO;IDA;IMP

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

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=ISO;ISS

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

GO:0001889 "liver development" evidence=ISO

GO:0003143 "embryonic heart tube morphogenesis" evidence=ISO

GO:0003151 "outflow tract morphogenesis" evidence=ISO

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

GO:0003281 "ventricular septum development" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA;ISO

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

GO:0005515 "protein binding" evidence=IPI

GO:0005622 "intracellular" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO;ISS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005737 "cytoplasm" evidence=ISO

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

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

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

GO:0006461 "protein complex assembly" evidence=ISO;ISS

GO:0007155 "cell adhesion" evidence=ISO

GO:0007219 "Notch signaling pathway" evidence=ISO

GO:0007224 "smoothened signaling pathway" evidence=ISO

GO:0007262 "STAT protein import into nucleus" evidence=ISO;ISS

GO:0007389 "pattern specification process" evidence=ISO

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0016477 "cell migration" evidence=ISO

GO:0021537 "telencephalon development" evidence=ISO

GO:0021555 "midbrain-hindbrain boundary morphogenesis" evidence=ISO

GO:0021557 "oculomotor nerve development" evidence=ISO

GO:0021558 "trochlear nerve development" evidence=ISO

GO:0021575 "hindbrain morphogenesis" evidence=ISO

GO:0021861 "forebrain radial glial cell differentiation" evidence=IDA

GO:0021915 "neural tube development" evidence=ISO

GO:0021983 "pituitary gland development" evidence=ISO

GO:0021984 "adenohypophysis development" evidence=ISO

GO:0030324 "lung development" evidence=ISO

GO:0030513 "positive regulation of BMP signaling pathway" evidence=ISO

GO:0030901 "midbrain development" evidence=ISO

GO:0031016 "pancreas development" evidence=ISO

GO:0035019 "somatic stem cell maintenance" evidence=ISO

GO:0035909 "aorta morphogenesis" evidence=ISO

GO:0035910 "ascending aorta morphogenesis" evidence=ISO

GO:0042102 "positive regulation of T cell proliferation" evidence=ISO

GO:0042491 "auditory receptor cell differentiation" evidence=ISO

GO:0042517 "positive regulation of tyrosine phosphorylation of Stat3 protein" evidence=ISO;ISS

GO:0042668 "auditory receptor cell fate determination" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO;ISS

GO:0042826 "histone deacetylase binding" evidence=ISO

GO:0043388 "positive regulation of DNA binding" evidence=ISO;ISS

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

GO:0045165 "cell fate commitment" evidence=ISO

GO:0045596 "negative regulation of cell differentiation" evidence=ISO

GO:0045598 "regulation of fat cell differentiation" evidence=ISO

GO:0045608 "negative regulation of auditory receptor cell differentiation" evidence=ISO

GO:0045665 "negative regulation of neuron differentiation" evidence=ISO

GO:0045747 "positive regulation of Notch signaling pathway" evidence=ISO

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISO;IDA

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

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

GO:0045977 "positive regulation of mitotic cell cycle, embryonic" evidence=ISO

GO:0046331 "lateral inhibition" evidence=ISO

GO:0046427 "positive regulation of JAK-STAT cascade" evidence=ISO;ISS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0048469 "cell maturation" evidence=ISO

GO:0048505 "regulation of timing of cell differentiation" evidence=ISO

GO:0048538 "thymus development" evidence=ISO

GO:0048667 "cell morphogenesis involved in neuron differentiation" evidence=ISO

GO:0048711 "positive regulation of astrocyte differentiation" evidence=ISO;ISS

GO:0048715 "negative regulation of oligodendrocyte differentiation" evidence=ISO;ISS

GO:0048844 "artery morphogenesis" evidence=ISO

GO:0050767 "regulation of neurogenesis" evidence=ISO

GO:0060037 "pharyngeal system development" evidence=ISO

GO:0060164 "regulation of timing of neuron differentiation" evidence=ISO

GO:0060253 "negative regulation of glial cell proliferation" evidence=ISO;ISS

GO:0060412 "ventricular septum morphogenesis" evidence=ISO

GO:0060716 "labyrinthine layer blood vessel development" evidence=ISO

GO:0061009 "common bile duct development" evidence=ISO

GO:0061106 "negative regulation of stomach neuroendocrine cell differentiation" evidence=ISO

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

GO:0071820 "N-box binding" evidence=ISO;ISS

GO:0090102 "cochlea development" evidence=ISO

GO:0097084 "vascular smooth muscle cell development" evidence=ISO

GO:0097150 "neuronal stem cell maintenance" evidence=ISO;IDA

GO:2000227 "negative regulation of pancreatic A cell differentiation" evidence=ISO

GO:2000737 "negative regulation of stem cell differentiation" evidence=ISO

GO:2000974 "negative regulation of pro-B cell differentiation" evidence=ISO;ISS

GO:2000978 "negative regulation of forebrain neuron differentiation" evidence=IDA

GO:2000981 "negative regulation of inner ear receptor cell differentiation" evidence=ISO

ZFIN\|ZDB-GENE-980526-144 her6 "hairy-related 6" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		314
cd00083		60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-14
pfam00010		52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	1e-13
smart00353		53	smart00353, HLH, helix loop helix domain	2e-11
smart00511		45	smart00511, ORANGE, Orange domain	1e-04
pfam07527		42	pfam07527, Hairy_orange, Hairy Orange	0.001

>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	Back alignment and domain information

 Score = 66.1 bits (162), Expect = 2e-14
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
           +    + E+RRR RIN+  +EL+SL+            KL KA+IL   V +++++Q   
Sbjct: 5   REAHNLRERRRRERINDAFDELRSLLPTL-----PPSKKLSKAEILRKAVDYIKSLQELL 59

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	Back alignment and domain information

>gnl\|CDD\|197674 smart00353, HLH, helix loop helix domain	Back alignment and domain information

>gnl\|CDD\|128787 smart00511, ORANGE, Orange domain	Back alignment and domain information

>gnl\|CDD\|219453 pfam07527, Hairy_orange, Hairy Orange	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		314
KOG4304\|consensus		250		99.98
PF00010		55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.38
cd00083		60	HLH Helix-loop-helix domain, found in specific DNA	99.27
smart00353		53	HLH helix loop helix domain.	99.14
KOG1318\|consensus		411		98.87
KOG3561\|consensus		803		98.64
KOG1319\|consensus		229		98.51
PF07527		43	Hairy_orange: Hairy Orange; InterPro: IPR003650 Th	98.47
smart00511		45	ORANGE Orange domain. This domain confers specific	98.41
KOG3560\|consensus		712		97.37
KOG0561\|consensus		373		97.11
KOG2483\|consensus		232		96.8
KOG3960\|consensus		284		96.72
KOG2588\|consensus		953		96.65
PF07527		43	Hairy_orange: Hairy Orange; InterPro: IPR003650 Th	96.46
smart00511		45	ORANGE Orange domain. This domain confers specific	95.75
KOG4029\|consensus		228		95.46
KOG3910\|consensus		632		94.5
KOG4304\|consensus		250		93.9
PLN03217		93	transcription factor ATBS1; Provisional	93.48
KOG3558\|consensus		768		93.16
KOG3559\|consensus		598		84.37
KOG4395\|consensus		285		81.43

>KOG4304\|consensus	Back alignment and domain information

Probab=99.98  E-value=3.5e-33  Score=260.11  Aligned_cols=108  Identities=49%  Similarity=0.772  Sum_probs=97.5

Q ss_pred             hhHHHHHhhhccchHHHHHHHHHHHhHHHHHHHHHHHHhcCCcccchhhHHHHHHHHHHHHHHHHHhhhhhccc-CChhH
Q psy11625        206 NTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVA-SDPTV  284 (314)
Q Consensus       206 ~~~~~~~RK~~k~liEKRRReRIN~sL~eLk~Llp~~~~~~~~~~sKlEKAdILE~TV~yLk~Lq~qq~~~~~~-~~~~~  284 (314)
                      .....++||++|++||||||||||+||++||.||+++++++..++.||||||||||||+|||+|++.+...... .+...
T Consensus        25 ~~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~~~~~~~~~~~  104 (250)
T KOG4304|consen   25 SSKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQAAAQAAPAALP  104 (250)
T ss_pred             chhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccccccccccccc
Confidence            44667899999999999999999999999999999999999888999999999999999999999887654433 45677


Q ss_pred             HhhHHHHHHHHHHHHhhccccCCCCCCCC
Q psy11625        285 LQKFKSGFGDCAVEINRYISRLDGLDTEV  313 (314)
Q Consensus       285 ~~~f~~Gf~~C~~EV~rFLs~~eg~d~~v  313 (314)
                      ++.|++||++|+.||.+||+.+||+|.++
T Consensus       105 ~d~f~~Gf~ec~~EVsr~ls~~~~~~~~~  133 (250)
T KOG4304|consen  105 VDSFRAGFRECAAEVSRYLSICPGMDAAK  133 (250)
T ss_pred             chhhhccHHHHHHHHHHHHhhCCCCChHH
Confidence            89999999999999999999999999754

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

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

>smart00353 HLH helix loop helix domain	Back alignment and domain information

>KOG1318\|consensus	Back alignment and domain information

>KOG3561\|consensus	Back alignment and domain information

>KOG1319\|consensus	Back alignment and domain information

>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family	Back alignment and domain information

>smart00511 ORANGE Orange domain	Back alignment and domain information

>KOG3560\|consensus	Back alignment and domain information

>KOG0561\|consensus	Back alignment and domain information

>KOG2483\|consensus	Back alignment and domain information

>KOG3960\|consensus	Back alignment and domain information

>KOG2588\|consensus	Back alignment and domain information

>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family	Back alignment and domain information

>smart00511 ORANGE Orange domain	Back alignment and domain information

>KOG4029\|consensus	Back alignment and domain information

>KOG3910\|consensus	Back alignment and domain information

>KOG4304\|consensus	Back alignment and domain information

>PLN03217 transcription factor ATBS1; Provisional	Back alignment and domain information

>KOG3558\|consensus	Back alignment and domain information

>KOG3559\|consensus	Back alignment and domain information

>KOG4395\|consensus	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		314
1a0a_A		63	BHLH, protein (phosphate system positive regulator	3e-10
1an4_A		65	Protein (upstream stimulatory factor); protein-DNA	1e-09
1am9_A		82	Srebp-1A, protein (sterol regulatory element bindi	2e-07
1nkp_B		83	MAX protein, MYC proto-oncogene protein; transcrip	5e-07
1hlo_A		80	Protein (transcription factor MAX); transcriptiona	1e-06
1nkp_A		88	C-MYC, MYC proto-oncogene protein; transcription,	9e-06
1nlw_A		80	MAD protein, MAX dimerizer; transcription factor,	1e-05
4f3l_A		361	Mclock, circadian locomoter output cycles protein	3e-05
2db7_A		64	Hairy/enhancer-OF-split related with YRPW motif 1;	1e-04
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
4f3l_B		387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-04

>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 Length = 63	Back alignment and structure

 Score = 54.4 bits (131), Expect = 3e-10
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQ 272
             E+ RR R+   L+EL SLI     K     +   KA  +E   ++++++Q+ 
Sbjct: 8   HAEQARRNRLAVALHELASLIPAEW-KQQNVSAAPSKATTVEAACRYIRHLQQN 60

PyMOL of 1a0a

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

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

>2db7_A Hairy/enhancer-OF-split related with YRPW motif 1; structural genomics, unknown function, DNA binding protein, NPPSFA; 1.90A {Homo sapiens} SCOP: a.273.1.1 Length = 64	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		314
4h10_A		73	ARYL hydrocarbon receptor nuclear translocator-LI	99.66
1a0a_A		63	BHLH, protein (phosphate system positive regulator	99.66
4h10_B		71	Circadian locomoter output cycles protein kaput; B	99.56
1an4_A		65	Protein (upstream stimulatory factor); protein-DNA	99.45
1am9_A		82	Srebp-1A, protein (sterol regulatory element bindi	99.4
4ati_A		118	MITF, microphthalmia-associated transcription fact	99.34
1hlo_A		80	Protein (transcription factor MAX); transcriptiona	99.22
1nkp_B		83	MAX protein, MYC proto-oncogene protein; transcrip	99.22
4f3l_A		361	Mclock, circadian locomoter output cycles protein	99.11
4f3l_B		387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.11
3u5v_A		76	Protein MAX, transcription factor E2-alpha chimer;	99.06
1nkp_A		88	C-MYC, MYC proto-oncogene protein; transcription,	99.05
1nlw_A		80	MAD protein, MAX dimerizer; transcription factor,	98.79
1mdy_A		68	Protein (MYOD BHLH domain); protein-DNA complex, t	98.59
2ql2_B		60	Neurod1, neurogenic differentiation factor 1; basi	98.57
2lfh_A		68	DNA-binding protein inhibitor ID-3; structural gen	98.38
2db7_A		64	Hairy/enhancer-OF-split related with YRPW motif 1;	98.22
4ath_A		83	MITF, microphthalmia-associated transcription fact	98.03
4aya_A		97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.69
2db7_A		64	Hairy/enhancer-OF-split related with YRPW motif 1;	96.55

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

Probab=99.66  E-value=3.8e-17  Score=126.25  Aligned_cols=58  Identities=31%  Similarity=0.490  Sum_probs=51.7

Q ss_pred             HHHhhhccchHHHHHHHHHHHhHHHHHHHHHHHHhcCCcccchhhHHHHHHHHHHHHHHHHH
Q psy11625        210 IWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQR  271 (314)
Q Consensus       210 ~~~RK~~k~liEKRRReRIN~sL~eLk~Llp~~~~~~~~~~sKlEKAdILE~TV~yLk~Lq~  271 (314)
                      ...||.+|.++|||||+|||++|++|+.|||.+..    ...|+|||+||++||+|||.|+.
T Consensus         6 ~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~----~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            6 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNA----MSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHT----CSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHHHHcccccc----ccccccHHHHHHHHHHHHHHHhc
Confidence            35688899999999999999999999999998753    25799999999999999999853

PyMOL of 4h10

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

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

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

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

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

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

>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*	Back alignment and structure

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

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

>2db7_A Hairy/enhancer-OF-split related with YRPW motif 1; structural genomics, unknown function, DNA binding protein, NPPSFA; 1.90A {Homo sapiens} SCOP: a.273.1.1	Back alignment and structure

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

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

>2db7_A Hairy/enhancer-OF-split related with YRPW motif 1; structural genomics, unknown function, DNA binding protein, NPPSFA; 1.90A {Homo sapiens} SCOP: a.273.1.1	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		314
d1an4a_		65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	3e-13
d1a0aa_		63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-11
d1nkpb_		83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	4e-10
d1am9a_		80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-09
d1nlwa_		79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-07
d1nkpa_		88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	3e-07
d1mdya_		68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	3e-07
d2db7a1		55	a.273.1.1 (A:3-57) Hairy/enhancer-of-split related	1e-05
d1uklc_		61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	7e-05

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65	Back information, alignment and structure


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 = 61.3 bits (149), Expect = 3e-13
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 215 SNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQ 272
           +    +E+RRR +INN + +L  +I ++  +     S   K  IL     ++Q +++ 
Sbjct: 7   AQHNEVERRRRDKINNWIVQLSKIIPDSSMEST--KSGQSKGGILSKASDYIQELRQS 62

PyMOL of d1an4a_

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

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83	Back information, alignment and structure

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

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79	Back information, alignment and structure

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68	Back information, alignment and structure

>d2db7a1 a.273.1.1 (A:3-57) Hairy/enhancer-of-split related with YRPW motif protein 1; HESR-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 55	Back information, alignment and structure

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		314
d1a0aa_		63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.56
d1an4a_		65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.35
d1am9a_		80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.34
d1mdya_		68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.27
d1nkpb_		83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.23
d1nkpa_		88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.19
d1nlwa_		79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.18
d1uklc_		61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.67
d2db7a1		55	Hairy/enhancer-of-split related with YRPW motif pr	98.36
d2db7a1		55	Hairy/enhancer-of-split related with YRPW motif pr	97.61

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

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=99.56  E-value=6.4e-16  Score=113.53  Aligned_cols=59  Identities=24%  Similarity=0.331  Sum_probs=52.1

Q ss_pred             hhhccchHHHHHHHHHHHhHHHHHHHHHHHHhcCCcccchhhHHHHHHHHHHHHHHHHHh
Q psy11625        213 FQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQ  272 (314)
Q Consensus       213 RK~~k~liEKRRReRIN~sL~eLk~Llp~~~~~~~~~~sKlEKAdILE~TV~yLk~Lq~q  272 (314)
                      ||..|.++||+||++||++|++|+.|||.+...+. ...|++||+||++||+||+.|+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~-~~~k~sKa~iL~~Av~yI~~Lq~~   60 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQN-VSAAPSKATTVEAACRYIRHLQQN   60 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSS-CCCCSCTTHHHHHHHHHHHHHHTC
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccC-CcccccHHHHHHHHHHHHHHHHHh
Confidence            57889999999999999999999999998755432 368999999999999999999764

PyMOL of d1a0aa_

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2db7a1 a.273.1.1 (A:3-57) Hairy/enhancer-of-split related with YRPW motif protein 1; HESR-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2db7a1 a.273.1.1 (A:3-57) Hairy/enhancer-of-split related with YRPW motif protein 1; HESR-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure