Citrus Sinensis ID: 048534

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-
Protein Sequence
MSSRRSRSRQSGSSRITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTDTAQAAIIRSLLMQ
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHHHHHHHHcHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mssrrsrsrqsgssritdDQINDLVSKLQQLLPelrnnrsdkvsAGKVLQETCNYIRSLHREVDDLSERLSELLATTDTAQAAIIRSLLMQ
Flexible Loop (DISEMBL)
mssrrsrsrqsgssritddqinDLVSKLQQLLPelrnnrsdkvsagkvLQETCNYIRSLHREVDDLSERLSELLATTDTAQAAIIRSLLMQ
Low Complexity Region (SEG)
MssrrsrsrqsgssrITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTDTAQAAIIRSLLMQ
Disordered region (IsUnstruct)
**********************************************KVLQETCNYIRSLHREVDDLSERLSELLATTDTAQAAII******
Disordered Region (DISOPRED)
********************INDLVSKLQ*********************ETCNYIRSLHREVDDLSERLSELLATTDTAQAAIIRSLLM*
Disordered Region (DISEMBL)
****************TDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTDTAQAAIIRSLLMQ
Disordered Region (DISPRO)
***************ITDDQINDLVSKLQQLLPELRNN**DKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTDTAQ*AIIRSLLMQ
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSSRRSRSRQSGSSRITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYxxxxxxxxxxxxxxxxxxxxxTDTAQAAIIRSLLMQ
Positional Conservation
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	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	91	2.2.26 [Sep-21-2011]
Q9CA64	93	Transcription factor bHLH	no	no	0.835	0.817	0.805	7e-28

>sp|Q9CA64|BH135_ARATH Transcription factor bHLH135 OS=Arabidopsis thaliana GN=BHLH135 PE=1 SV=1

 Score =  122 bits (306), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 62/77 (80%), Positives = 72/77 (93%), Gaps = 1/77 (1%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL 74
          I++DQINDL+ KLQQLLPELR++R SDKVSA +VLQ+TCNYIR+LHREVDDLSERLSELL
Sbjct: 17 ISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL 76

Query: 75 ATTDTAQAAIIRSLLMQ 91
          A +DTAQAA+IRSLL Q
Sbjct: 77 ANSDTAQAALIRSLLTQ 93

Atypical bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo. Promotes the correct definition of the hypophysis cell division plane. Transcriptionally controlled by MONOPTEROS. Probably unable to bind DNA. BHLH135 moves from its site of synthesis in pro-embryos cells into the hypophysis. Regulates brassinosteroid (BR) signaling by sequestering negative BR signaling components. May function as positive regulator of gibberellin signaling.
Arabidopsis thaliana (taxid: 3702)

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	91
351724407	92	uncharacterized protein LOC100527636 [Gl	0.835	0.826	0.934	3e-32
255540973	91	transcription regulator, putative [Ricin	0.835	0.835	0.934	6e-32
388496106	92	unknown [Lotus japonicus]	0.835	0.826	0.921	2e-31
449440772	92	PREDICTED: transcription factor bHLH135-	0.835	0.826	0.907	3e-31
356516770	92	PREDICTED: transcription factor bHLH135-	0.835	0.826	0.907	2e-30
225456723	91	PREDICTED: transcription factor bHLH135	0.835	0.835	0.894	8e-30
388510854	92	unknown [Medicago truncatula]	0.835	0.826	0.881	1e-29
147810883	91	hypothetical protein VITISV_022020 [Viti	0.835	0.835	0.894	1e-29
22331645	92	protein banquo 3 [Arabidopsis thaliana]	1.0	0.989	0.75	2e-29
356550791	91	PREDICTED: transcription factor bHLH135-	0.967	0.967	0.780	2e-29

>gi|351724407|ref|NP_001235265.1| uncharacterized protein LOC100527636 [Glycine max] gi|255632824|gb|ACU16765.1| unknown [Glycine max]

 Score =  142 bits (357), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQINDLVSKLQQLLPE+R+ RSDKVSA KVLQETCNYIRSLHREVDDLSERLSELLA
Sbjct: 17 ITDDQINDLVSKLQQLLPEIRDRRSDKVSASKVLQETCNYIRSLHREVDDLSERLSELLA 76

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTDTAQAAIIR+LLMQ
Sbjct: 77 TTDTAQAAIIRNLLMQ 92

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540973|ref|XP_002511551.1| transcription regulator, putative [Ricinus communis] gi|223550666|gb|EEF52153.1| transcription regulator, putative [Ricinus communis]

 Score =  140 bits (354), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQI DLVSKLQQLLPE+RN RSDKVSA KVLQETCNYIRSLHREVDDLSERLSELLA
Sbjct: 16 ITDDQILDLVSKLQQLLPEIRNRRSDKVSAAKVLQETCNYIRSLHREVDDLSERLSELLA 75

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTDTAQAAIIR+LLMQ
Sbjct: 76 TTDTAQAAIIRNLLMQ 91

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388496106|gb|AFK36119.1| unknown [Lotus japonicus]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 70/76 (92%), Positives = 73/76 (96%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQI+DLVSKLQQLLPE+R  RSDKVSA KVLQETCNYIRSLHREVDDLSERLSELLA
Sbjct: 17 ITDDQIHDLVSKLQQLLPEIRERRSDKVSASKVLQETCNYIRSLHREVDDLSERLSELLA 76

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTDTAQAAIIR+LLMQ
Sbjct: 77 TTDTAQAAIIRNLLMQ 92

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440772|ref|XP_004138158.1| PREDICTED: transcription factor bHLH135-like [Cucumis sativus] gi|449477285|ref|XP_004154981.1| PREDICTED: transcription factor bHLH135-like [Cucumis sativus]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 74/76 (97%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQINDLVSKLQQLLPE+R+ +SDKVSA KVLQETCNYIR+LHREVDDLSERLSELLA
Sbjct: 17 ITDDQINDLVSKLQQLLPEIRHRQSDKVSASKVLQETCNYIRNLHREVDDLSERLSELLA 76

Query: 76 TTDTAQAAIIRSLLMQ 91
          T+DTAQAAIIRSLLMQ
Sbjct: 77 TSDTAQAAIIRSLLMQ 92

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516770|ref|XP_003527066.1| PREDICTED: transcription factor bHLH135-like [Glycine max]

 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 72/76 (94%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQINDLVSKLQQLLPE+R+ RSDKVSA KVLQETCNYIRSLHREV DLSERLSELL 
Sbjct: 17 ITDDQINDLVSKLQQLLPEIRDRRSDKVSASKVLQETCNYIRSLHREVGDLSERLSELLD 76

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTDTAQAAIIR+LLMQ
Sbjct: 77 TTDTAQAAIIRNLLMQ 92

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225456723|ref|XP_002274840.1| PREDICTED: transcription factor bHLH135 [Vitis vinifera] gi|297734002|emb|CBI15249.3| unnamed protein product [Vitis vinifera]

 Score =  134 bits (337), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 68/76 (89%), Positives = 71/76 (93%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQINDLVSKLQQLLPE+R   SDKVSA KVLQETCNYIRSL+REVDDLSERLSELLA
Sbjct: 16 ITDDQINDLVSKLQQLLPEIRGRHSDKVSAAKVLQETCNYIRSLNREVDDLSERLSELLA 75

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTD+AQAAIIRSLL Q
Sbjct: 76 TTDSAQAAIIRSLLTQ 91

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510854|gb|AFK43493.1| unknown [Medicago truncatula]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 73/76 (96%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQI+DLVSKLQQLLPE+RN  SDKVSA +VLQETCNYIR+L+REVDDLSERLSELLA
Sbjct: 17 ITDDQIHDLVSKLQQLLPEIRNRSSDKVSASRVLQETCNYIRNLNREVDDLSERLSELLA 76

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTDTAQAAIIR+LLMQ
Sbjct: 77 TTDTAQAAIIRNLLMQ 92

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147810883|emb|CAN67278.1| hypothetical protein VITISV_022020 [Vitis vinifera]

 Score =  133 bits (334), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 68/76 (89%), Positives = 70/76 (92%)

Query: 16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
          ITDDQINDLVSKLQQLLPE+R   SDKVSA KVLQETCNYIRSL+REVDDLSERLSELLA
Sbjct: 16 ITDDQINDLVSKLQQLLPEIRGRHSDKVSAAKVLQETCNYIRSLNREVDDLSERLSELLA 75

Query: 76 TTDTAQAAIIRSLLMQ 91
          TTD AQAAIIRSLL Q
Sbjct: 76 TTDXAQAAIIRSLLTQ 91

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22331645|ref|NP_190355.2| protein banquo 3 [Arabidopsis thaliana] gi|332644800|gb|AEE78321.1| protein banquo 3 [Arabidopsis thaliana]

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 69/92 (75%), Positives = 83/92 (90%), Gaps = 1/92 (1%)

Query: 1  MSSRRSRSRQSGSSRITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSL 59
          MSSR+SRSRQ+G+S ITD+QINDLV +L +LLPEL NNR S KVSA +VLQETC+YIR+L
Sbjct: 1  MSSRKSRSRQTGASMITDEQINDLVLQLHRLLPELANNRRSGKVSASRVLQETCSYIRNL 60

Query: 60 HREVDDLSERLSELLATTDTAQAAIIRSLLMQ 91
           +EVDDLSERLS+LL +TD+AQAA+IRSLLMQ
Sbjct: 61 SKEVDDLSERLSQLLESTDSAQAALIRSLLMQ 92

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550791|ref|XP_003543767.1| PREDICTED: transcription factor bHLH135-like [Glycine max]

 Score =  132 bits (332), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 71/91 (78%), Positives = 82/91 (90%), Gaps = 3/91 (3%)

Query: 1  MSSRRSRSRQSGSSRITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLH 60
          MSSRRSR +QS S+RI+DDQI DLVSKL+QL+PE+R+ RSDKVSA KVLQETCNYIRSLH
Sbjct: 1  MSSRRSR-QQSASTRISDDQIIDLVSKLRQLVPEIRDRRSDKVSASKVLQETCNYIRSLH 59

Query: 61 REVDDLSERLSELLAT--TDTAQAAIIRSLL 89
          REVDDLSERLS+LLAT   D+ +AAIIRSL+
Sbjct: 60 REVDDLSERLSQLLATIDADSPEAAIIRSLI 90

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	91
TAIR|locus:2019210	93	BS1 "AT1G74500" [Arabidopsis t	0.835	0.817	0.805	5.7e-27
TAIR|locus:1005716685	94	KDR "KIDARI" [Arabidopsis thal	0.813	0.787	0.815	2.5e-26
TAIR|locus:2100342	92	BNQ3 "AT3G47710" [Arabidopsis	0.835	0.826	0.753	3.3e-24
TAIR|locus:1006230235	92	PRE5 "Paclobutrazol Resistance	0.824	0.815	0.692	1.5e-21
TAIR|locus:2178002	92	PRE1 "AT5G39860" [Arabidopsis	0.824	0.815	0.666	1e-20
TAIR|locus:2150916	94	BNQ2 "AT5G15160" [Arabidopsis	0.813	0.787	0.636	4.4e-20

TAIR|locus:2019210 BS1 "AT1G74500" [Arabidopsis thaliana (taxid:3702)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 62/77 (80%), Positives = 72/77 (93%)

Query:    16 ITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL 74
             I++DQINDL+ KLQQLLPELR++R SDKVSA +VLQ+TCNYIR+LHREVDDLSERLSELL
Sbjct:    17 ISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL 76

Query:    75 ATTDTAQAAIIRSLLMQ 91
             A +DTAQAA+IRSLL Q
Sbjct:    77 ANSDTAQAALIRSLLTQ 93

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009742 "brassinosteroid mediated signaling pathway" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0010086 "embryonic root morphogenesis" evidence=IMP

TAIR|locus:1005716685 KDR "KIDARI" [Arabidopsis thaliana (taxid:3702)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 62/76 (81%), Positives = 70/76 (92%)

Query:    16 ITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLA 75
             I+DDQI+DLVSKLQ L+PELR  RSDKVSA KVLQETCNYIR+LHREVDDLS+RLSELLA
Sbjct:    17 ISDDQISDLVSKLQHLIPELRRRRSDKVSASKVLQETCNYIRNLHREVDDLSDRLSELLA 76

Query:    76 TTD--TAQAAIIRSLL 89
             +TD  +A+AAIIRSLL
Sbjct:    77 STDDNSAEAAIIRSLL 92

GO:0005634 "nucleus" evidence=ISM

GO:0009416 "response to light stimulus" evidence=IMP

TAIR|locus:2100342 BNQ3 "AT3G47710" [Arabidopsis thaliana (taxid:3702)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 58/77 (75%), Positives = 69/77 (89%)

Query:    16 ITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL 74
             ITD+QINDLV +L +LLPEL NNR S KVSA +VLQETC+YIR+L +EVDDLSERLS+LL
Sbjct:    16 ITDEQINDLVLQLHRLLPELANNRRSGKVSASRVLQETCSYIRNLSKEVDDLSERLSQLL 75

Query:    75 ATTDTAQAAIIRSLLMQ 91
              +TD+AQAA+IRSLLMQ
Sbjct:    76 ESTDSAQAALIRSLLMQ 92

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0009640 "photomorphogenesis" evidence=IMP

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

TAIR|locus:1006230235 PRE5 "Paclobutrazol Resistance 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 54/78 (69%), Positives = 65/78 (83%)

Query:    16 ITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL 74
             I+DDQ+ DLVSKL+Q LPE+   R SDKVSA KVLQETCNYIR LHREVD+LS+RLS+LL
Sbjct:    15 ISDDQMIDLVSKLRQFLPEIHERRRSDKVSASKVLQETCNYIRKLHREVDNLSDRLSQLL 74

Query:    75 ATTD--TAQAAIIRSLLM 90
              + D  + +AA+IRSLLM
Sbjct:    75 DSVDEDSPEAAVIRSLLM 92

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2178002 PRE1 "AT5G39860" [Arabidopsis thaliana (taxid:3702)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 52/78 (66%), Positives = 67/78 (85%)

Query:    16 ITDDQINDLVSKLQQLLPEL-RNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL 74
             I+D+Q+ DLVSKL+Q+LPE+ +  RSDK SA KVLQETCNYIR+L+REVD+LSERLS+LL
Sbjct:    15 ISDNQMIDLVSKLRQILPEIGQRRRSDKASASKVLQETCNYIRNLNREVDNLSERLSQLL 74

Query:    75 ATTD--TAQAAIIRSLLM 90
              + D  + +AA+IRSLLM
Sbjct:    75 ESVDEDSPEAAVIRSLLM 92

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0009741 "response to brassinosteroid stimulus" evidence=IEP

GO:0009826 "unidimensional cell growth" evidence=IMP

GO:0009640 "photomorphogenesis" evidence=IMP

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

TAIR|locus:2150916 BNQ2 "AT5G15160" [Arabidopsis thaliana (taxid:3702)]

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 49/77 (63%), Positives = 65/77 (84%)

Query:    16 ITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL 74
             I+DDQI DL+SKL+Q +PE+R NR S+ VSA KVLQETCNYIR+L++E DDLS+RL++LL
Sbjct:    16 ISDDQITDLISKLRQSIPEIRQNRRSNTVSASKVLQETCNYIRNLNKEADDLSDRLTQLL 75

Query:    75 ATTD--TAQAAIIRSLL 89
              + D  + QAA+IRSL+
Sbjct:    76 ESIDPNSPQAAVIRSLI 92


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.315   0.129   0.335    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       91        77   0.00091  102 3  10 22  0.37    29
                                                     29  0.50    29


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  509 (54 KB)
  Total size of DFA:  103 KB (2072 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  16.44u 0.14s 16.58t   Elapsed:  00:00:01
  Total cpu time:  16.44u 0.14s 16.58t   Elapsed:  00:00:01
  Start:  Sat May 11 06:14:51 2013   End:  Sat May 11 06:14:52 2013

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0005773 "vacuole" evidence=IDA

GO:0009640 "photomorphogenesis" evidence=IMP

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

---

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)
Q9CA64	BH135_ARATH	No assigned EC number	0.8051	0.8351	0.8172	no	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	91
PLN03217	93	PLN03217, PLN03217, transcription factor ATBS1; Pr	4e-28
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	0.004

>gnl|CDD|178756 PLN03217, PLN03217, transcription factor ATBS1; Provisional

 Score = 96.8 bits (240), Expect = 4e-28
 Identities = 75/93 (80%), Positives = 86/93 (92%), Gaps = 2/93 (2%)

Query: 1  MSSRRSRSRQS-GSSRITDDQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRS 58
          MS RRSRSRQS G+SRI++DQINDL+ KLQQLLPELR++R SDKVSA +VLQ+TCNYIR+
Sbjct: 1  MSGRRSRSRQSSGTSRISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRN 60

Query: 59 LHREVDDLSERLSELLATTDTAQAAIIRSLLMQ 91
          LHREVDDLSERLSELLA +DTAQAA+IRSLL Q
Sbjct: 61 LHREVDDLSERLSELLANSDTAQAALIRSLLTQ 93

Length = 93

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

 Score = 32.0 bits (74), Expect = 0.004
 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLH 60
          D+IND   +L++LLP   N +  K     +L+    YI+ L 
Sbjct: 14 DRINDAFEELRELLPTPPNKKLSKAE---ILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	91
PLN03217	93	transcription factor ATBS1; Provisional	100.0
smart00353	53	HLH helix loop helix domain.	98.56
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	98.48
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	98.45
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	95.98
KOG1318	411	consensus Helix loop helix transcription factor EB	95.35
PF07606	152	DUF1569: Protein of unknown function (DUF1569); In	80.24

>PLN03217 transcription factor ATBS1; Provisional

Probab=100.00  E-value=2.1e-53  Score=293.39  Aligned_cols=91  Identities=81%  Similarity=1.122  Sum_probs=87.7

Q ss_pred             CCCcccccc-CCCCCCCCHHHHHHHHHHHHHhchhhhh-ccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 048534            1 MSSRRSRSR-QSGSSRITDDQINDLVSKLQQLLPELRN-NRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTD   78 (91)
Q Consensus         1 MSsrrsrs~-~~~~s~isddqi~dLvsKLQaLLPe~~~-r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s~D   78 (91)
                      |||||||++ ++++++||||||+|||+|||+|||++++ |+++++||+|||||||||||+||||||||||||+|||++.|
T Consensus         1 MSsRRSrsrq~s~s~risddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t~~   80 (93)
T PLN03217          1 MSGRRSRSRQSSGTSRISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLANSD   80 (93)
T ss_pred             CCcccccccccCCCCCCCHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            999999998 4688999999999999999999999986 88999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHhcC
Q 048534           79 TAQAAIIRSLLMQ   91 (91)
Q Consensus        79 ~~~a~iiRsLL~~   91 (91)
                      .|+|+||||||||
T Consensus        81 s~~a~iIRSlL~~   93 (93)
T PLN03217         81 TAQAALIRSLLTQ   93 (93)
T ss_pred             CchHHHHHHHhcC
Confidence            9999999999997

>smart00353 HLH helix loop helix domain

Probab=98.56  E-value=1.9e-07  Score=54.26  Aligned_cols=44  Identities=34%  Similarity=0.619  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      ++||+.+..|+.++|...  .+.+.+-+-||++||+||+.|+.+++
T Consensus         9 ~~~n~~~~~L~~lip~~~--~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        9 RKINEAFDELRSLLPTLP--NNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             HHHHHHHHHHHHHCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            689999999999999875  45677888999999999999999986

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

Probab=98.48  E-value=3.8e-07  Score=53.45  Aligned_cols=44  Identities=36%  Similarity=0.657  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      ++||+.+..|+.++|...  .+.+.+-+.||+.||+||+.|+.+++
T Consensus        17 ~~~n~~~~~L~~llp~~~--~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083          17 ERINDAFDELRSLLPTLP--PSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHHHHHHHHHCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            789999999999999986  55678889999999999999998863

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

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

Probab=98.45  E-value=5.1e-07  Score=53.50  Aligned_cols=42  Identities=38%  Similarity=0.652  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLH   60 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~Lh   60 (91)
                      +.||+.+..|+.+||........+.+-+.||+.||+||+.|+
T Consensus        14 ~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen   14 DRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            689999999999999954455667899999999999999986

; 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 ....

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=95.98  E-value=0.02  Score=45.27  Aligned_cols=58  Identities=33%  Similarity=0.452  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHhchhhhhcc-C-CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 048534           19 DQINDLVSKLQQLLPELRNNR-S-DKVSAGKVLQETCNYIRSLHREVDDLSERLSELLAT   76 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~-~-~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s   76 (91)
                      |-|+.=-+-||.|+|.-...- + -|.|-+-|||.||.||--||.|..+--+-+++|=+.
T Consensus        75 dAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~  134 (229)
T KOG1319|consen   75 DAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKD  134 (229)
T ss_pred             HHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346666677999999986443 2 388999999999999999999999999999998654

>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]

Probab=95.35  E-value=0.03  Score=47.01  Aligned_cols=52  Identities=31%  Similarity=0.601  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLS   71 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs   71 (91)
                      +-||+-|-+|-.|||..+--. .+..-.-||+-+|.|||.||++-....|...
T Consensus       246 ~nIN~~IkeLg~liP~~~~~~-~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~  297 (411)
T KOG1318|consen  246 ENINDRIKELGQLIPKCNSED-MKSNKGTILKASCDYIRELQQTLQRARELEN  297 (411)
T ss_pred             HHHHHHHHHHHHhCCCCCcch-hhcccchhhHHHHHHHHHHHHHHHHHHHHHh
Confidence            679999999999999985222 2222456999999999999998876666443

>PF07606 DUF1569: Protein of unknown function (DUF1569); InterPro: IPR011463 This entry represents a family of hypothetical proteins identified in Rhodopirellula baltica and other bacteria

Probab=80.24  E-value=3.9  Score=29.02  Aligned_cols=47  Identities=21%  Similarity=0.487  Sum_probs=37.0

Q ss_pred             CCCccccccCCCCCCCCHHHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHH
Q 048534            1 MSSRRSRSRQSGSSRITDDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIR   57 (91)
Q Consensus         1 MSsrrsrs~~~~~s~isddqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr   57 (91)
                      |+.||.         ++-+-++|++.+|+.|.|+. .+.-.+-|++.+|.--|..|+
T Consensus         1 ~~~~r~---------l~f~~l~e~~~ri~~L~~~~-~~~wGkms~~Qml~Hc~~~~~   47 (152)
T PF07606_consen    1 MSDRRE---------LQFEDLDEIINRINRLTPDT-QPQWGKMSVSQMLAHCAQSIE   47 (152)
T ss_pred             CCcccc---------CcccCHHHHHHHHHHhCcCC-CCCcCCcCHHHHHHHHHHHHH
Confidence            676764         67777899999999999975 444578899999987766665

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	91
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	5e-05
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-04
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	6e-04
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	7e-04

>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 = 37.3 bits (87), Expect = 5e-05
 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL 73
          D I D    L+  +P L+  ++ +     +L +   YI+ + R+     + + +L
Sbjct: 25 DHIKDSFHSLRDSVPSLQGEKASRAQ---ILDKATEYIQYMRRKNHTHQQDIDDL 76

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

 Score = 36.1 bits (83), Expect = 5e-04
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 5/61 (8%)

Query: 2  SSRRSRSRQSGSSRITDDQINDLVSKLQQLLPELRNNRS--DKVSAGKVLQETCNYIRSL 59
            + +R   S   +   D++N  + +L  L+P         DK++   VL+    ++++L
Sbjct: 9  RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLT---VLRMAVQHMKTL 65

Query: 60 H 60
           
Sbjct: 66 R 66

>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 = 34.3 bits (79), Expect = 6e-04
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 4/64 (6%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTD 78
            IND + +L+ L+         K++   VL++  +YIR L      L +    L     
Sbjct: 19 SSINDKIIELKDLVVGTEA----KLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVH 74

Query: 79 TAQA 82
           +++
Sbjct: 75 KSKS 78

>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 = 34.3 bits (79), Expect = 7e-04
 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL 73
          D I D    L+  +P L+  ++ +     +L +   YI+ + R+     + + +L
Sbjct: 15 DHIKDSFHSLRDSVPSLQGEKASRAQ---ILDKATEYIQYMRRKNHTHQQDIDDL 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	91
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	98.66
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	98.64
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	98.56
1a0a_A	63	BHLH, protein (phosphate system positive regulator	98.42
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	98.22
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	98.1
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	98.05
4h10_B	71	Circadian locomoter output cycles protein kaput; B	97.98
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	97.98
4ati_A	118	MITF, microphthalmia-associated transcription fact	97.97
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.41
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	97.21
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	97.1
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	96.74
4f3l_A	361	Mclock, circadian locomoter output cycles protein	96.51
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	96.25
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	95.81
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	95.09
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	81.73
3coq_A	89	Regulatory protein GAL4; helix bundle, protein-DNA	80.93

>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=98.66  E-value=7.6e-08  Score=61.86  Aligned_cols=54  Identities=26%  Similarity=0.386  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLAT   76 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s   76 (91)
                      +.||+.+..|+.++|..    +.+.+-+-||++|+.||+.|+.+|..|.+...+|=..
T Consensus        19 ~~in~~f~~L~~lvP~~----~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   72 (82)
T 1am9_A           19 SSINDKIIELKDLVVGT----EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (82)
T ss_dssp             HHHHHHHHHHHHHHTCS----SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999999973    4688889999999999999999999999988877543

>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=98.64  E-value=1.1e-07  Score=60.37  Aligned_cols=52  Identities=25%  Similarity=0.523  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL   73 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~L   73 (91)
                      +.||+.+..|+.++|...   +.+.|=+.||+.|+.||+.|+.++..|.+.+.+|
T Consensus        25 ~~in~~f~~Lr~lvP~~~---~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           25 DHIKDSFHSLRDSVPSLQ---GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHSGGGT---TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHCcCCC---CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999999875   3578889999999999999999999999988766

>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=98.56  E-value=2.9e-07  Score=58.42  Aligned_cols=53  Identities=25%  Similarity=0.500  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL   74 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll   74 (91)
                      +.||+.+..|+.++|...   +.+.|-+.||+.|++||+.|+.++..|.+.+.+|-
T Consensus        15 ~~in~~f~~Lr~lvP~~~---~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~   67 (83)
T 1nkp_B           15 DHIKDSFHSLRDSVPSLQ---GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHTTSGGGT---TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999875   46788899999999999999987777776665553

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

Probab=98.42  E-value=2e-07  Score=57.94  Aligned_cols=46  Identities=22%  Similarity=0.443  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHhchhhhhcc--CCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNR--SDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~--~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      +-||+.+..|+.|||......  +.+.|=+-+|+.||.||+.|++||.
T Consensus        15 ~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A           15 NRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             HHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            579999999999999986443  5677889999999999999999874

>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=98.22  E-value=2.1e-07  Score=56.77  Aligned_cols=46  Identities=24%  Similarity=0.520  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHhchhhhhcc-CCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNR-SDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~-~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      +.||+.+..|+.|+|...... ..+.+-+-||++||.||+.|+.|+.
T Consensus        18 ~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A           18 DKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             HHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            689999999999999986432 3467888899999999999998863

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

Probab=98.10  E-value=1e-05  Score=52.19  Aligned_cols=53  Identities=17%  Similarity=0.194  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL   73 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~L   73 (91)
                      +.|++.+.+|..++|.+.  .+.+.|-..||+.||.||+.|+.+...|.+...+|
T Consensus        14 ~~lk~~f~~Lr~~vP~~~--~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L   66 (80)
T 1nlw_A           14 AHLRLSLEKLKGLVPLGP--DSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (80)
T ss_dssp             HHHHHHHHHHHHSSCCCS--SSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999873  24567777999999999999999998887766554

>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=98.05  E-value=1.9e-05  Score=51.48  Aligned_cols=53  Identities=25%  Similarity=0.376  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL   73 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~L   73 (91)
                      +.||+-+..|+.++|.+..  +.+.|=+.||+.|+.||+.|+.+...+.+-..+|
T Consensus        19 ~~ln~~f~~Lr~~vP~~~~--~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L   71 (88)
T 1nkp_A           19 NELKRSFFALRDQIPELEN--NEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHTTCGGGTT--CTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6799999999999998853  4578888999999999999999988776554443

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

Probab=97.98  E-value=1.3e-05  Score=51.54  Aligned_cols=44  Identities=30%  Similarity=0.474  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDL   66 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddL   66 (91)
                      +.||+-+..|+.|+|.    .+.+..=+-||+.||.||+.|+.++.=|
T Consensus        21 d~IN~~i~eL~~LvP~----~~~K~dK~sIL~~aI~yik~Lq~~~~~~   64 (71)
T 4h10_B           21 DQFNVLIKELGSMLPG----NARKMDKSTVLQKSIDFLRKHKEITAWL   64 (71)
T ss_dssp             HHHHHHHHHHHTTSSS----CCSCCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCC----CCCCCcHHHHHHHHHHHHHHHHHhhhHH
Confidence            7899999999999994    3457777889999999999999998643

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

Probab=97.98  E-value=1.2e-05  Score=51.81  Aligned_cols=46  Identities=24%  Similarity=0.314  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcc-hHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKV-SAGKVLQETCNYIRSLHREVDDL   66 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~-SaskvLqETC~YIr~LhrEVddL   66 (91)
                      +.||+-+..|+.++|...  .+++. |-..||+.||.||+.|+++|.++
T Consensus        18 ~~IN~~f~~Lr~~vP~~~--~~~K~~sK~~IL~~AieYI~~Lq~~l~e~   64 (76)
T 3u5v_A           18 RDINEAFRELGRMCQMHL--KSDKAQTKLLILQQAVQVILGLEQQVRER   64 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHH--CCCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCCC--CccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999753  23444 67789999999999999999864

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

Probab=97.97  E-value=1.4e-05  Score=54.45  Aligned_cols=50  Identities=28%  Similarity=0.499  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSER   69 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeR   69 (91)
                      +.||+-+..|+.|+|..... ..+.+=+-||+.|+.||+.|+.++..|.+-
T Consensus        40 ~~In~~~~~L~~lvP~~~~~-~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           40 FNINDRIKELGTLIPKSNDP-DMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             HHHHHHHHHHHHHSCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhccCc-cccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57999999999999988532 236677889999999999999999999864

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

Probab=97.41  E-value=0.00042  Score=46.21  Aligned_cols=53  Identities=26%  Similarity=0.461  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSE   72 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~   72 (91)
                      +-||+=|..|-.|+|..+.. ..+.+=+-||+-||.||+.|+.|+..+.|...+
T Consensus         5 ~nIN~~I~EL~~LiP~~~~~-~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r   57 (83)
T 4ath_A            5 FNINDRIKELGTLIPKSNDP-DMRWNKGTILKASVDYIRKLQREQQRAKDLENR   57 (83)
T ss_dssp             HHHHHHHHHHHHHSCCCCCT-TCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred             hhHHHhhhhhhccCCCCCCc-ccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45999999999999987432 346677889999999999999999988876653

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

Probab=97.21  E-value=0.00056  Score=43.66  Aligned_cols=42  Identities=24%  Similarity=0.421  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHR   61 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~Lhr   61 (91)
                      +.||+-+..|+.|+|.... ..++..=+-||+.|..||+.|+-
T Consensus        22 ~rIN~~l~eL~~LvP~~~~-~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           22 DKMNSFIDELASLVPTCNA-MSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHSHHHHT-CSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHcccccc-ccccccHHHHHHHHHHHHHHHhc
Confidence            7899999999999998753 34677888999999999999863

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

Probab=97.10  E-value=0.00079  Score=41.41  Aligned_cols=44  Identities=23%  Similarity=0.379  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      .+||+-...|+.++|...  .+.|.|=..+|+.+.+||..|+.-++
T Consensus        15 ~~iN~af~~LR~~lP~~~--~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B           15 HGLNAALDNLRKVVPCYS--KTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHTSSSCC--SSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHccCCC--CcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            579999999999999874  35678888999999999999987654

>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=96.74  E-value=0.0016  Score=41.01  Aligned_cols=43  Identities=14%  Similarity=0.315  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      ..||+-...|+.++|...   +.+.|=..+|+.+.+||..|+.-++
T Consensus        25 ~~iN~af~~LR~~iP~~~---~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           25 SKVNEAFETLKRSTSSNP---NQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHTTSCSCT---TSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCCCC---CCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            579999999999999753   4688889999999999999997654

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

Probab=96.51  E-value=0.0035  Score=46.65  Aligned_cols=40  Identities=30%  Similarity=0.554  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHH
Q 048534           18 DDQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHR   61 (91)
Q Consensus        18 ddqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~Lhr   61 (91)
                      -|+||+.+..|..|||.    ..+|..=+-||+.||+|||.++.
T Consensus        24 r~~~n~~~~~l~~~~p~----~~~~~dk~~il~~~~~~~~~~~~   63 (361)
T 4f3l_A           24 RDQFNVLIKELGSMLPG----NARKMDKSTVLQKSIDFLRKHKE   63 (361)
T ss_dssp             HHHHHHHHHHHHHTCCS----SSCCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCC----CCCCcCHHHHHHHHHHHHHHHHh
Confidence            38999999999999993    23466666799999999999873

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

Probab=96.25  E-value=0.0066  Score=39.16  Aligned_cols=41  Identities=32%  Similarity=0.555  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHR   61 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~Lhr   61 (91)
                      ..+|+-..+|+.++|...  .+.|.|=-++||-+.+||.-|+.
T Consensus        27 ~~lN~aF~~LR~~VP~~p--~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           27 DDMNHCYSRLRELVPGVP--RGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             SHHHHHHHHHHHHCCCCC--TTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCCC--CCCCccHHHHHHHHHHHHHHHHc
Confidence            579999999999999984  34678888999999999999873

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

Probab=95.81  E-value=0.013  Score=44.22  Aligned_cols=42  Identities=24%  Similarity=0.421  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHR   61 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~Lhr   61 (91)
                      |+||+.+..|..|||..+. ...|..=+-||+.||+|||.|+.
T Consensus        26 ~~~n~~~~~L~~l~p~~~~-~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           26 DKMNSFIDELASLVPTCNA-MSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             HHHHHHHHHHHHHCHHHHH-CSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhcCCCCc-cccccCHHHHHHHHHHHHHHhhc
Confidence            7899999999999998742 34566677899999999999874

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

Probab=95.09  E-value=0.046  Score=37.08  Aligned_cols=42  Identities=38%  Similarity=0.605  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           21 INDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        21 i~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      +|+-..+|+..+|...  .+.|.|=-++|+-+.+||..|+.-++
T Consensus        40 lN~AF~~LR~~vP~~p--~~kKLSKIETLRlAi~YI~~Lq~~L~   81 (97)
T 4aya_A           40 MNDCYSKLKELVPSIP--QNKKVSKMEILQHVIDYILDLQIALD   81 (97)
T ss_dssp             HHHHHHHHHHHCTTSC--SSSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCC--CCCcccHHHHHHHHHHHHHHHHHHHh
Confidence            8999999999999874  34577778999999999998876554

>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=81.73  E-value=1.1  Score=28.73  Aligned_cols=26  Identities=38%  Similarity=0.704  Sum_probs=23.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHhchhhh
Q 048534           11 SGSSRITDDQINDLVSKLQQLLPELR   36 (91)
Q Consensus        11 ~~~s~isddqi~dLvsKLQaLLPe~~   36 (91)
                      +|++.+++-++..+|+.++.|+|++.
T Consensus         3 ~~~~~~~~~~l~s~I~qV~DLfPdLG   28 (71)
T 2di0_A            3 SGSSGMCGVELDSLISQVKDLLPDLG   28 (71)
T ss_dssp             CCCSCCSSHHHHHHHHHHHHHCCSSC
T ss_pred             CCCCCCcHHHHHHHHHHHHHHcccCC
Confidence            46778999999999999999999994

>3coq_A Regulatory protein GAL4; helix bundle, protein-DNA complex; HET: DNA; 2.40A {Saccharomyces cerevisiae} SCOP: g.38.1.1 h.1.3.1

Probab=80.93  E-value=2.4  Score=25.28  Aligned_cols=37  Identities=14%  Similarity=0.234  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCh------hHHHHHHHHhc
Q 048534           54 NYIRSLHREVDDLSERLSELLATTDT------AQAAIIRSLLM   90 (91)
Q Consensus        54 ~YIr~LhrEVddLSeRLs~Ll~s~D~------~~a~iiRsLL~   90 (91)
                      .||..|+..|+.|-..|.+|....|.      +..+-|+..|.
T Consensus        45 ~~~~~L~~r~~~le~~l~~l~~~~~l~~~~~~~s~~~i~~~l~   87 (89)
T 3coq_A           45 AHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLT   87 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSSCHHHHHHCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCchhhHHhhcCCCHHHHHHHHh
Confidence            48999999999999999999888776      33455555543

---

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	91
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	2e-04
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	0.002
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	0.002
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	0.003

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

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

 Score = 33.9 bits (78), Expect = 2e-04
 Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL 73
            IND + +L+ L+         K+    VL++  +YI+ L +    L +    L
Sbjct: 2  SSINDKIIELKDLVM----GTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVL 52

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

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

 Score = 32.1 bits (73), Expect = 0.002
 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL 73
          D I D    L+  +P L+  ++ +     +L +   YI+ + R+     + + +L
Sbjct: 15 DHIKDSFHSLRDSVPSLQGEKASRAQ---ILDKATEYIQYMRRKNHTHQQDIDDL 66

>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 = 31.8 bits (72), Expect = 0.002
 Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 2/47 (4%)

Query: 19 DQINDLVSKLQQLLPEL--RNNRSDKVSAGKVLQETCNYIRSLHREV 63
          +++   + +L  L+P    + N S   S    ++  C YIR L +  
Sbjct: 15 NRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

>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 = 31.4 bits (71), Expect = 0.003
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSEL 73
          +++      L+  +PEL NN   K     +L++   YI S+  E   L      L
Sbjct: 19 NELKRSFFALRDQIPELENNE--KAPKVVILKKATAYILSVQAEEQKLISEEDLL 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	91
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.59
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	98.54
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	98.45
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	98.41
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	98.38
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	98.36
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	97.52

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

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

Probab=98.59  E-value=2.9e-08  Score=59.34  Aligned_cols=52  Identities=25%  Similarity=0.350  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELL   74 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll   74 (91)
                      +.||+.+..|+.++|..    ..+.+-+-||++|+.||+.|+.+|..|.+-..+|=
T Consensus         2 ~~in~~f~~L~~lvP~~----~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           2 SSINDKIIELKDLVMGT----DAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCHHHHHHHHHHHHSCS----SCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHhhCCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999999954    24667788999999999999999999998777663

>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=98.54  E-value=1.4e-07  Score=58.73  Aligned_cols=58  Identities=22%  Similarity=0.342  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTD   78 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s~D   78 (91)
                      +.||+.+..|+.+||....  +.+.|=+.||+.||.||+.|+.+++.|.+...+|-...+
T Consensus        19 ~~in~~f~~Lr~llP~~~~--~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~   76 (88)
T d1nkpa_          19 NELKRSFFALRDQIPELEN--NEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRRE   76 (88)
T ss_dssp             HHHHHHHHHHHTTCGGGTT--CTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999998743  246778889999999999999999999988887765544

>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=98.48  E-value=2.3e-07  Score=57.31  Aligned_cols=54  Identities=26%  Similarity=0.386  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLAT   76 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s   76 (91)
                      +.||+.+..|+.|+|..    ..+.+=+-||++|++||+.|+++++.|.+...+|-..
T Consensus        19 ~~in~~~~~L~~llP~~----~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~   72 (80)
T d1am9a_          19 SSINDKIIELKDLVVGT----EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (80)
T ss_dssp             HHHHHHHHHHHHHHTCS----SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999963    3466778899999999999999999999888776443

>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=98.45  E-value=3e-07  Score=56.24  Aligned_cols=56  Identities=16%  Similarity=0.185  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLAT   76 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s   76 (91)
                      +.||+.+..|..+||....  +.+.|-+-||++|++||+.|+.++..+.+...+|...
T Consensus        14 ~~in~~f~~L~~llP~~~~--~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~   69 (79)
T d1nlwa_          14 AHLRLSLEKLKGLVPLGPD--SSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQRE   69 (79)
T ss_dssp             HHHHHHHHHHHHSSCCCSS--SCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999997632  3456777899999999999999999998888777643

>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=98.41  E-value=5.6e-07  Score=55.42  Aligned_cols=57  Identities=23%  Similarity=0.463  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVDDLSERLSELLATTD   78 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVddLSeRLs~Ll~s~D   78 (91)
                      +.||+.+..|+.+||...   +.+.|=+.||+.|++||+.|+.++.+|-+.+..|....+
T Consensus        15 ~~in~~f~~L~~llP~~~---~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~   71 (83)
T d1nkpb_          15 DHIKDSFHSLRDSVPSLQ---GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNA   71 (83)
T ss_dssp             HHHHHHHHHHHTTSGGGT---TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999763   346788899999999999999999999998888765443

>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=98.38  E-value=1.5e-07  Score=56.25  Aligned_cols=46  Identities=24%  Similarity=0.440  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHhchhhh--hccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELR--NNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~--~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      +.||+-+..|+.|||...  ...+.+.+=+.||++||.||+.|+++|.
T Consensus        15 ~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v~   62 (63)
T d1a0aa_          15 NRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             HHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhhc
Confidence            689999999999999874  3345677888899999999999999873

>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=98.36  E-value=1.7e-07  Score=56.98  Aligned_cols=43  Identities=14%  Similarity=0.315  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHhchhhhhccCCcchHHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRNNRSDKVSAGKVLQETCNYIRSLHREVD   64 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~r~~~~~SaskvLqETC~YIr~LhrEVd   64 (91)
                      +.||+-+..|+.+||...   +.+.|-+.||++||+||+.|+..|.
T Consensus        25 ~~in~~~~~L~~llP~~~---~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          25 SKVNEAFETLKRSTSSNP---NQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHTTSCSCT---TSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHCCCCC---CCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            679999999999999874   3567888999999999999998775

>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=97.52  E-value=1e-05  Score=48.18  Aligned_cols=45  Identities=24%  Similarity=0.528  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHhchhhhh-ccCCcchHHHHHHHHHHHHHHHHHHH
Q 048534           19 DQINDLVSKLQQLLPELRN-NRSDKVSAGKVLQETCNYIRSLHREV   63 (91)
Q Consensus        19 dqi~dLvsKLQaLLPe~~~-r~~~~~SaskvLqETC~YIr~LhrEV   63 (91)
                      +.||+.+..|+.+||.... .++.+.|=+-||+.|.+||+.|+.|.
T Consensus        18 ~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_          18 DKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             HHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            6799999999999999853 33456677779999999999998764