Citrus Sinensis ID: 039972

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
Protein Sequence
MEYVNAKTLASGKGNKKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAPVPQQDSMQASETQPFQDFNVFQGEESETLMHLDGFMKY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHccccccHHHccccccccccEEEEEEEEEEc
Coil and Loop (DISEMBL)
meyvnaktlasgkgnkkkkssgsksnpmklstdpqsVAARQRRHRISDRFKILqsmvpggtkmdtASMLDEAINYVKFLKAVIWFHENIINfadhhhhehdppvafgqlpgsfpyspeslyssinnlaaapvpqqdsmqasetqpfqdfnvfqgeesetlmhldgfmky
Flexible Loop (DISEMBL)
meyvnaktlasgkgnkkkkssgsksnpmklstdpqsvaarqrRHRIsdrfkilqsmvpggTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAPVPQQDSMQASETQPFQDFNVFQGEESetlmhldgfmky
Low Complexity Region (SEG)
MEYVNAKTLAsgkgnkkkkssgsksnPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAPVPQQDSMQASETQPFQDFNVFQGEESETLMHLDGFMKY
Disordered region (IsUnstruct)
***************************************************IL**********DTASMLDEAINYVKFLKAVIWFHENIINF*****************************************************************************
Disordered Region (DISOPRED)
*******************************************HRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHE***************************************************************************LDGFMKY
Disordered Region (DISEMBL)
*******************************************HRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAP***********TQPFQDFNVFQGEESETLMHLDGFMKY
Disordered Region (DISPRO)
**********************************QSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAPVPQQDSMQASETQPFQDFNVFQGEESETLMHLDGFMKY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEYVNAKTLASGKGNKKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAPVPQQDSMQASETQPFQDFNVFQGEESETLMHLDGFMKY
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	169	2.2.26 [Sep-21-2011]
Q9M041	912	Transcription factor bHLH	yes	no	0.585	0.108	0.583	1e-27
Q7XAQ6	215	Transcription factor LAX	yes	no	0.366	0.288	0.709	2e-21
Q8S3D2	373	Transcription factor bHLH	no	no	0.502	0.227	0.538	5e-21
O81313	198	Transcription factor IND	no	no	0.313	0.267	0.660	4e-15
Q9C707	298	Transcription factor bHLH	no	no	0.396	0.224	0.535	1e-13
Q3E7L7	223	Transcription factor bHLH	no	no	0.562	0.426	0.364	1e-13
Q84WK0	352	Transcription factor bHLH	no	no	0.313	0.150	0.584	2e-13
Q7XHI9	328	Transcription factor bHLH	no	no	0.313	0.161	0.584	3e-13
Q9FJ00	307	Putative transcription fa	no	no	0.396	0.218	0.521	7e-13
Q8LEG1	258	Transcription factor bHLH	no	no	0.479	0.313	0.404	1e-12

>sp|Q9M041|BH140_ARATH Transcription factor bHLH140 OS=Arabidopsis thaliana GN=BHLH140 PE=4 SV=1

 Score =  122 bits (306), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 63/108 (58%), Positives = 76/108 (70%), Gaps = 9/108 (8%)

Query: 11  SGKGNKKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLD 70
           S  GN K+  S S      LSTDPQSVAAR RRHRISDRFKILQSMVPGG KMDT SMLD
Sbjct: 29  SETGNTKRSRSTST-----LSTDPQSVAARDRRHRISDRFKILQSMVPGGAKMDTVSMLD 83

Query: 71  EAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPE 118
           EAI+YVKFLKA IW+H+N++ F +    +H+   +    PG+  + P+
Sbjct: 84  EAISYVKFLKAQIWYHQNMLLFIN----DHETTSSCTYSPGAGEFGPK 127

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XAQ6|LAX_ORYSJ Transcription factor LAX PANICLE OS=Oryza sativa subsp. japonica GN=LAX PE=1 SV=1

 Score =  102 bits (253), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 56/62 (90%)

Query: 29  KLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHEN 88
           KLSTDPQSVAAR+RRHRISDRF++L+S+VPGG+KMDT SML++AI+YVKFLKA +  H+ 
Sbjct: 39  KLSTDPQSVAARERRHRISDRFRVLRSLVPGGSKMDTVSMLEQAIHYVKFLKAQVTLHQA 98

Query: 89  II 90
            +
Sbjct: 99  AL 100

Transcription factor that seems to regulate organogenesis in postembryonic development. Involved in regulating shoot branching by controlling axillary meristem initiation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8S3D2|BH087_ARATH Transcription factor bHLH87 OS=Arabidopsis thaliana GN=BHLH87 PE=2 SV=1

 Score =  100 bits (248), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 65/91 (71%), Gaps = 6/91 (6%)

Query: 24  KSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVI 83
           K   +K+STDPQ+VAARQRR RIS++ ++LQ++VPGGTKMDTASMLDEA NY+KFL+A +
Sbjct: 269 KRKNVKISTDPQTVAARQRRERISEKIRVLQTLVPGGTKMDTASMLDEAANYLKFLRAQV 328

Query: 84  WFHENIINFADHHHHEHDPPVAFGQLPGSFP 114
              EN+    D  +      ++F   P SFP
Sbjct: 329 KALENLRPKLDQTN------LSFSSAPTSFP 353

Arabidopsis thaliana (taxid: 3702)

>sp|O81313|IND_ARATH Transcription factor IND OS=Arabidopsis thaliana GN=IND PE=1 SV=3

 Score = 80.9 bits (198), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 35/53 (66%), Positives = 45/53 (84%)

Query: 28  MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLK 80
           +++S DPQ+V AR+RR RIS++ +IL+ +VPGG KMDTASMLDEAI Y KFLK
Sbjct: 116 VRISDDPQTVVARRRRERISEKIRILKRIVPGGAKMDTASMLDEAIRYTKFLK 168

Transcription regulator required for seed dispersal. Involved in the differentiation of all three cell types required for fruit dehiscence. Acts as the key regulator in a network including SHP and ALC that controls specification of the valve margin. Works with ALC, SHP, and FUL to allow differentiation of the lignified valve layer, the spring-loaded mechanism of fruit that promotes opening. Regulates the expression of the YJ80 marker.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C707|BH083_ARATH Transcription factor bHLH83 OS=Arabidopsis thaliana GN=BHLH83 PE=2 SV=1

 Score = 76.3 bits (186), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 38/71 (53%), Positives = 50/71 (70%), Gaps = 4/71 (5%)

Query: 17  KKKSSG----SKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEA 72
           KK SSG    +K  P     DPQS+AA+ RR RIS+R KILQ +VP GTK+D  +ML++A
Sbjct: 184 KKLSSGVTGKTKPKPTTSPKDPQSLAAKNRRERISERLKILQELVPNGTKVDLVTMLEKA 243

Query: 73  INYVKFLKAVI 83
           I+YVKFL+  +
Sbjct: 244 ISYVKFLQVQV 254

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E7L7|BH139_ARATH Transcription factor bHLH139 OS=Arabidopsis thaliana GN=BHLH139 PE=4 SV=1

 Score = 75.9 bits (185), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/118 (36%), Positives = 69/118 (58%), Gaps = 23/118 (19%)

Query: 3   YVNAKTLASGKGNKKKKSSGSKSNPMK-----------LSTDPQSVAARQRRHRISDRFK 51
           + + ++L+S   +  +K+ G  SN  K           +++DPQS+ AR+RR RI+DR K
Sbjct: 100 WRDGQSLSSYNSSDDEKALGLVSNTSKSLKRKAKANRGIASDPQSLYARKRRERINDRLK 159

Query: 52  ILQSMVPGGTKMDTASMLDEAINYVKFLKAVI--------WFH----ENIINFADHHH 97
            LQS+VP GTK+D ++ML++A++YVKFL+  I        W +     N +N   HH+
Sbjct: 160 TLQSLVPNGTKVDISTMLEDAVHYVKFLQLQIKLLSSEDLWMYAPLAHNGLNMGLHHN 217

Arabidopsis thaliana (taxid: 3702)

>sp|Q84WK0|BH085_ARATH Transcription factor bHLH85 OS=Arabidopsis thaliana GN=BHLH85 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 31/53 (58%), Positives = 46/53 (86%)

Query: 31  STDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVI 83
           +TDPQS+ AR+RR RI++R +ILQ++VP GTK+D ++ML+EA++YVKFL+  I
Sbjct: 273 ATDPQSLYARKRRERINERLRILQNLVPNGTKVDISTMLEEAVHYVKFLQLQI 325

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XHI9|BH084_ARATH Transcription factor bHLH84 OS=Arabidopsis thaliana GN=BHLH84 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 31/53 (58%), Positives = 44/53 (83%)

Query: 31  STDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVI 83
           +TDPQS+ AR+RR RI++R +ILQ +VP GTK+D ++ML+EA+ YVKFL+  I
Sbjct: 244 ATDPQSLYARKRRERINERLRILQHLVPNGTKVDISTMLEEAVQYVKFLQLQI 296

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJ00|BH086_ARATH Putative transcription factor bHLH086 OS=Arabidopsis thaliana GN=BHLH86 PE=4 SV=2

 Score = 73.2 bits (178), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 37/71 (52%), Positives = 51/71 (71%), Gaps = 4/71 (5%)

Query: 17  KKKSSGS--KSNPMKLST--DPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEA 72
           KK SSG+  K  P   ++  DPQS+AA+ RR RIS+R K+LQ +VP GTK+D  +ML++A
Sbjct: 190 KKPSSGTNGKIKPKATTSPKDPQSLAAKNRRERISERLKVLQELVPNGTKVDLVTMLEKA 249

Query: 73  INYVKFLKAVI 83
           I YVKFL+  +
Sbjct: 250 IGYVKFLQVQV 260

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LEG1|BH054_ARATH Transcription factor bHLH54 OS=Arabidopsis thaliana GN=BHLH54 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 58/84 (69%), Gaps = 3/84 (3%)

Query: 3   YVNAKTLASGKGNKKKKSSGSKSNPMKL---STDPQSVAARQRRHRISDRFKILQSMVPG 59
           +V+ ++L++   ++K   +  K         +TDPQS+ AR+RR +I++R K LQ++VP 
Sbjct: 143 WVDGQSLSNSSDDEKASVTSVKGKTRATKGTATDPQSLYARKRREKINERLKTLQNLVPN 202

Query: 60  GTKMDTASMLDEAINYVKFLKAVI 83
           GTK+D ++ML+EA++YVKFL+  I
Sbjct: 203 GTKVDISTMLEEAVHYVKFLQLQI 226

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	169
147838921	161	hypothetical protein VITISV_022410 [Viti	0.668	0.701	0.541	3e-27
449461799	195	PREDICTED: transcription factor bHLH87-l	0.721	0.625	0.534	3e-27
224091024	165	predicted protein [Populus trichocarpa]	0.810	0.830	0.477	6e-27
15240948	912	aprataxin [Arabidopsis thaliana] gi|7533	0.585	0.108	0.583	6e-26
297810265	898	basic helix-loop-helix family protein [A	0.479	0.090	0.686	2e-25
357506069	153	LAX [Medicago truncatula] gi|355498338|g	0.585	0.647	0.559	2e-25
224091579	163	predicted protein [Populus trichocarpa]	0.414	0.429	0.771	1e-24
357131240	228	PREDICTED: transcription factor LAX PANI	0.461	0.342	0.594	6e-21
227016421	211	barren stalk1-like protein [Leymus ciner	0.366	0.293	0.709	4e-20
227016419	211	barren stalk1-like protein [Leymus ciner	0.366	0.293	0.709	4e-20

>gi|147838921|emb|CAN77067.1| hypothetical protein VITISV_022410 [Vitis vinifera] gi|297735648|emb|CBI18142.3| unnamed protein product [Vitis vinifera]

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 71/131 (54%), Positives = 85/131 (64%), Gaps = 18/131 (13%)

Query: 30  LSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENI 89
           LSTDPQSVAAR+RRHRISDRFKILQS+VPGGTKMDT SML+EAI+YVK+LK  IW H+ +
Sbjct: 36  LSTDPQSVAARERRHRISDRFKILQSLVPGGTKMDTVSMLEEAIHYVKYLKTQIWLHQTM 95

Query: 90  INFADHHHHEHDPPVAFGQLPGSFP-YSPESLYSSINNLAAAPVPQQDSMQ--ASETQPF 146
           INF D      DP + +     S P +  E+ YS    LA         MQ   + T P 
Sbjct: 96  INFVD-----DDPSLLYQS--DSLPSHQQEAFYSPDETLAM--------MQPYITTTAPV 140

Query: 147 QDFNVFQGEES 157
           +D   FQGEE+
Sbjct: 141 RDSYCFQGEET 151

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461799|ref|XP_004148629.1| PREDICTED: transcription factor bHLH87-like [Cucumis sativus] gi|449532778|ref|XP_004173357.1| PREDICTED: transcription factor bHLH87-like [Cucumis sativus]

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 70/131 (53%), Positives = 85/131 (64%), Gaps = 9/131 (6%)

Query: 14  GNKKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAI 73
           G   K+S G     +KLSTDPQSVAAR+RRHRISDRFKILQS+VPGGTKMDT SMLDEAI
Sbjct: 36  GGAGKRSKGV----VKLSTDPQSVAARERRHRISDRFKILQSLVPGGTKMDTVSMLDEAI 91

Query: 74  NYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYS--PESLYSSINNLAAAP 131
           +YVKFLK  IW H+ +INF D+  +      A       FP+       Y+++NNL    
Sbjct: 92  HYVKFLKTQIWLHQTMINFVDYDSNSSAAVSAAATANSGFPFEQIASGEYNNMNNLL--- 148

Query: 132 VPQQDSMQASE 142
            PQ D ++  E
Sbjct: 149 YPQNDVVKMEE 159

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091024|ref|XP_002309150.1| predicted protein [Populus trichocarpa] gi|222855126|gb|EEE92673.1| predicted protein [Populus trichocarpa]

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 75/157 (47%), Positives = 95/157 (60%), Gaps = 20/157 (12%)

Query: 13  KGNKKKKSSGSKSNP-MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDE 71
           K  ++K++ G KSN  +KLSTDPQSVAAR+RRHRISDRFKILQS+VPGGTKMDT SML+E
Sbjct: 19  KNGREKRTGGKKSNGGVKLSTDPQSVAARERRHRISDRFKILQSLVPGGTKMDTVSMLEE 78

Query: 72  AINYVKFLKAVIWFHENIINFADHHHH-EHDPPVAFGQLPGSFP-YSPESLYSSINNLAA 129
           AINYVKFLK  I  H+ I+N  D     ++  P     LP   P Y   +L S ++  ++
Sbjct: 79  AINYVKFLKNQILLHQTIMNSVDDERSLDYHLPAGSASLPTEQPSYLDSNLASVVHPSSS 138

Query: 130 APVPQQDSMQASETQPFQDFNVFQGEESETLMHLDGF 166
            P P                + FQ +E+ T  H D F
Sbjct: 139 LPCPD---------------SYFQADENYT--HYDAF 158

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240948|ref|NP_195751.1| aprataxin [Arabidopsis thaliana] gi|75335734|sp|Q9M041.1|BH140_ARATH RecName: Full=Transcription factor bHLH140; AltName: Full=Basic helix-loop-helix protein 140; Short=AtbHLH140; Short=bHLH 140; AltName: Full=Transcription factor EN 122; AltName: Full=bHLH transcription factor bHLH140 gi|7320709|emb|CAB81914.1| putative protein [Arabidopsis thaliana] gi|332002943|gb|AED90326.1| aprataxin [Arabidopsis thaliana]

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 63/108 (58%), Positives = 76/108 (70%), Gaps = 9/108 (8%)

Query: 11  SGKGNKKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLD 70
           S  GN K+  S S      LSTDPQSVAAR RRHRISDRFKILQSMVPGG KMDT SMLD
Sbjct: 29  SETGNTKRSRSTST-----LSTDPQSVAARDRRHRISDRFKILQSMVPGGAKMDTVSMLD 83

Query: 71  EAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLPGSFPYSPE 118
           EAI+YVKFLKA IW+H+N++ F +    +H+   +    PG+  + P+
Sbjct: 84  EAISYVKFLKAQIWYHQNMLLFIN----DHETTSSCTYSPGAGEFGPK 127

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297810265|ref|XP_002873016.1| basic helix-loop-helix family protein [Arabidopsis lyrata subsp. lyrata] gi|297318853|gb|EFH49275.1| basic helix-loop-helix family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/86 (68%), Positives = 68/86 (79%), Gaps = 5/86 (5%)

Query: 11  SGKGNKKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLD 70
           S  GN K+  S S      LSTDPQSVAAR+RRHRIS+RFKILQSMVPGG KMDT SML+
Sbjct: 29  SETGNTKRSRSTST-----LSTDPQSVAARERRHRISERFKILQSMVPGGAKMDTVSMLE 83

Query: 71  EAINYVKFLKAVIWFHENIINFADHH 96
           EAI YVKFLKA IWFH+N++ F ++H
Sbjct: 84  EAIRYVKFLKAQIWFHQNMLLFLNNH 109

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357506069|ref|XP_003623323.1| LAX [Medicago truncatula] gi|355498338|gb|AES79541.1| LAX [Medicago truncatula]

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 61/109 (55%), Positives = 73/109 (66%), Gaps = 10/109 (9%)

Query: 30  LSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENI 89
           LSTDPQSVAAR+RRHRISDRFKILQSM+PGG+K+DT SML+EAI+YVKFLK  IW HE +
Sbjct: 32  LSTDPQSVAARERRHRISDRFKILQSMIPGGSKLDTVSMLEEAIHYVKFLKKQIWLHETL 91

Query: 90  INFADHHHHEHDPPVAFGQLPGSFPYS----PESLYSSINNLAAAPVPQ 134
           INF D     H        LP  +  +    P   + S+ NL   P+ Q
Sbjct: 92  INFVDDIGESH------MLLPQDYSSNDKNIPSGTFESMQNLPQLPLEQ 134

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091579|ref|XP_002334947.1| predicted protein [Populus trichocarpa] gi|222875273|gb|EEF12404.1| predicted protein [Populus trichocarpa]

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 54/70 (77%), Positives = 61/70 (87%)

Query: 25  SNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIW 84
           S  +KLSTDPQSVAAR+RRHRISDRFKILQS+VPGGTKMDT SML+EAINYVKFLK  + 
Sbjct: 32  SGGVKLSTDPQSVAARERRHRISDRFKILQSLVPGGTKMDTVSMLEEAINYVKFLKTQVL 91

Query: 85  FHENIINFAD 94
            H+ I+NF D
Sbjct: 92  LHQTIMNFVD 101

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357131240|ref|XP_003567247.1| PREDICTED: transcription factor LAX PANICLE-like [Brachypodium distachyon]

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 47/79 (59%), Positives = 63/79 (79%), Gaps = 1/79 (1%)

Query: 13  KGNKKKKSSGSKSNP-MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDE 71
           +G   + + G +  P  KLSTDPQSVAAR+RRHRISDRF++L+S+VPGG+KMDT SML++
Sbjct: 43  EGRPMRVAGGGRRRPGTKLSTDPQSVAARERRHRISDRFRVLRSLVPGGSKMDTVSMLEQ 102

Query: 72  AINYVKFLKAVIWFHENII 90
           AI+YVKFLKA +  H+  +
Sbjct: 103 AIHYVKFLKAQVTLHQAAL 121

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|227016421|gb|ACP18672.1| barren stalk1-like protein [Leymus cinereus x Leymus triticoides]

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 56/62 (90%)

Query: 29  KLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHEN 88
           KLSTDPQSVAAR+RRHRISDRF++L+S+VPGG+KMDT SML++AI+YVKFLKA +  H+ 
Sbjct: 52  KLSTDPQSVAARERRHRISDRFRVLRSLVPGGSKMDTVSMLEQAIHYVKFLKAQVSLHQA 111

Query: 89  II 90
            +
Sbjct: 112 AL 113

Source: Leymus cinereus x Leymus triticoides

Species: Leymus cinereus x Leymus triticoides

Genus: Leymus

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|227016419|gb|ACP18671.1| barren stalk1-like protein [Leymus cinereus x Leymus triticoides]

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 56/62 (90%)

Query: 29  KLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHEN 88
           KLSTDPQSVAAR+RRHRISDRF++L+S+VPGG+KMDT SML++AI+YVKFLKA +  H+ 
Sbjct: 52  KLSTDPQSVAARERRHRISDRFRVLRSLVPGGSKMDTVSMLEQAIHYVKFLKAQVSLHQA 111

Query: 89  II 90
            +
Sbjct: 112 AL 113

Source: Leymus cinereus x Leymus triticoides

Species: Leymus cinereus x Leymus triticoides

Genus: Leymus

Family: Poaceae

Order: Poales

Class: Liliopsida

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	169
TAIR|locus:2179122	912	APTX "APRATAXIN-like" [Arabido	0.781	0.144	0.485	5.7e-24
UNIPROTKB|Q5MP56	219	BA1 "Uncharacterized protein"	0.349	0.269	0.745	1.2e-19
TAIR|locus:2144791	224	HEC3 "AT5G09750" [Arabidopsis	0.331	0.25	0.75	2.4e-19
TAIR|locus:2089418	373	AT3G21330 "AT3G21330" [Arabido	0.514	0.233	0.531	4.3e-19
UNIPROTKB|Q6Z9R3	246	P0461F06.33 "BHLH protein fami	0.502	0.345	0.545	6.5e-19
UNIPROTKB|Q67TR8	236	B1342C04.6 "Basic helix-loop-h	0.331	0.237	0.732	4.1e-17
TAIR|locus:2074865	231	HEC2 "AT3G50330" [Arabidopsis	0.313	0.229	0.773	4.1e-17
TAIR|locus:2155543	241	HEC1 "HECATE 1" [Arabidopsis t	0.313	0.219	0.773	4.1e-17
UNIPROTKB|Q657D1	484	P0697C12.40 "BHLH transcriptio	0.331	0.115	0.678	6.7e-16
UNIPROTKB|Q69TX2	211	P0021C04.13 "BHLH protein-like	0.550	0.440	0.478	7.7e-16

TAIR|locus:2179122 APTX "APRATAXIN-like" [Arabidopsis thaliana (taxid:3702)]

 Score = 286 (105.7 bits), Expect = 5.7e-24, P = 5.7e-24
 Identities = 68/140 (48%), Positives = 86/140 (61%)

Query:    30 LSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENI 89
             LSTDPQSVAAR RRHRISDRFKILQSMVPGG KMDT SMLDEAI+YVKFLKA IW+H+N+
Sbjct:    43 LSTDPQSVAARDRRHRISDRFKILQSMVPGGAKMDTVSMLDEAISYVKFLKAQIWYHQNM 102

Query:    90 INFADHHHHEHDPPVAFGQLPGSFPYSPESLYSSINNLAAAPVPQQDSMQASETQPFQDF 149
             + F + H  E      +   PG+  + P+ L+   ++ A  P+    S     T     +
Sbjct:   103 LLFINDH--ETTSSCTYS--PGAGEFGPK-LFGYDDDYA--PIMDTYSQGVPLTVADSKY 155

Query:   150 NVFQGEESETLMHLDGFMKY 169
               + G   +   H+  F KY
Sbjct:   156 TPWFGSVDDEQEHVTYF-KY 174

GO:0003824 "catalytic activity" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0006790 "sulfur compound metabolic process" evidence=IDA

GO:0009150 "purine ribonucleotide metabolic process" evidence=IDA

GO:0047627 "adenylylsulfatase activity" evidence=IDA

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0006259 "DNA metabolic process" evidence=RCA

GO:0006310 "DNA recombination" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007126 "meiosis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0010332 "response to gamma radiation" evidence=RCA

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0032204 "regulation of telomere maintenance" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0043247 "telomere maintenance in response to DNA damage" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

UNIPROTKB|Q5MP56 BA1 "Uncharacterized protein" [Zea mays (taxid:4577)]

 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 44/59 (74%), Positives = 54/59 (91%)

Query:    29 KLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHE 87
             KLSTDPQSVAAR+RRHRISDRF++L+S+VPGG+KMDT SML++AI+YVKFLK  I  H+
Sbjct:    51 KLSTDPQSVAARERRHRISDRFRVLRSLVPGGSKMDTVSMLEQAIHYVKFLKTQISLHQ 109

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2144791 HEC3 "AT5G09750" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 2.4e-19, Sum P(2) = 2.4e-19
 Identities = 42/56 (75%), Positives = 48/56 (85%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVI 83
             +++S DPQSVAAR RR RIS+R +ILQ +VPGGTKMDTASMLDEAI YVKFLK  I
Sbjct:   123 VRISDDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIRYVKFLKRQI 178

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

TAIR|locus:2089418 AT3G21330 "AT3G21330" [Arabidopsis thaliana (taxid:3702)]

 Score = 231 (86.4 bits), Expect = 4.3e-19, P = 4.3e-19
 Identities = 50/94 (53%), Positives = 67/94 (71%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHE 87
             +K+STDPQ+VAARQRR RIS++ ++LQ++VPGGTKMDTASMLDEA NY+KFL+A +   E
Sbjct:   273 VKISTDPQTVAARQRRERISEKIRVLQTLVPGGTKMDTASMLDEAANYLKFLRAQVKALE 332

Query:    88 NIINFADHHHHEHDPPVAFGQLPGSFP-YSPESL 120
             N+    D  +      ++F   P SFP + P  L
Sbjct:   333 NLRPKLDQTN------LSFSSAPTSFPLFHPSFL 360

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|Q6Z9R3 P0461F06.33 "BHLH protein family-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 48/88 (54%), Positives = 61/88 (69%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHE 87
             +++STDPQSVAAR RR RIS+R +ILQ +VPGGTKMDTASMLDEAI+YVKFLK  +   +
Sbjct:   155 VRISTDPQSVAARMRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKTQV---Q 211

Query:    88 NIINFADHHHHEHDPPVAFGQLPGSFPY 115
             ++   A  + H   PP A      +  Y
Sbjct:   212 SLERAAAANGHRPPPPTATSAAAATVAY 239

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q67TR8 B1342C04.6 "Basic helix-loop-helix (BHLH)-like protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 41/56 (73%), Positives = 50/56 (89%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVI 83
             +++S DPQSVAAR RR RIS+R +ILQ +VPGGTKMDTASMLDEAI+YVKFLK+ +
Sbjct:   145 VRISKDPQSVAARLRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKSQV 200

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2074865 HEC2 "AT3G50330" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 41/53 (77%), Positives = 48/53 (90%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLK 80
             +++S DPQSVAAR RR RIS+R +ILQ +VPGGTKMDTASMLDEAI+YVKFLK
Sbjct:   123 VRISKDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLK 175

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

GO:0080126 "ovary septum development" evidence=IGI

TAIR|locus:2155543 HEC1 "HECATE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 41/53 (77%), Positives = 48/53 (90%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLK 80
             +++S DPQSVAAR RR RIS+R +ILQ +VPGGTKMDTASMLDEAI+YVKFLK
Sbjct:   126 VRISKDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLK 178

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

GO:0048445 "carpel morphogenesis" evidence=RCA

UNIPROTKB|Q657D1 P0697C12.40 "BHLH transcription-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 206 (77.6 bits), Expect = 6.7e-16, P = 6.7e-16
 Identities = 38/56 (67%), Positives = 50/56 (89%)

Query:    28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVI 83
             +++S+DPQ+VAARQRR RIS+R ++LQ +VPGG KMDTASMLDEA NY++FLK+ I
Sbjct:   368 VRISSDPQTVAARQRRERISERLRVLQKLVPGGAKMDTASMLDEAANYLRFLKSQI 423

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q69TX2 P0021C04.13 "BHLH protein-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 45/94 (47%), Positives = 57/94 (60%)

Query:    29 KLSTDPQSVAARQRRHRISDRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHEN 88
             ++S++PQSVAAR RR R+S R + LQ +VPGG ++DTASML+EAI YVKFLK  +   E 
Sbjct:   119 RVSSEPQSVAARLRRERVSQRMRALQRLVPGGARLDTASMLEEAIRYVKFLKGHVQSLER 178

Query:    89 IINFADHHHHEHDPPVAFGQLPGSFPYSPESLYS 122
                 A H H  H     F    G   YS  S Y+
Sbjct:   179 AAA-ALHMHGGHAAAAGFAGDAGDAVYSCPSYYA 211

GO:0005634 "nucleus" evidence=IC

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	169
smart00353	53	smart00353, HLH, helix loop helix domain	3e-13
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	7e-13
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	4e-10

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

 Score = 60.3 bits (147), Expect = 3e-13
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 36 SVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAV 82
          +   R+RR +I++ F  L+S++P      K+  A +L  AI Y+K L+  
Sbjct: 1  NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEE 50

Length = 53

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 59.5 bits (145), Expect = 7e-13
 Identities = 17/51 (33%), Positives = 33/51 (64%), Gaps = 3/51 (5%)

Query: 36 SVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVI 83
          ++  R+RR RI+D F  L+S++P      K+  A +L +A++Y+K L+ ++
Sbjct: 9  NLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59

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

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

 Score = 52.5 bits (127), Expect = 4e-10
 Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 2/43 (4%)

Query: 40 RQRRHRISDRFKILQSMVP--GGTKMDTASMLDEAINYVKFLK 80
          R+RR RI+D F+ L+ ++P     K+  A +L  AI Y+K L+
Sbjct: 10 RRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	169
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.53
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.52
smart00353	53	HLH helix loop helix domain.	99.51
KOG1318	411	consensus Helix loop helix transcription factor EB	99.22
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.98
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.96
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.68
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.57
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.21
KOG0561	373	consensus bHLH transcription factor [Transcription	98.05
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.02
PLN03217	93	transcription factor ATBS1; Provisional	97.98
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.86
KOG3910	632	consensus Helix loop helix transcription factor [T	95.7
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	95.68
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	95.13
KOG3898	254	consensus Transcription factor NeuroD and related	93.62
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	92.71
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	91.31
KOG4395	285	consensus Transcription factor Atonal, contains HT	80.24

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

Probab=99.53  E-value=1.7e-14  Score=95.24  Aligned_cols=51  Identities=33%  Similarity=0.660  Sum_probs=48.6

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG---TKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~---~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      ..|+..||+||++||++|..|+++||..   .|+||++||+.||+||+.|+.++
T Consensus         6 ~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           6 EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4699999999999999999999999987   89999999999999999999876

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=99.52  E-value=2e-14  Score=94.49  Aligned_cols=48  Identities=38%  Similarity=0.655  Sum_probs=45.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC-----CCCChhhHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG-----TKMDTASMLDEAINYVKFLK   80 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~-----~K~dkasiL~~aI~YIk~Lq   80 (169)
                      ..|+..||+||++||++|..|+.+||.+     .|+||++||+.||+||++||
T Consensus         3 ~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    3 QKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            3599999999999999999999999976     78999999999999999997

; 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 ....

>smart00353 HLH helix loop helix domain

Probab=99.51  E-value=5.4e-14  Score=91.20  Aligned_cols=49  Identities=33%  Similarity=0.581  Sum_probs=45.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHHH
Q 039972           36 SVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVIW   84 (169)
Q Consensus        36 ~~~ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~~v~   84 (169)
                      +..||+||++||++|..|+++||.   ..|+||++||+.||+||+.|+.+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            368999999999999999999994   6899999999999999999999875

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

Probab=99.22  E-value=1.8e-11  Score=109.60  Aligned_cols=56  Identities=25%  Similarity=0.475  Sum_probs=49.9

Q ss_pred             CCCCCCcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHH
Q 039972           28 MKLSTDPQSVAARQRRHRISDRFKILQSMVPGG----TKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        28 ~~~~~~~h~~~ER~RR~kin~~~~~Lr~lvP~~----~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      .+..++.|+.+|||||++||++|.+|..|||.|    .|..|..||..+++||+.||+..
T Consensus       230 dr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~  289 (411)
T KOG1318|consen  230 DRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTL  289 (411)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHH
Confidence            344567899999999999999999999999987    57779999999999999999854

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

Probab=98.98  E-value=2.8e-10  Score=96.47  Aligned_cols=52  Identities=21%  Similarity=0.415  Sum_probs=46.7

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCC--------CCCCChhhHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPG--------GTKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~--------~~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      +..+-+.||+||+|||++|.+|++||+.        -.|++||.||+-||+|++.|+...
T Consensus        33 k~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~   92 (250)
T KOG4304|consen   33 KVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ   92 (250)
T ss_pred             hhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence            3457899999999999999999999994        278999999999999999999854

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.96  E-value=3.5e-10  Score=92.29  Aligned_cols=57  Identities=28%  Similarity=0.470  Sum_probs=49.9

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhhHHHHHHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPGG-------TKMDTASMLDEAINYVKFLKAVIWFHEN   88 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~~-------~K~dkasiL~~aI~YIk~Lq~~v~~L~~   88 (169)
                      +..|.-+||+||+-||..+..|+.|||.|       .|+.||.||..+|+||.+|+.++...+.
T Consensus        63 r~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~  126 (229)
T KOG1319|consen   63 RRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEE  126 (229)
T ss_pred             HHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34699999999999999999999999954       4888999999999999999998755444

>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]

Probab=98.68  E-value=9e-08  Score=80.48  Aligned_cols=58  Identities=24%  Similarity=0.281  Sum_probs=48.9

Q ss_pred             CCCCCCCcccHHHHHHHHHHHHHHHHHHhcCCCC--CCCC-hhhHHHHHHHHHHHHHHHHH
Q 039972           27 PMKLSTDPQSVAARQRRHRISDRFKILQSMVPGG--TKMD-TASMLDEAINYVKFLKAVIW   84 (169)
Q Consensus        27 ~~~~~~~~h~~~ER~RR~kin~~~~~Lr~lvP~~--~K~d-kasiL~~aI~YIk~Lq~~v~   84 (169)
                      .....+..|+..||+||+.|+++|..|+.+||.+  .+.. .++||+.|++||+.|+.+..
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~  115 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSA  115 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHH
Confidence            3444556799999999999999999999999974  3444 79999999999999998753

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

Probab=98.57  E-value=7.6e-08  Score=92.49  Aligned_cols=51  Identities=24%  Similarity=0.421  Sum_probs=48.0

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPGG----TKMDTASMLDEAINYVKFLKAV   82 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~~----~K~dkasiL~~aI~YIk~Lq~~   82 (169)
                      ++.|+.+||+||+++|..|.+|.+|||.|    .|+||.+||.+||++||.+++.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            56799999999999999999999999985    6999999999999999999985

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.21  E-value=8.6e-07  Score=86.02  Aligned_cols=54  Identities=24%  Similarity=0.484  Sum_probs=49.6

Q ss_pred             CCCCcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHH
Q 039972           30 LSTDPQSVAARQRRHRISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        30 ~~~~~h~~~ER~RR~kin~~~~~Lr~lvP~~-~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      ..+..|+++||+.|..|||+|.+|+++||+. .|+.|..+|..||+||++|+..-
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~n  329 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYN  329 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccc
Confidence            4456799999999999999999999999985 89999999999999999999854

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.05  E-value=3.6e-06  Score=73.25  Aligned_cols=50  Identities=24%  Similarity=0.490  Sum_probs=45.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCChhhHHHHHHHHHHHHHHHH
Q 039972           34 PQSVAARQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        34 ~h~~~ER~RR~kin~~~~~Lr~lvP~--~~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      --+..||+|=.-||-.|..||+|+|.  +.|++||.||+.+.+||.+|+.+.
T Consensus        63 IANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K  114 (373)
T KOG0561|consen   63 IANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK  114 (373)
T ss_pred             hhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence            34567999999999999999999996  799999999999999999999854

>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]

Probab=98.02  E-value=2.8e-05  Score=66.24  Aligned_cols=58  Identities=17%  Similarity=0.356  Sum_probs=49.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHh-cCCC-CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           36 SVAARQRRHRISDRFKILQS-MVPG-GTKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        36 ~~~ER~RR~kin~~~~~Lr~-lvP~-~~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      .+.||+|=.|+||.|.+|+. -.++ ...+-|..||..||+||..||.-++++......+
T Consensus       123 TMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  123 TMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            46799999999999999985 5565 5889999999999999999999999887655544

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.98  E-value=2.6e-05  Score=56.48  Aligned_cols=51  Identities=22%  Similarity=0.310  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHhcCCC------CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           43 RHRISDRFKILQSMVPG------GTKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        43 R~kin~~~~~Lr~lvP~------~~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      -+.|+|.+..|+.|+|.      ..|...+-||.||+.||+.|+.+|..|.+....+
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~L   75 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL   75 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36899999999999994      3567778899999999999999999998766554

>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]

Probab=97.86  E-value=2.4e-05  Score=64.97  Aligned_cols=55  Identities=22%  Similarity=0.462  Sum_probs=48.7

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC----CCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG----GTKMDTASMLDEAINYVKFLKAVIWFHE   87 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~----~~K~dkasiL~~aI~YIk~Lq~~v~~L~   87 (169)
                      ..++..||.|=+.+|..|..||.+||.    ..|+.|..+|..||.||++|+.-++..+
T Consensus       111 ~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~  169 (228)
T KOG4029|consen  111 QARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE  169 (228)
T ss_pred             hhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence            346777999999999999999999994    5789999999999999999999887654

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=95.70  E-value=0.0054  Score=56.90  Aligned_cols=52  Identities=19%  Similarity=0.220  Sum_probs=41.9

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHH
Q 039972           34 PQSVAARQRRHRISDRFKILQSMVPGG----TKMDTASMLDEAINYVKFLKAVIWF   85 (169)
Q Consensus        34 ~h~~~ER~RR~kin~~~~~Lr~lvP~~----~K~dkasiL~~aI~YIk~Lq~~v~~   85 (169)
                      ..++.||.|-..||+.|++|..+.---    ....|.-||..||.-|-.|++||.+
T Consensus       529 aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  529 ANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             hhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            445667777778999999999887532    3345899999999999999999965

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=95.68  E-value=0.0024  Score=51.01  Aligned_cols=51  Identities=27%  Similarity=0.498  Sum_probs=45.9

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC--CCCCChhhHHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~--~~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      ..|++-||+|-..+|+.|.+||.++|.  ..|++|.--|.-|..||-+|=+-+
T Consensus        80 v~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   80 VMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            458999999999999999999999996  589999999999999999986543

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=95.13  E-value=0.022  Score=53.55  Aligned_cols=39  Identities=26%  Similarity=0.526  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHhcCCC----CCCCChhhHHHHHHHHHH
Q 039972           39 ARQRRHRISDRFKILQSMVPG----GTKMDTASMLDEAINYVK   77 (169)
Q Consensus        39 ER~RR~kin~~~~~Lr~lvP~----~~K~dkasiL~~aI~YIk   77 (169)
                      -|+-|+|+|-.++.|.+|+|-    .+|+||.|||.-+|-|++
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            566799999999999999994    599999999999999985

>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]

Probab=93.62  E-value=0.064  Score=45.71  Aligned_cols=50  Identities=26%  Similarity=0.453  Sum_probs=42.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHH
Q 039972           34 PQSVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        34 ~h~~~ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      .=+.-||+|=..+|+-|+.||.+||.   ..|+.|+..|.-|-.||..|++-.
T Consensus        75 kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~  127 (254)
T KOG3898|consen   75 KANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL  127 (254)
T ss_pred             cccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence            34566888888999999999999994   589999999999999999998644

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]

Probab=92.71  E-value=0.075  Score=51.14  Aligned_cols=46  Identities=28%  Similarity=0.527  Sum_probs=39.7

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC----CCCCChhhHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG----GTKMDTASMLDEAINYVKF   78 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~----~~K~dkasiL~~aI~YIk~   78 (169)
                      +...-+.|-||.|-|+-|.+|..++|-    ..-+|||+|+.-||-|++-
T Consensus        48 EkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   48 EKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            344567899999999999999999993    3779999999999999874

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=91.31  E-value=0.24  Score=45.44  Aligned_cols=42  Identities=31%  Similarity=0.486  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCC----CCCCChhhHHHHHHHHHHH
Q 039972           37 VAARQRRHRISDRFKILQSMVPG----GTKMDTASMLDEAINYVKF   78 (169)
Q Consensus        37 ~~ER~RR~kin~~~~~Lr~lvP~----~~K~dkasiL~~aI~YIk~   78 (169)
                      .+.|.||++-|-.|.+|..++|-    ...+|||+|+.-|..|||.
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            46899999999999999999994    2569999999999999985

>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]

Probab=80.24  E-value=2.9  Score=36.10  Aligned_cols=49  Identities=22%  Similarity=0.354  Sum_probs=42.2

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHHH
Q 039972           36 SVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVIW   84 (169)
Q Consensus        36 ~~~ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~~v~   84 (169)
                      +..||+|=..+|..|+.||..||.   ..|++|-..|..|-.||-.|-..+.
T Consensus       179 narErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  179 NARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             chHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            466888888999999999999996   4788999999999999998876653

---

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	169
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-10
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	1e-07
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-07
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	6e-07
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-06

>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 = 53.2 bits (128), Expect = 2e-10
 Identities = 13/46 (28%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 36 SVAARQRRHRISDRFKILQSMVPG-GTKMDTASMLDEAINYVKFLK 80
          +   ++ R  I+D+   L+ +V G   K++ +++L +AI+Y++FL+
Sbjct: 11 NAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQ 56

>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 = 46.2 bits (110), Expect = 1e-07
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLK 80
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++
Sbjct: 11 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 53

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

 Score = 46.2 bits (110), Expect = 1e-07
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 40 RQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLK 80
          RQRR+ +   F  L+  +P      K     +L +A  Y+  ++
Sbjct: 15 RQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58

>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 = 44.2 bits (105), Expect = 6e-07
 Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKA 81
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++ 
Sbjct: 21 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 64

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 6/48 (12%)

Query: 40 RQRRHRISDRFKILQSMVPG------GTKMDTASMLDEAINYVKFLKA 81
          R+RR +I++    L  ++P        +      +L +A +Y++ L+ 
Sbjct: 14 RRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.72
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.66
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.66
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.65
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.64
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.61
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.61
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.61
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.58
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.51
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.51
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.26
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.23
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.17
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.03
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.88
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.84
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.44
1pyi_A	96	Protein (pyrimidine pathway regulator 1); protein-	84.19

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

Probab=99.72  E-value=6.8e-18  Score=119.53  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=57.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFLKAVIWFHENIINFAD   94 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~-~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~~   94 (169)
                      ..|+.+||+||++||++|..|++|||++ .|+|||+||++||+||++|+.+++.|+.....+.
T Consensus         8 ~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~   70 (82)
T 1am9_A            8 TAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4699999999999999999999999997 9999999999999999999999999988666553

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

Probab=99.66  E-value=1.4e-16  Score=119.91  Aligned_cols=60  Identities=22%  Similarity=0.462  Sum_probs=52.2

Q ss_pred             CCCcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 039972           31 STDPQSVAARQRRHRISDRFKILQSMVPGG----TKMDTASMLDEAINYVKFLKAVIWFHENII   90 (169)
Q Consensus        31 ~~~~h~~~ER~RR~kin~~~~~Lr~lvP~~----~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~   90 (169)
                      .+..|+.+||+||++||++|..|++|||++    .|++||+||+.||+||++|+.+++.|+...
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445799999999999999999999999986    378899999999999999999999987643

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

Probab=99.66  E-value=1e-16  Score=111.10  Aligned_cols=56  Identities=27%  Similarity=0.479  Sum_probs=51.6

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFLKAVIWFHE   87 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~~-~K~dkasiL~~aI~YIk~Lq~~v~~L~   87 (169)
                      +.+|+.+||+||++||++|.+|++|||++ .|+||++||+.||+||+.|+.++.-|+
T Consensus         9 R~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            9 RVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            35799999999999999999999999974 799999999999999999999987664

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

Probab=99.65  E-value=3.6e-17  Score=110.76  Aligned_cols=53  Identities=21%  Similarity=0.362  Sum_probs=48.1

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhhHHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPGG-------TKMDTASMLDEAINYVKFLKAVIW   84 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~~-------~K~dkasiL~~aI~YIk~Lq~~v~   84 (169)
                      +.+|..+||+||++||++|..|++|||++       .|++||+||+.||+||++||++|+
T Consensus         3 r~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            45799999999999999999999999953       678899999999999999998763

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

Probab=99.64  E-value=5e-17  Score=109.98  Aligned_cols=52  Identities=19%  Similarity=0.401  Sum_probs=48.0

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCCC------CCChhhHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPGGT------KMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~~~------K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      +..|+.+||+||++||++|..|++|||.+.      |+|||+||+.||+||++|+++.
T Consensus         6 r~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            457999999999999999999999999864      7899999999999999999764

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

Probab=99.61  E-value=8.2e-16  Score=108.03  Aligned_cols=61  Identities=28%  Similarity=0.452  Sum_probs=56.5

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG--TKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~--~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      ..|+..||+||.+||++|..|+++||.+  .|++|++||..||+||+.|+.+++.|+.....+
T Consensus        14 ~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           14 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4699999999999999999999999975  799999999999999999999999999876654

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

Probab=99.61  E-value=1.1e-15  Score=107.96  Aligned_cols=61  Identities=30%  Similarity=0.512  Sum_probs=54.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~--~~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      ..|+..||+||++||++|..|+++||.  +.|++|++||..||+||+.|+.+++.|+.....+
T Consensus         4 ~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L   66 (83)
T 1nkp_B            4 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999999999999999997  4899999999999999999999888777654443

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

Probab=99.61  E-value=1.1e-16  Score=111.31  Aligned_cols=51  Identities=25%  Similarity=0.432  Sum_probs=47.0

Q ss_pred             CCCcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHH
Q 039972           31 STDPQSVAARQRRHRISDRFKILQSMVPGG----TKMDTASMLDEAINYVKFLKA   81 (169)
Q Consensus        31 ~~~~h~~~ER~RR~kin~~~~~Lr~lvP~~----~K~dkasiL~~aI~YIk~Lq~   81 (169)
                      .+..|+.+||+||++||++|.+|++|||.|    .|+|||+||+.||+||+.|+.
T Consensus         9 rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            345799999999999999999999999975    799999999999999999974

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

Probab=99.58  E-value=2.7e-15  Score=107.56  Aligned_cols=58  Identities=22%  Similarity=0.237  Sum_probs=52.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG---TKMDTASMLDEAINYVKFLKAVIWFHENII   90 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~---~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~   90 (169)
                      ..|+..||+||++||++|..|+++||.+   .|++|++||..||+||++|+.+.+.+....
T Consensus         8 ~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~   68 (88)
T 1nkp_A            8 RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEE   68 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999999999999999974   699999999999999999999987765543

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

Probab=99.51  E-value=3.8e-14  Score=100.00  Aligned_cols=61  Identities=20%  Similarity=0.191  Sum_probs=54.1

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      ..|+..||+||..||++|..|+++||.   +.|.+|++||..|++||+.|+++.+.|....+.+
T Consensus         3 ~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L   66 (80)
T 1nlw_A            3 STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            359999999999999999999999995   4789999999999999999999998777655443

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

Probab=99.51  E-value=9e-15  Score=102.39  Aligned_cols=57  Identities=19%  Similarity=0.247  Sum_probs=49.5

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCC---CCCC-ChhhHHHHHHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPG---GTKM-DTASMLDEAINYVKFLKAVIWFHEN   88 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~---~~K~-dkasiL~~aI~YIk~Lq~~v~~L~~   88 (169)
                      +..|+..||+||+.||++|..|+.+||.   +.|. +|++||..||+||++|++++++++.
T Consensus         6 R~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            6 RAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3569999999999999999999999994   4555 7999999999999999999998763

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

Probab=99.26  E-value=6.5e-12  Score=86.11  Aligned_cols=51  Identities=20%  Similarity=0.468  Sum_probs=47.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC--CCCCChhhHHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~--~~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      ..|+..||+|+..||+.|..|+++||.  ..|++|+.||..||+||.+|++.+
T Consensus        14 ~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           14 KAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            358999999999999999999999996  489999999999999999999865

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

Probab=99.23  E-value=1.3e-11  Score=82.67  Aligned_cols=51  Identities=24%  Similarity=0.358  Sum_probs=47.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHHH
Q 039972           34 PQSVAARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVIW   84 (169)
Q Consensus        34 ~h~~~ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~~v~   84 (169)
                      .|+..||+|+..||+.|..||.+||.   ..|++|+.+|..||+||.+|++.++
T Consensus         5 ~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            5 KANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            47889999999999999999999996   4799999999999999999998764

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

Probab=99.17  E-value=2.2e-11  Score=104.49  Aligned_cols=51  Identities=25%  Similarity=0.458  Sum_probs=42.7

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCC-CCCCCChhhHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVP-GGTKMDTASMLDEAINYVKFLKAV   82 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP-~~~K~dkasiL~~aI~YIk~Lq~~   82 (169)
                      +.+|+.+||+||++||+.|.+|++||| ...|+||++||..||+||+.|+..
T Consensus        13 ~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           13 RVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            356999999999999999999999999 468999999999999999999864

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

Probab=99.03  E-value=7e-11  Score=102.60  Aligned_cols=51  Identities=25%  Similarity=0.425  Sum_probs=47.2

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCC----CCCCCChhhHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVP----GGTKMDTASMLDEAINYVKFLKAV   82 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP----~~~K~dkasiL~~aI~YIk~Lq~~   82 (169)
                      +.+|+.+||+||++||+.|..|+.|||    ...|+||++||..||+|||.|+..
T Consensus        14 ~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           14 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            457999999999999999999999999    568999999999999999999853

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

Probab=98.88  E-value=4.8e-10  Score=76.78  Aligned_cols=44  Identities=23%  Similarity=0.476  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHH
Q 039972           38 AARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKA   81 (169)
Q Consensus        38 ~ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~   81 (169)
                      -||+|+..||+.|..||.+||.   ..|++|..+|..||+||..||.
T Consensus        21 rER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           21 EPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            3888999999999999999996   4899999999999999999984

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

Probab=98.84  E-value=6.1e-09  Score=73.83  Aligned_cols=45  Identities=22%  Similarity=0.465  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHH
Q 039972           43 RHRISDRFKILQSMVPGG----TKMDTASMLDEAINYVKFLKAVIWFHE   87 (169)
Q Consensus        43 R~kin~~~~~Lr~lvP~~----~K~dkasiL~~aI~YIk~Lq~~v~~L~   87 (169)
                      |..||++|..|..|||.+    .|.+|++||..|||||++||+.++.+.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~   52 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAK   52 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence            889999999999999964    579999999999999999988765443

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

Probab=98.44  E-value=4e-07  Score=66.23  Aligned_cols=48  Identities=21%  Similarity=0.354  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHHHHH
Q 039972           39 ARQRRHRISDRFKILQSMVPG---GTKMDTASMLDEAINYVKFLKAVIWFH   86 (169)
Q Consensus        39 ER~RR~kin~~~~~Lr~lvP~---~~K~dkasiL~~aI~YIk~Lq~~v~~L   86 (169)
                      ||.|=..||+.|..||.+||.   ..|++|..+|..||+||..|++.++..
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~   83 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSH   83 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            466778899999999999995   479999999999999999999988653

>1pyi_A Protein (pyrimidine pathway regulator 1); protein-DNA complex, transcription/DNA complex, GAL4, zinc finger, Zn2Cys6, binuclear cluster; HET: DNA; 3.20A {Saccharomyces cerevisiae} SCOP: g.38.1.1 h.1.3.1

Probab=84.19  E-value=2.9  Score=28.38  Aligned_cols=25  Identities=16%  Similarity=0.143  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhccCC
Q 039972           73 INYVKFLKAVIWFHENIINFADHHH   97 (169)
Q Consensus        73 I~YIk~Lq~~v~~L~~~~~~~~~~~   97 (169)
                      -.||..|+++|+.||.....+....
T Consensus        47 ~~~~~~Le~rl~~le~~l~~~~~~~   71 (96)
T 1pyi_A           47 RSYVFFLEDRLAVMMRVLKEYGVDP   71 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            4599999999999998877765544

---

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	169
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	3e-13
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	4e-12
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-11
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-10
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-10
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	5e-10
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-09
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	9e-09

>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 = 59.0 bits (143), Expect = 3e-13
 Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 1/40 (2%)

Query: 43 RHRISDRFKILQSMVPGGT-KMDTASMLDEAINYVKFLKA 81
          R  I+D+   L+ +V G   KM  + +L +AI+Y+K+L+ 
Sbjct: 1  RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQ 40

>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 = 56.0 bits (135), Expect = 4e-12
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 7/52 (13%)

Query: 36 SVAARQRRHRISDRFKILQSMVPG-------GTKMDTASMLDEAINYVKFLK 80
            A + RR+R++     L S++P              A+ ++ A  Y++ L+
Sbjct: 7  KHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58

>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 = 55.3 bits (133), Expect = 1e-11
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHE 87
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++     H+
Sbjct: 11 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQ 60

>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 = 53.0 bits (127), Expect = 1e-10
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 36 SVAARQRRHRISDRFKILQSMVP---GGTKMDTASMLDEAINYVKFLKAVI 83
          +V  RQRR+ +   F  L+  +P      K     +L +A  Y+  ++A  
Sbjct: 11 NVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEE 61

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

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.8 bits (124), Expect = 2e-10
 Identities = 11/70 (15%), Positives = 32/70 (45%), Gaps = 7/70 (10%)

Query: 16 KKKKSSGSKSNPMKLSTDPQSVAARQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAI 73
          + K+ + +            ++  R+R  ++++ F+ L+         ++    +L  AI
Sbjct: 2  ELKRKTTNADRRKA-----ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAI 56

Query: 74 NYVKFLKAVI 83
           Y++ L+A++
Sbjct: 57 RYIEGLQALL 66

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

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

 Score = 50.5 bits (121), Expect = 5e-10
 Identities = 10/47 (21%), Positives = 23/47 (48%), Gaps = 6/47 (12%)

Query: 40 RQRRHRISDRFKILQSMVP------GGTKMDTASMLDEAINYVKFLK 80
          R+RR +I++    L  ++P        +      +L +A +Y++ L+
Sbjct: 14 RRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

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

 Score = 50.3 bits (120), Expect = 1e-09
 Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 40 RQRRHRISDRFKILQSMVPGG---TKMDTASMLDEAINYVKFLKAVI 83
          + RR  +    + L+ +VP G   ++  T S+L +A  ++K L+   
Sbjct: 10 KNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSD 56

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

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

 Score = 48.0 bits (114), Expect = 9e-09
 Identities = 13/49 (26%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 36 SVAARQRRHRISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFLKAVI 83
          +   ++ R  I+D+   L+ +V G   K++ +++L +AI+Y++FL+   
Sbjct: 11 NAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSN 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	169
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.64
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.59
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.58
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.57
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.54
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.53

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

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

Probab=99.64  E-value=1.6e-16  Score=109.95  Aligned_cols=61  Identities=21%  Similarity=0.340  Sum_probs=55.7

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~-~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      ..|+.+||+||++||++|..|++|||++ .|+||++||..||+||+.|+.+++.|......+
T Consensus         8 ~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~l   69 (80)
T d1am9a_           8 TAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999999999999999985 799999999999999999999999888755544

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

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.64  E-value=5.3e-17  Score=107.94  Aligned_cols=52  Identities=21%  Similarity=0.397  Sum_probs=48.1

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCC-------CCCCChhhHHHHHHHHHHHHHHHH
Q 039972           32 TDPQSVAARQRRHRISDRFKILQSMVPG-------GTKMDTASMLDEAINYVKFLKAVI   83 (169)
Q Consensus        32 ~~~h~~~ER~RR~kin~~~~~Lr~lvP~-------~~K~dkasiL~~aI~YIk~Lq~~v   83 (169)
                      +..|+.+||+||++||++|..|++|||+       +.|+|||+||+.||+||++|+++|
T Consensus         3 R~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            3579999999999999999999999994       579999999999999999999865

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

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

Probab=99.63  E-value=2.3e-16  Score=108.65  Aligned_cols=61  Identities=21%  Similarity=0.225  Sum_probs=54.6

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG---TKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~---~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      ..|+..||+||++||++|..|+++||++   .|++|++||..||+||+.|+.+++.|......+
T Consensus         3 ~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L   66 (79)
T d1nlwa_           3 STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4699999999999999999999999964   689999999999999999999998887655443

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=2.8e-16  Score=106.02  Aligned_cols=52  Identities=19%  Similarity=0.449  Sum_probs=48.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG--TKMDTASMLDEAINYVKFLKAVIW   84 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~--~K~dkasiL~~aI~YIk~Lq~~v~   84 (169)
                      ..|+..||+||++||++|..|++|||++  .|+||++||..||+||++|++.|+
T Consensus        14 ~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          14 KAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            4699999999999999999999999984  689999999999999999998764

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

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

Probab=99.58  E-value=2e-15  Score=104.77  Aligned_cols=60  Identities=30%  Similarity=0.527  Sum_probs=53.6

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHENIINF   92 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~--~~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~   92 (169)
                      ..|+..||+||++||+.|..|+++||+  +.|++|++||..||+||+.|+++++.|......
T Consensus         4 ~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   65 (83)
T d1nkpb_           4 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD   65 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            369999999999999999999999996  579999999999999999999998877654443

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.57  E-value=2.2e-15  Score=105.64  Aligned_cols=61  Identities=21%  Similarity=0.242  Sum_probs=54.2

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG---TKMDTASMLDEAINYVKFLKAVIWFHENIINFA   93 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~---~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~   93 (169)
                      ..|+.+||+||++||++|..|+++||++   .|++|++||..||+||+.|+++++.|+.....+
T Consensus         8 ~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   71 (88)
T d1nkpa_           8 RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999999999999999963   689999999999999999999998877654443

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.54  E-value=1.3e-15  Score=101.68  Aligned_cols=50  Identities=20%  Similarity=0.436  Sum_probs=46.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC------CCCChhhHHHHHHHHHHHHHHH
Q 039972           33 DPQSVAARQRRHRISDRFKILQSMVPGG------TKMDTASMLDEAINYVKFLKAV   82 (169)
Q Consensus        33 ~~h~~~ER~RR~kin~~~~~Lr~lvP~~------~K~dkasiL~~aI~YIk~Lq~~   82 (169)
                      ..|+.+||+||++||++|..|++|||.+      .|++|++||..||+||++||++
T Consensus         7 ~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~   62 (65)
T d1an4a_           7 AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            4699999999999999999999999953      4899999999999999999875

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

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

Probab=99.53  E-value=2.1e-15  Score=99.59  Aligned_cols=52  Identities=29%  Similarity=0.419  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 039972           43 RHRISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFLKAVIWFHENIINFAD   94 (169)
Q Consensus        43 R~kin~~~~~Lr~lvP~~-~K~dkasiL~~aI~YIk~Lq~~v~~L~~~~~~~~   94 (169)
                      |++||++|..|++|||++ .|+|||+||.+||+||++|+.+++.|+.....+.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999986 6999999999999999999999999988666553