Citrus Sinensis ID: 041198

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90---
Protein Sequence
MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASIDSNSAEAAIIRSLLM
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHc
Coil and Loop (DISEMBL)
mssrrsrsrqssgvsrisyDQIGDLVSKLQQLIPElrsrrsdkvSASKILQETCDYIRSLHREVDDLSDRLSELLASIDSNSAEAAIIRSLLM
Flexible Loop (DISEMBL)
mssrrsrsrqssgvsrisydqigDLVSKLQQLIPElrsrrsdkvsaskILQETCDYIRSLHREVDDLSDRLSELlasidsnsaeaaIIRSLLM
Low Complexity Region (SEG)
MssrrsrsrqssgvsrisYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASIDSNSAEAAIIRSLLM
Disordered region (IsUnstruct)
*********************IGDLVS*L*******************ILQETCDYIRSLHREV*****************************
Disordered Region (DISOPRED)
*********************IGDLVSKLQQ********************ETCDYIRSLHREVDDLSDRLSELLASIDSNSAEAAIIRSLLM
Disordered Region (DISEMBL)
****************ISYDQIGDLVSKLQQLIPELR********ASKILQETCDYIRSLHREVDDLSDRLSELLASIDSNSAEAAIIRSLLM
Disordered Region (DISPRO)
****************ISYDQIGDLVSKLQQLIPELRSR**DKVSASKILQETCDYIRSLHREVDDLSDRLSELLASIDSNSAE*AIIRSLLM
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYxxxxxxxxxxxxxxxxxxxxxIDSNSAEAAIIRSLLM
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	93	2.2.26 [Sep-21-2011]
Q9CA64	93	Transcription factor bHLH	no	no	0.795	0.795	0.740	1e-23

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

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/77 (74%), Positives = 71/77 (92%), Gaps = 3/77 (3%)

Query: 17 ISYDQIGDLVSKLQQLIPELR-SRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELL 75
          IS DQI DL+ KLQQL+PELR SRRSDKVSA+++LQ+TC+YIR+LHREVDDLS+RLSELL
Sbjct: 17 ISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL 76

Query: 76 ASIDSNSAEAAIIRSLL 92
          A  +S++A+AA+IRSLL
Sbjct: 77 A--NSDTAQAALIRSLL 91

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	93
225425746	92	PREDICTED: transcription factor bHLH135	0.870	0.880	0.839	7e-30
356550791	91	PREDICTED: transcription factor bHLH135-	0.967	0.989	0.771	1e-29
356500403	93	PREDICTED: transcription factor bHLH135-	0.903	0.903	0.785	3e-29
356526903	93	PREDICTED: transcription factor bHLH135-	0.881	0.881	0.819	3e-29
351726902	91	uncharacterized protein LOC100305611 [Gl	0.967	0.989	0.760	4e-29
356531780	92	PREDICTED: transcription factor bHLH135-	0.967	0.978	0.760	4e-29
356498222	93	PREDICTED: transcription factor bHLH135-	0.903	0.903	0.773	8e-29
359806909	92	uncharacterized protein LOC100784537 [Gl	0.967	0.978	0.75	9e-29
357501781	93	Transcription factor style2.1 [Medicago	0.978	0.978	0.760	2e-28
255552902	90	transcription regulator, putative [Ricin	0.967	1.0	0.720	2e-28

>gi|225425746|ref|XP_002276549.1| PREDICTED: transcription factor bHLH135 [Vitis vinifera] gi|147833933|emb|CAN68305.1| hypothetical protein VITISV_041983 [Vitis vinifera] gi|296086398|emb|CBI31987.3| unnamed protein product [Vitis vinifera]

 Score =  134 bits (337), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 68/81 (83%), Positives = 76/81 (93%)

Query: 13 GVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLS 72
          GVSRIS DQI DLVSKLQQLIPE+R+RRSDKVSASK+LQETC+YIR+LHREVDDLSDRLS
Sbjct: 12 GVSRISDDQIADLVSKLQQLIPEIRNRRSDKVSASKVLQETCNYIRNLHREVDDLSDRLS 71

Query: 73 ELLASIDSNSAEAAIIRSLLM 93
           LLAS D++S +AAIIRSLLM
Sbjct: 72 ALLASTDTDSDQAAIIRSLLM 92

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  133 bits (334), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 71/92 (77%), Positives = 83/92 (90%), Gaps = 2/92 (2%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSL 60
          MSSRRSR  Q S  +RIS DQI DLVSKL+QL+PE+R RRSDKVSASK+LQETC+YIRSL
Sbjct: 1  MSSRRSR--QQSASTRISDDQIIDLVSKLRQLVPEIRDRRSDKVSASKVLQETCNYIRSL 58

Query: 61 HREVDDLSDRLSELLASIDSNSAEAAIIRSLL 92
          HREVDDLS+RLS+LLA+ID++S EAAIIRSL+
Sbjct: 59 HREVDDLSERLSQLLATIDADSPEAAIIRSLI 90

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500403|ref|XP_003519021.1| PREDICTED: transcription factor bHLH135-like [Glycine max]

 Score =  132 bits (332), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 66/84 (78%), Positives = 76/84 (90%)

Query: 10 QSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSD 69
          QS   + I+  QI DLVSKLQQLIPELR+RRSDKVSA+K+LQETC+YI++LHREVDDLSD
Sbjct: 10 QSGASAEITDAQITDLVSKLQQLIPELRARRSDKVSAAKVLQETCNYIKNLHREVDDLSD 69

Query: 70 RLSELLASIDSNSAEAAIIRSLLM 93
          RLSELLA+ DSNSA+AAIIRSLLM
Sbjct: 70 RLSELLANTDSNSAQAAIIRSLLM 93

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526903|ref|XP_003532055.1| PREDICTED: transcription factor bHLH135-like [Glycine max]

 Score =  132 bits (331), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 68/83 (81%), Positives = 77/83 (92%), Gaps = 1/83 (1%)

Query: 12 SGVS-RISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDR 70
          SGVS  I+  QI DL+SKLQQLIPELR+RRSDKVSASK+LQETC+YI+SLHREVDDLSDR
Sbjct: 11 SGVSTEITDAQITDLISKLQQLIPELRARRSDKVSASKVLQETCNYIKSLHREVDDLSDR 70

Query: 71 LSELLASIDSNSAEAAIIRSLLM 93
          LS+LLA+ DSNSA+AAIIRSLLM
Sbjct: 71 LSQLLATTDSNSAQAAIIRSLLM 93

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726902|ref|NP_001237910.1| uncharacterized protein LOC100305611 [Glycine max] gi|255626077|gb|ACU13383.1| unknown [Glycine max]

 Score =  132 bits (331), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 83/92 (90%), Gaps = 2/92 (2%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSL 60
          MSSRRSR  Q S  +RIS DQI DLVSKL+QL+PE+R RRSDKVSASK+LQETC+YIRSL
Sbjct: 1  MSSRRSR--QQSASTRISDDQIIDLVSKLRQLVPEIRDRRSDKVSASKVLQETCNYIRSL 58

Query: 61 HREVDDLSDRLSELLASIDSNSAEAAIIRSLL 92
          HREV+DLS+RLS+LLA+ID++S EAAIIRSL+
Sbjct: 59 HREVNDLSERLSQLLATIDADSPEAAIIRSLI 90

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531780|ref|XP_003534454.1| PREDICTED: transcription factor bHLH135-like [Glycine max]

 Score =  131 bits (330), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 83/92 (90%), Gaps = 2/92 (2%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSL 60
          MSSRRSR  Q SG +RIS DQI +LVSKL+QL+PE+R+RRSDKVSASK+LQETC+YIRSL
Sbjct: 1  MSSRRSR--QHSGSTRISDDQIIELVSKLRQLVPEIRNRRSDKVSASKVLQETCNYIRSL 58

Query: 61 HREVDDLSDRLSELLASIDSNSAEAAIIRSLL 92
          HREV DLS+RLS+LL +ID++SAEA IIRSLL
Sbjct: 59 HREVSDLSERLSQLLTTIDADSAEAGIIRSLL 90

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498222|ref|XP_003517952.1| PREDICTED: transcription factor bHLH135-like [Glycine max]

 Score =  130 bits (328), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 65/84 (77%), Positives = 76/84 (90%)

Query: 10 QSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSD 69
          QS   + I+  QI DLVSKLQQLIPELR+RRSDKVS++K+LQETC+YI++LHREVDDLSD
Sbjct: 10 QSGASAEITDAQITDLVSKLQQLIPELRARRSDKVSSAKVLQETCNYIKNLHREVDDLSD 69

Query: 70 RLSELLASIDSNSAEAAIIRSLLM 93
          RLSELLA+ DSNSA+AAIIRSLLM
Sbjct: 70 RLSELLANTDSNSAQAAIIRSLLM 93

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359806909|ref|NP_001241066.1| uncharacterized protein LOC100784537 [Glycine max] gi|255637698|gb|ACU19172.1| unknown [Glycine max]

 Score =  130 bits (327), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 69/92 (75%), Positives = 82/92 (89%), Gaps = 2/92 (2%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSL 60
          MSSRRSR  Q SG +RIS DQI +LVSKL+QL+PE+R+RRSDKVSASK+LQETC+YIR L
Sbjct: 1  MSSRRSR--QHSGSTRISDDQIIELVSKLRQLVPEIRNRRSDKVSASKVLQETCNYIRGL 58

Query: 61 HREVDDLSDRLSELLASIDSNSAEAAIIRSLL 92
          HREV DLS+RLS+LL +ID++SAEA IIRSLL
Sbjct: 59 HREVSDLSERLSQLLTTIDADSAEAGIIRSLL 90

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357501781|ref|XP_003621179.1| Transcription factor style2.1 [Medicago truncatula] gi|355496194|gb|AES77397.1| Transcription factor style2.1 [Medicago truncatula]

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 83/92 (90%), Gaps = 1/92 (1%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSL 60
          MSSRRSR +QS G +RIS DQI DLV KL+QL+PE+R+RRSDKV ASK+LQETC+YIR+L
Sbjct: 1  MSSRRSR-QQSGGSTRISDDQIIDLVCKLRQLVPEIRNRRSDKVPASKVLQETCNYIRNL 59

Query: 61 HREVDDLSDRLSELLASIDSNSAEAAIIRSLL 92
           REVDDLS RLS+LLA+IDS+SAEA+IIRSLL
Sbjct: 60 QREVDDLSLRLSQLLATIDSDSAEASIIRSLL 91

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552902|ref|XP_002517494.1| transcription regulator, putative [Ricinus communis] gi|223543505|gb|EEF45036.1| transcription regulator, putative [Ricinus communis]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 67/93 (72%), Positives = 80/93 (86%), Gaps = 3/93 (3%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSL 60
          MS RRSR      V RI+ DQI DLVSKL+QL+PE+R RR DKVSASK+LQETC+YIR+L
Sbjct: 1  MSGRRSRQ---PSVPRITDDQIIDLVSKLRQLLPEIRQRRPDKVSASKVLQETCNYIRNL 57

Query: 61 HREVDDLSDRLSELLASIDSNSAEAAIIRSLLM 93
          HREVDDLS+RLS+LLA+ID++S EAAIIRSL+M
Sbjct: 58 HREVDDLSERLSQLLATIDADSPEAAIIRSLIM 90

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	93
TAIR|locus:1005716685	94	KDR "KIDARI" [Arabidopsis thal	0.784	0.776	0.890	5e-28
TAIR|locus:1006230235	92	PRE5 "Paclobutrazol Resistance	0.795	0.804	0.733	2.3e-23
TAIR|locus:2019210	93	BS1 "AT1G74500" [Arabidopsis t	0.763	0.763	0.743	7.8e-23
TAIR|locus:2150916	94	BNQ2 "AT5G15160" [Arabidopsis	0.784	0.776	0.689	1.1e-21
TAIR|locus:2178002	92	PRE1 "AT5G39860" [Arabidopsis	0.795	0.804	0.68	1.1e-21
TAIR|locus:2100342	92	BNQ3 "AT3G47710" [Arabidopsis	0.774	0.782	0.666	4e-19
FB|FBgn0029711	437	Usf "Usf" [Drosophila melanoga	0.419	0.089	0.435	0.00076

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

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 65/73 (89%), Positives = 68/73 (93%)

Query:    20 DQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASID 79
             DQI DLVSKLQ LIPELR RRSDKVSASK+LQETC+YIR+LHREVDDLSDRLSELLAS D
Sbjct:    20 DQISDLVSKLQHLIPELRRRRSDKVSASKVLQETCNYIRNLHREVDDLSDRLSELLASTD 79

Query:    80 SNSAEAAIIRSLL 92
              NSAEAAIIRSLL
Sbjct:    80 DNSAEAAIIRSLL 92

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 55/75 (73%), Positives = 66/75 (88%)

Query:    20 DQIGDLVSKLQQLIPELRSRR-SDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI 78
             DQ+ DLVSKL+Q +PE+  RR SDKVSASK+LQETC+YIR LHREVD+LSDRLS+LL S+
Sbjct:    18 DQMIDLVSKLRQFLPEIHERRRSDKVSASKVLQETCNYIRKLHREVDNLSDRLSQLLDSV 77

Query:    79 DSNSAEAAIIRSLLM 93
             D +S EAA+IRSLLM
Sbjct:    78 DEDSPEAAVIRSLLM 92

GO:0005634 "nucleus" evidence=ISM

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

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 55/74 (74%), Positives = 69/74 (93%)

Query:    20 DQIGDLVSKLQQLIPELR-SRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI 78
             DQI DL+ KLQQL+PELR SRRSDKVSA+++LQ+TC+YIR+LHREVDDLS+RLSELLA+ 
Sbjct:    20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN- 78

Query:    79 DSNSAEAAIIRSLL 92
              S++A+AA+IRSLL
Sbjct:    79 -SDTAQAALIRSLL 91

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

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 51/74 (68%), Positives = 66/74 (89%)

Query:    20 DQIGDLVSKLQQLIPELR-SRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI 78
             DQI DL+SKL+Q IPE+R +RRS+ VSASK+LQETC+YIR+L++E DDLSDRL++LL SI
Sbjct:    19 DQITDLISKLRQSIPEIRQNRRSNTVSASKVLQETCNYIRNLNKEADDLSDRLTQLLESI 78

Query:    79 DSNSAEAAIIRSLL 92
             D NS +AA+IRSL+
Sbjct:    79 DPNSPQAAVIRSLI 92

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

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

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 51/75 (68%), Positives = 68/75 (90%)

Query:    20 DQIGDLVSKLQQLIPEL-RSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI 78
             +Q+ DLVSKL+Q++PE+ + RRSDK SASK+LQETC+YIR+L+REVD+LS+RLS+LL S+
Sbjct:    18 NQMIDLVSKLRQILPEIGQRRRSDKASASKVLQETCNYIRNLNREVDNLSERLSQLLESV 77

Query:    79 DSNSAEAAIIRSLLM 93
             D +S EAA+IRSLLM
Sbjct:    78 DEDSPEAAVIRSLLM 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:2100342 BNQ3 "AT3G47710" [Arabidopsis thaliana (taxid:3702)]

 Score = 229 (85.7 bits), Expect = 4.0e-19, P = 4.0e-19
 Identities = 50/75 (66%), Positives = 63/75 (84%)

Query:    20 DQIGDLVSKLQQLIPEL-RSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI 78
             +QI DLV +L +L+PEL  +RRS KVSAS++LQETC YIR+L +EVDDLS+RLS+LL S 
Sbjct:    19 EQINDLVLQLHRLLPELANNRRSGKVSASRVLQETCSYIRNLSKEVDDLSERLSQLLEST 78

Query:    79 DSNSAEAAIIRSLLM 93
             DS  A+AA+IRSLLM
Sbjct:    79 DS--AQAALIRSLLM 91

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

FB|FBgn0029711 Usf "Usf" [Drosophila melanogaster (taxid:7227)]

 Score = 72 (30.4 bits), Expect = 0.00076, Sum P(2) = 0.00076
 Identities = 17/39 (43%), Positives = 24/39 (61%)

Query:    45 SASKILQETCDYIRSLHREVDDLSDRLSELLASIDSNSA 83
             S S+IL + C+YI+S+  E+D L D L E  +   SN A
Sbjct:   327 SKSQILIKACEYIKSMQGEIDTLRDCLRETDSLRASNQA 365

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

GO:0005634 "nucleus" evidence=ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

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	93
PLN03217	93	PLN03217, PLN03217, transcription factor ATBS1; Pr	2e-25

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

 Score = 90.6 bits (224), Expect = 2e-25
 Identities = 71/93 (76%), Positives = 84/93 (90%), Gaps = 3/93 (3%)

Query: 1  MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELR-SRRSDKVSASKILQETCDYIRS 59
          MS RRSRSRQSSG SRIS DQI DL+ KLQQL+PELR SRRSDKVSA+++LQ+TC+YIR+
Sbjct: 1  MSGRRSRSRQSSGTSRISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRN 60

Query: 60 LHREVDDLSDRLSELLASIDSNSAEAAIIRSLL 92
          LHREVDDLS+RLSELLA+ D  +A+AA+IRSLL
Sbjct: 61 LHREVDDLSERLSELLANSD--TAQAALIRSLL 91

Length = 93

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	93
PLN03217	93	transcription factor ATBS1; Provisional	100.0
smart00353	53	HLH helix loop helix domain.	98.71
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	98.62
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	98.59
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	97.16
KOG1318	411	consensus Helix loop helix transcription factor EB	96.94
KOG4304	250	consensus Transcriptional repressors of the hairy/	95.27
KOG0561	373	consensus bHLH transcription factor [Transcription	83.19
PF07606	152	DUF1569: Protein of unknown function (DUF1569); In	80.6
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	80.58

>PLN03217 transcription factor ATBS1; Provisional

Probab=100.00  E-value=6.3e-52  Score=286.53  Aligned_cols=91  Identities=77%  Similarity=1.079  Sum_probs=87.9

Q ss_pred             CCCcccccccCCCCCCCcHhHHHHHHHHHHHhchhhhh-hccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 041198            1 MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRS-RRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASID   79 (93)
Q Consensus         1 mssrrsrsr~~~~asrisddqI~dLvsKLQ~LLP~~~~-r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s~D   79 (93)
                      |||||||+||.+|+++||||||+|||+|||+|||++++ |+++++|++|||||||||||+||||||||||||+|||++  
T Consensus         1 MSsRRSrsrq~s~s~risddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t--   78 (93)
T PLN03217          1 MSGRRSRSRQSSGTSRISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN--   78 (93)
T ss_pred             CCcccccccccCCCCCCCHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--
Confidence            99999999988899999999999999999999999986 889999999999999999999999999999999999999  


Q ss_pred             CCcHHHHHHHHhhC
Q 041198           80 SNSAEAAIIRSLLM   93 (93)
Q Consensus        80 ~ns~~a~iirsLL~   93 (93)
                      .|++||+|||||||
T Consensus        79 ~~s~~a~iIRSlL~   92 (93)
T PLN03217         79 SDTAQAALIRSLLT   92 (93)
T ss_pred             cCCchHHHHHHHhc
Confidence            67899999999997

>smart00353 HLH helix loop helix domain

Probab=98.71  E-value=4e-08  Score=57.48  Aligned_cols=48  Identities=31%  Similarity=0.560  Sum_probs=41.9

Q ss_pred             CCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           16 RISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        16 risddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      +-..++|++.+..|+.++|...  .+.+.+.+.||++||+||+.|+.+++
T Consensus         5 r~RR~~~n~~~~~L~~lip~~~--~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        5 RRRRRKINEAFDELRSLLPTLP--NNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            3456899999999999999875  45677899999999999999999986

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

Probab=98.62  E-value=9.6e-08  Score=56.39  Aligned_cols=50  Identities=34%  Similarity=0.565  Sum_probs=44.0

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      .++...++|++.+..|+.+||...  .+.+.+.+.||+.||+||+.|+.+++
T Consensus        11 ~Er~RR~~~n~~~~~L~~llp~~~--~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083          11 RERRRRERINDAFDELRSLLPTLP--PSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            456678999999999999999996  55677999999999999999998863

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=98.59  E-value=1.1e-07  Score=56.70  Aligned_cols=46  Identities=37%  Similarity=0.593  Sum_probs=39.7

Q ss_pred             CCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHH
Q 041198           16 RISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLH   61 (93)
Q Consensus        16 risddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLh   61 (93)
                      +-..++|++.+..|+.+||........+.+.+.||+.||+||+.||
T Consensus        10 r~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen   10 RRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            3456899999999999999964455667899999999999999987

; 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=97.16  E-value=0.00095  Score=52.71  Aligned_cols=63  Identities=32%  Similarity=0.421  Sum_probs=52.3

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhc-c-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRR-S-DKVSASKILQETCDYIRSLHREVDDLSDRLSELLAS   77 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~-~-~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s   77 (93)
                      ++=..|-|+-=-+-||.|+|.+..-- + -|.+.|-|||.||.||.-||.|..+--+-+++|=..
T Consensus        70 EqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~  134 (229)
T KOG1319|consen   70 EQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKD  134 (229)
T ss_pred             HHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44456677777888999999996443 2 388999999999999999999999999999998554

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

Probab=96.94  E-value=0.0015  Score=54.85  Aligned_cols=57  Identities=32%  Similarity=0.522  Sum_probs=44.4

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLS   72 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLs   72 (93)
                      +|=..+-||+.|.+|-+|||.++--. .+....-||+-+|.|||.||++-....|...
T Consensus       241 ERRRR~nIN~~IkeLg~liP~~~~~~-~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~  297 (411)
T KOG1318|consen  241 ERRRRENINDRIKELGQLIPKCNSED-MKSNKGTILKASCDYIRELQQTLQRARELEN  297 (411)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCcch-hhcccchhhHHHHHHHHHHHHHHHHHHHHHh
Confidence            34456899999999999999995322 3334778999999999999998876666543

>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]

Probab=95.27  E-value=0.035  Score=43.49  Aligned_cols=50  Identities=28%  Similarity=0.460  Sum_probs=42.3

Q ss_pred             CCcHhHHHHHHHHHHHhchhhhhh---ccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           16 RISYDQIGDLVSKLQQLIPELRSR---RSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        16 risddqI~dLvsKLQ~LLP~~~~r---~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      +=..+.||+.+..|+.|||+.-..   +..|--.|.||+=|.+|.|.||+-..
T Consensus        41 KkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   41 KKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            335789999999999999999654   45678899999999999999998543

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=83.19  E-value=1.8  Score=36.60  Aligned_cols=42  Identities=33%  Similarity=0.547  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           21 QIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        21 qI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      -||-=..-|.+|||-   .-+.|.|.|-|||.|..||-.|..+--
T Consensus        74 SINAGFqsLr~LlPr---~eGEKLSKAAILQQTa~yI~~Le~~Kt  115 (373)
T KOG0561|consen   74 SINAGFQSLRALLPR---KEGEKLSKAAILQQTADYIHQLEGHKT  115 (373)
T ss_pred             hhhHHHHHHHHhcCc---ccchhhHHHHHHHHHHHHHHHHHhccc
Confidence            377778889999994   346688999999999999999976643

>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=80.60  E-value=3.7  Score=29.28  Aligned_cols=47  Identities=23%  Similarity=0.563  Sum_probs=37.0

Q ss_pred             CCCcccccccCCCCCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHH
Q 041198            1 MSSRRSRSRQSSGVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIR   58 (93)
Q Consensus         1 mssrrsrsr~~~~asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIr   58 (93)
                      |+.||.          ++-+-+.|++.+|+.|.|+. .+.-.+-|++.||.--+..|+
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            666665          77788899999999999974 455578899999987666554

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]

Probab=80.58  E-value=4.4  Score=37.10  Aligned_cols=50  Identities=22%  Similarity=0.374  Sum_probs=40.8

Q ss_pred             CCCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHH
Q 041198           13 GVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREV   64 (93)
Q Consensus        13 ~asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEV   64 (93)
                      .++|=..||+|-+|.-|-.+||.+.. -+-|.-...||++|..+||.+ +|+
T Consensus        26 ~~EKrRRdq~N~yI~ELs~Mvp~~~~-~~RK~DK~tVLr~aV~~lr~~-k~~   75 (803)
T KOG3561|consen   26 EIEKRRRDQMNKYIEELSEMVPTNAS-LSRKPDKLTVLRMAVDHLRLI-KEQ   75 (803)
T ss_pred             hHHHHHHHHHHHHHHHHHHhhhcchh-cccCchHHHHHHHHHHHHHHH-hhh
Confidence            35777899999999999999999863 334567789999999999865 555

---

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	93
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	9e-05
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	4e-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 = 36.5 bits (85), Expect = 9e-05
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 20 DQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSEL 74
          D I D    L+  +P L+  ++ +     IL +  +YI+ + R+       + +L
Sbjct: 25 DHIKDSFHSLRDSVPSLQGEKASRAQ---ILDKATEYIQYMRRKNHTHQQDIDDL 76

>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 = 35.0 bits (81), Expect = 4e-04
 Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 20 DQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASID 79
            I D + +L+ L+    +    K++ S +L++  DYIR L      L      L  ++ 
Sbjct: 19 SSINDKIIELKDLVVGTEA----KLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVH 74

Query: 80 SN 81
           +
Sbjct: 75 KS 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	93
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	98.87
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	98.81
1a0a_A	63	BHLH, protein (phosphate system positive regulator	98.76
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	98.74
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	98.48
4ati_A	118	MITF, microphthalmia-associated transcription fact	98.46
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	98.36
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	98.33
4h10_B	71	Circadian locomoter output cycles protein kaput; B	98.3
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	98.26
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	98.0
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.87
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	97.54
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	97.41
4f3l_A	361	Mclock, circadian locomoter output cycles protein	97.08
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	96.97
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	96.74
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	96.14
2di0_A	71	Activating signal cointegrator 1 complex subunit 2	82.85

>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=98.87  E-value=6.4e-09  Score=67.28  Aligned_cols=60  Identities=23%  Similarity=0.356  Sum_probs=52.1

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI   78 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s~   78 (93)
                      ++-..+.||+.+..|+.|||..    +.+.+.+.||++|+.||+.||.+++.|.+...+|=..+
T Consensus        14 ErrRR~~in~~f~~L~~lvP~~----~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   73 (82)
T 1am9_A           14 EKRYRSSINDKIIELKDLVVGT----EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAV   73 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCS----SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhccCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445689999999999999984    46789999999999999999999999999988876543

>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=98.81  E-value=1.5e-08  Score=64.74  Aligned_cols=55  Identities=25%  Similarity=0.482  Sum_probs=49.2

Q ss_pred             CcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           17 ISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSEL   74 (93)
Q Consensus        17 isddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqL   74 (93)
                      =..+.||+.+..|+.+||.+.   +.+.|.+.||+.|++||+.|+.+++.|.+.+.+|
T Consensus        22 ~RR~~in~~f~~Lr~lvP~~~---~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           22 KRRDHIKDSFHSLRDSVPSLQ---GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHSGGGT---TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHHHHCcCCC---CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345789999999999999886   3578999999999999999999999999988766

>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=98.76  E-value=4.3e-09  Score=65.88  Aligned_cols=52  Identities=21%  Similarity=0.395  Sum_probs=45.5

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhhc--cccchHHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSRR--SDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r~--~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      +++-..+.||+.+..|+.|||.+....  +.+.|.|.+|+.||.||+.||+||.
T Consensus         9 aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            9 AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             GTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            566678999999999999999996544  5688999999999999999999874

>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=98.74  E-value=3.8e-08  Score=62.88  Aligned_cols=54  Identities=26%  Similarity=0.503  Sum_probs=45.6

Q ss_pred             cHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           18 SYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSEL   74 (93)
Q Consensus        18 sddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqL   74 (93)
                      ..+.||+.+..|+.+||.+.   +.+.|.+.||+.|++||+.|+.++..|.+.+.+|
T Consensus        13 RR~~in~~f~~Lr~lvP~~~---~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L   66 (83)
T 1nkp_B           13 RRDHIKDSFHSLRDSVPSLQ---GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHTTSGGGT---TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45889999999999999875   4678999999999999999997777666655554

>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=98.48  E-value=2.1e-08  Score=61.65  Aligned_cols=52  Identities=27%  Similarity=0.455  Sum_probs=43.3

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhh-ccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSR-RSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r-~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      .++-..+.||+.+..|+.|||.+... +..+.+.+.||++||+||+.|+.|+.
T Consensus        12 ~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A           12 VERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            34556789999999999999998643 23477999999999999999998863

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

Probab=98.46  E-value=3.1e-07  Score=63.06  Aligned_cols=56  Identities=30%  Similarity=0.439  Sum_probs=46.5

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDR   70 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSer   70 (93)
                      +++-..+.||+-+..|+.|+|.+... ..+.+.+-||+.|+.||+.||.+++.|.+-
T Consensus        34 ~ERrRR~~In~~~~~L~~lvP~~~~~-~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           34 IERRRRFNINDRIKELGTLIPKSNDP-DMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCc-cccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566789999999999999998542 346789999999999999999999999864

>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=98.36  E-value=1.8e-06  Score=56.72  Aligned_cols=55  Identities=24%  Similarity=0.314  Sum_probs=45.9

Q ss_pred             CcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           17 ISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSE   73 (93)
Q Consensus        17 isddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsq   73 (93)
                      =..+.|++.+..|+.++|.+..  +.|.|.+.||+.|+.||+.|+.+...+.+-..+
T Consensus        16 ~RR~~ln~~f~~Lr~~vP~~~~--~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~   70 (88)
T 1nkp_A           16 QRRNELKRSFFALRDQIPELEN--NEKAPKVVILKKATAYILSVQAEEQKLISEEDL   70 (88)
T ss_dssp             HHHHHHHHHHHHHHTTCGGGTT--CTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3468899999999999999853  457899999999999999999988776654443

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

Probab=98.33  E-value=3e-07  Score=59.59  Aligned_cols=52  Identities=23%  Similarity=0.297  Sum_probs=43.8

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhhccccc-hHHHHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSRRSDKV-SASKILQETCDYIRSLHREVDDL   67 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r~~~~~-SaskvLqETC~YIrsLhrEVddL   67 (93)
                      .+|-..+.||+-+..|+.++|...  .+++. |...||+.||.||+.|+++|.++
T Consensus        12 ~ER~Rr~~IN~~f~~Lr~~vP~~~--~~~K~~sK~~IL~~AieYI~~Lq~~l~e~   64 (76)
T 3u5v_A           12 LERKRRRDINEAFRELGRMCQMHL--KSDKAQTKLLILQQAVQVILGLEQQVRER   64 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH--CCCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHhhhHHHHHHHHHHHHHHcCCCC--CccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677899999999999999754  24555 78899999999999999999875

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

Probab=98.30  E-value=1.1e-06  Score=56.90  Aligned_cols=49  Identities=24%  Similarity=0.414  Sum_probs=41.8

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHH
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDL   67 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddL   67 (93)
                      ++-..+.||+.+..|+.|||.    .+.+...+-||+.||.||+.|+.++.-|
T Consensus        16 ErrRRd~IN~~i~eL~~LvP~----~~~K~dK~sIL~~aI~yik~Lq~~~~~~   64 (71)
T 4h10_B           16 EKKRRDQFNVLIKELGSMLPG----NARKMDKSTVLQKSIDFLRKHKEITAWL   64 (71)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSS----CCSCCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HhhHHHHHHHHHHHHHHhCCC----CCCCCcHHHHHHHHHHHHHHHHHhhhHH
Confidence            444578999999999999994    3457899999999999999999998644

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

Probab=98.26  E-value=2.8e-06  Score=55.10  Aligned_cols=56  Identities=16%  Similarity=0.169  Sum_probs=46.9

Q ss_pred             CcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           17 ISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSEL   74 (93)
Q Consensus        17 isddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqL   74 (93)
                      -..+.|++.+.+|..++|.+.  .+.+.|...||+.||.||+.|+.+...|.+...+|
T Consensus        11 ~RR~~lk~~f~~Lr~~vP~~~--~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L   66 (80)
T 1nlw_A           11 NRRAHLRLSLEKLKGLVPLGP--DSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (80)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCS--SSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346899999999999999873  34577888999999999999999998887766554

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

Probab=98.00  E-value=9.5e-06  Score=52.22  Aligned_cols=48  Identities=17%  Similarity=0.390  Sum_probs=41.0

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHR   62 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhr   62 (93)
                      +++-..+.||+-+..|+.|||.+.. ...+...+-||+.|++||+.|+-
T Consensus        16 ~ERrRR~rIN~~l~eL~~LvP~~~~-~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           16 IEKRRRDKMNSFIDELASLVPTCNA-MSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSHHHHT-CSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHHcccccc-ccccccHHHHHHHHHHHHHHHhc
Confidence            4556679999999999999999863 34688999999999999999873

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

Probab=97.87  E-value=3.6e-05  Score=51.53  Aligned_cols=54  Identities=30%  Similarity=0.413  Sum_probs=45.5

Q ss_pred             HhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041198           19 YDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSE   73 (93)
Q Consensus        19 ddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsq   73 (93)
                      .+-||+-|..|-.|+|.++.. ..+.+.+-||+-||.||+.|+.|+..+.|....
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~-~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r   57 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDP-DMRWNKGTILKASVDYIRKLQREQQRAKDLENR   57 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCT-TCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCc-ccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456999999999999987432 347799999999999999999999988876653

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

Probab=97.54  E-value=0.00011  Score=45.47  Aligned_cols=48  Identities=19%  Similarity=0.347  Sum_probs=40.8

Q ss_pred             CCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           16 RISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        16 risddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      |-.-.+||+-...|+.+||...  .+.|.|...+|+.+++||..|+.-++
T Consensus        11 R~R~~~iN~af~~LR~~lP~~~--~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B           11 RNRMHGLNAALDNLRKVVPCYS--KTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSSSCC--SSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHccCCC--CcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            3445789999999999999874  35688999999999999999997664

>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=97.41  E-value=0.00015  Score=46.02  Aligned_cols=49  Identities=16%  Similarity=0.324  Sum_probs=40.9

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHH
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDD   66 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVdd   66 (93)
                      +|-.-..||+-...|+.+||...   +.|.|...+|+.+.+||..|+.-++|
T Consensus        20 ER~R~~~iN~af~~LR~~iP~~~---~~KlSKi~tLr~Ai~YI~~L~~~L~~   68 (68)
T 1mdy_A           20 ERRRLSKVNEAFETLKRSTSSNP---NQRLPKVEILRNAIRYIEGLQALLRD   68 (68)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCSCT---TSCCCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCC---CCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence            33445789999999999999753   56889999999999999999976653

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

Probab=97.08  E-value=0.00039  Score=52.21  Aligned_cols=46  Identities=24%  Similarity=0.456  Sum_probs=39.5

Q ss_pred             CCCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHH
Q 041198           13 GVSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHR   62 (93)
Q Consensus        13 ~asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhr   62 (93)
                      -++|-..|+||+.+..|..|||.    ...|...+-||+.||+|||.++.
T Consensus        18 ~~e~~rr~~~n~~~~~l~~~~p~----~~~~~dk~~il~~~~~~~~~~~~   63 (361)
T 4f3l_A           18 KSEKKRRDQFNVLIKELGSMLPG----NARKMDKSTVLQKSIDFLRKHKE   63 (361)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTCCS----SSCCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCC----CCCCcCHHHHHHHHHHHHHHHHh
Confidence            45777889999999999999993    35688889999999999999874

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

Probab=96.97  E-value=0.0011  Score=42.98  Aligned_cols=46  Identities=30%  Similarity=0.480  Sum_probs=39.2

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHH
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHR   62 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhr   62 (93)
                      +|-.-..+|+-..+|+.+||...  .+.|.|.-++||-+.+||.-||.
T Consensus        22 ER~Rm~~lN~aF~~LR~~VP~~p--~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           22 PLSLLDDMNHCYSRLRELVPGVP--RGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CSCSSSHHHHHHHHHHHHCCCCC--TTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCC--CCCCccHHHHHHHHHHHHHHHHc
Confidence            44455789999999999999985  34688999999999999999973

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

Probab=96.74  E-value=0.0022  Score=48.87  Aligned_cols=48  Identities=17%  Similarity=0.378  Sum_probs=40.8

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHR   62 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhr   62 (93)
                      ++|=..|+||+.+..|..|||..+ ....|...+-||+.||+|||.|+.
T Consensus        20 ~ek~rR~~~n~~~~~L~~l~p~~~-~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           20 IEKRRRDKMNSFIDELASLVPTCN-AMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHH-HCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hhhcchHHHHHHHHHHHHhcCCCC-ccccccCHHHHHHHHHHHHHHhhc
Confidence            455567999999999999999874 345678899999999999999874

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

Probab=96.14  E-value=0.01  Score=40.41  Aligned_cols=43  Identities=40%  Similarity=0.623  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           21 QIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        21 qI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      ++|+-..+|+..||...  .+.|.|.-++|+-+++||..|+.-++
T Consensus        39 ~lN~AF~~LR~~vP~~p--~~kKLSKIETLRlAi~YI~~Lq~~L~   81 (97)
T 4aya_A           39 NMNDCYSKLKELVPSIP--QNKKVSKMEILQHVIDYILDLQIALD   81 (97)
T ss_dssp             HHHHHHHHHHHHCTTSC--SSSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCC--CCCcccHHHHHHHHHHHHHHHHHHHh
Confidence            39999999999999874  34678999999999999998876544

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

Probab=82.85  E-value=0.9  Score=29.31  Aligned_cols=26  Identities=31%  Similarity=0.576  Sum_probs=23.8

Q ss_pred             CCCCCCcHhHHHHHHHHHHHhchhhh
Q 041198           12 SGVSRISYDQIGDLVSKLQQLIPELR   37 (93)
Q Consensus        12 ~~asrisddqI~dLvsKLQ~LLP~~~   37 (93)
                      +|++.++.-++...|+.++.|+|++.
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            47788999999999999999999995

---

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	93
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	2e-05
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	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 = 37.0 bits (86), Expect = 2e-05
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 4/63 (6%)

Query: 20 DQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASID 79
            I D + +L+ L+    +    K+  S +L++  DYI+ L +    L      L  +  
Sbjct: 2  SSINDKIIELKDLVMGTDA----KMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQ 57

Query: 80 SNS 82
           N 
Sbjct: 58 KNK 60

>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 = 31.8 bits (72), Expect = 0.003
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 20 DQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSEL 74
          D I D    L+  +P L+  ++ +     IL +  +YI+ + R+       + +L
Sbjct: 15 DHIKDSFHSLRDSVPSLQGEKASRAQ---ILDKATEYIQYMRRKNHTHQQDIDDL 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	93
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.93
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	98.71
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	98.7
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	98.64
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	98.6
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	98.6
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	98.58
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	97.97

>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=98.93  E-value=3.9e-10  Score=68.10  Aligned_cols=55  Identities=24%  Similarity=0.315  Sum_probs=48.0

Q ss_pred             hHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 041198           20 DQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI   78 (93)
Q Consensus        20 dqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s~   78 (93)
                      +.|||.+..|+.+||...    .|.+.+-||++|++||+.|+.+|..|.+-..+|=...
T Consensus         2 ~~in~~f~~L~~lvP~~~----~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           2 SSINDKIIELKDLVMGTD----AKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCHHHHHHHHHHHHSCSS----CCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHhhCCCCC----CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999999763    3668899999999999999999999999888775543

>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=98.71  E-value=1.7e-08  Score=62.86  Aligned_cols=59  Identities=24%  Similarity=0.345  Sum_probs=50.7

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLAS   77 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s   77 (93)
                      ++-..+.|++.+..|+.|||...    .+.+.+.||++|++||+.|+.+++.|.+...+|-..
T Consensus        14 Er~RR~~in~~~~~L~~llP~~~----~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~   72 (80)
T d1am9a_          14 EKRYRSSINDKIIELKDLVVGTE----AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCSS----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567899999999999999743    366899999999999999999999999988887544

>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=98.70  E-value=2.6e-08  Score=62.54  Aligned_cols=61  Identities=25%  Similarity=0.302  Sum_probs=51.2

Q ss_pred             CCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 041198           16 RISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLASI   78 (93)
Q Consensus        16 risddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s~   78 (93)
                      +-..+.||+.+..|+++||.+..  +.+.|.+.||+.||.||+.|+.+++.|.+...+|-...
T Consensus        15 r~RR~~in~~f~~Lr~llP~~~~--~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~   75 (88)
T d1nkpa_          15 RQRRNELKRSFFALRDQIPELEN--NEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRR   75 (88)
T ss_dssp             HHHHHHHHHHHHHHHTTCGGGTT--CTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34468999999999999998743  24678999999999999999999999998888775543

>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=98.64  E-value=4.1e-08  Score=60.56  Aligned_cols=58  Identities=16%  Similarity=0.172  Sum_probs=49.5

Q ss_pred             cHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041198           18 SYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLAS   77 (93)
Q Consensus        18 sddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s   77 (93)
                      ..+.|++.+..|..+||....  +.+.|.+.||++|++||+.|+.++..|.+...+|...
T Consensus        12 RR~~in~~f~~L~~llP~~~~--~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~   69 (79)
T d1nlwa_          12 RRAHLRLSLEKLKGLVPLGPD--SSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQRE   69 (79)
T ss_dssp             HHHHHHHHHHHHHHSSCCCSS--SCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCccCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999997642  3467889999999999999999999998888777643

>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=98.60  E-value=8.5e-08  Score=59.60  Aligned_cols=58  Identities=24%  Similarity=0.442  Sum_probs=50.1

Q ss_pred             CcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041198           17 ISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVDDLSDRLSELLAS   77 (93)
Q Consensus        17 isddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVddLSerLsqLl~s   77 (93)
                      -..+.||+.+..|+.+||...   +.+.|.+.||+.|++||+.|+.++..|-+.+..|-..
T Consensus        12 ~RR~~in~~f~~L~~llP~~~---~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~   69 (83)
T d1nkpb_          12 KRRDHIKDSFHSLRDSVPSLQ---GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   69 (83)
T ss_dssp             HHHHHHHHHHHHHHTTSGGGT---TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346899999999999999764   3467999999999999999999999999888877554

>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=98.60  E-value=1.7e-08  Score=60.72  Aligned_cols=52  Identities=21%  Similarity=0.365  Sum_probs=44.4

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhh--hccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRS--RRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~--r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      +++-..+.||+-+..|+.|||.+..  ..+.+.+.+.||++||+||+.|+++|.
T Consensus         9 ~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v~   62 (63)
T d1a0aa_           9 AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             GTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhhc
Confidence            4566789999999999999998753  345688999999999999999999873

>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=98.58  E-value=1.9e-08  Score=61.67  Aligned_cols=48  Identities=15%  Similarity=0.298  Sum_probs=41.6

Q ss_pred             CCCcHhHHHHHHHHHHHhchhhhhhccccchHHHHHHHHHHHHHHHHHHHH
Q 041198           15 SRISYDQIGDLVSKLQQLIPELRSRRSDKVSASKILQETCDYIRSLHREVD   65 (93)
Q Consensus        15 srisddqI~dLvsKLQ~LLP~~~~r~~~~~SaskvLqETC~YIrsLhrEVd   65 (93)
                      ++-..+.||+-+..|+.|||.+.   +.+.+.+.||++||+||+.|+..|.
T Consensus        20 Er~Rr~~in~~~~~L~~llP~~~---~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          20 ERRRLSKVNEAFETLKRSTSSNP---NQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCSCT---TSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCC---CCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            45567899999999999999874   3467999999999999999998875

>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=97.97  E-value=6.9e-07  Score=53.76  Aligned_cols=51  Identities=27%  Similarity=0.457  Sum_probs=43.2

Q ss_pred             CCCCcHhHHHHHHHHHHHhchhhhh-hccccchHHHHHHHHHHHHHHHHHHH
Q 041198           14 VSRISYDQIGDLVSKLQQLIPELRS-RRSDKVSASKILQETCDYIRSLHREV   64 (93)
Q Consensus        14 asrisddqI~dLvsKLQ~LLP~~~~-r~~~~~SaskvLqETC~YIrsLhrEV   64 (93)
                      .++-..+.||+.+..|+.|||.+.. ..+.+.+.+.||+.|.+||+.|+.|.
T Consensus        12 ~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_          12 VERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            4566778999999999999999853 34567888999999999999999764