Citrus Sinensis ID: 026943

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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-------170-------180-------190-------200-------210-------220-------230
Protein Sequence
MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPIYSPAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQVKQNTIQQAACSPSMQSNHMQGD
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHcccccccccccccccccccccccHHHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccHccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccHHHHHHHHHHHHHHHcccHHcccccccccccccccc
Coil and Loop (DISEMBL)
MMTWASYESLkslktkttdedsashgrsenqdedhetktgrshsskrRRTAAVHNQSERRRRDRINQKMKALQKlvpnasktdkasMLDEVIDYLKQLKAQVQMMNNVRnnmpqmnmmmplGMQQQLQMSLLARMGmgvglgtgmgmlDMNTMAAAAATArtapqslpppiyspaasvtlpdpyYAFLAQSMNVELYNKMAALFRQQVKQNTiqqaacspsmqsnhmqgd
Flexible Loop (DISEMBL)
mmtwasyeslkslktkttdedsashgrsenqdedhetktgrshsskrrrtaavhnqserrrrdrinQKMKalqklvpnasktdkasMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPIYSPAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQVKQNTIQQaacspsmqsnhmqgd
Low Complexity Region (SEG)
MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAqvqmmnnvrnnmpqmnmmmplgmqqqlqmSLLARmgmgvglgtgmgmldmntmaaaaatartaPQSLPPPIYSPAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQVKQNTIQQAACSPSMQSNHMQGD
Disordered region (IsUnstruct)
****************************************************************************************DEVIDYLKQLKAQV**************************MSLLARMGMGVGLGTGMGMLDMNT*******************Y*PAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQV**********************
Disordered Region (DISOPRED)
***************************************************************RINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKA**********************************************************************************************************************************
Disordered Region (DISEMBL)
MMTWASYESLKS**************************************************DRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPIYSPAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQVK*********************
Disordered Region (DISPRO)
*************************************************************RDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPIYSPAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQVKQNT******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSHSSKRRRTAAVHxxxxxxxxxxxxxxxxxxxxxVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPIYSPAASVTLPDPYYAFLAQSMNVELYNKMAALFRQQVKQNTIQQAACSPSMQSNHMQGD
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	230	2.2.26 [Sep-21-2011]
Q8GZ38	399	Transcription factor UNE1	yes	no	0.843	0.486	0.467	4e-30
Q570R7	366	Transcription factor PIF7	no	no	0.5	0.314	0.576	1e-23
O80536	524	Transcription factor PIF3	no	no	0.404	0.177	0.514	1e-20
Q8GZM7	478	Transcription factor PIF1	no	no	0.378	0.182	0.540	2e-19
Q9FUA4	373	Transcription factor SPAT	no	no	0.352	0.217	0.585	3e-19
Q8L5W8	416	Transcription factor PIL1	no	no	0.6	0.331	0.377	4e-19
Q9FHA2	210	Transcription factor ALC	no	no	0.365	0.4	0.528	2e-17
Q9SVU6	413	Transcription factor bHLH	no	no	0.517	0.288	0.464	4e-17
Q9SVU7	445	Putative transcription fa	no	no	0.421	0.217	0.457	9e-17
Q8L5W7	363	Transcription factor PIF6	no	no	0.530	0.336	0.382	1e-16

>sp|Q8GZ38|UNE10_ARATH Transcription factor UNE10 OS=Arabidopsis thaliana GN=UNE10 PE=2 SV=1

 Score =  131 bits (329), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 101/216 (46%), Positives = 135/216 (62%), Gaps = 22/216 (10%)

Query: 9   SLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSH-SSKRRRTAAVHNQSERRRRDRINQ 67
           S+ S      D DS  H R + +DE+ +   G+S  S+KR R AA+HNQSER+RRD+INQ
Sbjct: 172 SMGSHDNTIDDHDSVCHSRPQMEDEEEKKAGGKSSVSTKRSRAAAIHNQSERKRRDKINQ 231

Query: 68  KMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQL 127
           +MK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQV MM+  R NMP M + M +  QQQL
Sbjct: 232 RMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVSMMS--RMNMPSMMLPMAMQQQQQL 289

Query: 128 QMSLLAR--MGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPP----PIYSPAASVT-- 179
           QMSL++            G+G+LD+N+M  AAA+A     ++ P    P+  P+   +  
Sbjct: 290 QMSLMSNPMGLGMGMGMPGLGLLDLNSMNRAAASAPNIHANMMPNPFLPMNCPSWDASSN 349

Query: 180 --------LPDPYYAFLA---QSMNVELYNKMAALF 204
                   +PDP  AFLA   Q   +E Y++MA L+
Sbjct: 350 DSRFQSPLIPDPMSAFLACSTQPTTMEAYSRMATLY 385

Required during the fertilization of ovules by pollen.
Arabidopsis thaliana (taxid: 3702)

>sp|Q570R7|PIF7_ARATH Transcription factor PIF7 OS=Arabidopsis thaliana GN=BHLH72 PE=1 SV=2

 Score =  110 bits (274), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 72/125 (57%), Positives = 95/125 (76%), Gaps = 10/125 (8%)

Query: 2   MTWASYESLKSLKT-KTTDEDSASHGRSENQD---EDHETK--TGRSHSSKRRRTAAVHN 55
           M+WAS+ES +SLKT +T D D    G SE QD   ++ ET+   GRS+  +R R AA+HN
Sbjct: 115 MSWASFESGRSLKTARTGDRDYFRSG-SETQDTEGDEQETRGEAGRSNG-RRGRAAAIHN 172

Query: 56  QSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQM 115
           +SERRRRDRINQ+M+ LQKL+P ASK DK S+LD+VI++LKQL+AQVQ M ++R N+PQ 
Sbjct: 173 ESERRRRDRINQRMRTLQKLLPTASKADKVSILDDVIEHLKQLQAQVQFM-SLRANLPQQ 231

Query: 116 NMMMP 120
            MM+P
Sbjct: 232 -MMIP 235

Transcription factor acting negatively in the phytochrome B signaling pathway under prolonged red light. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. May regulate the expression of a subset of genes by binding to the G-box motif.

Arabidopsis thaliana (taxid: 3702)

>sp|O80536|PIF3_ARATH Transcription factor PIF3 OS=Arabidopsis thaliana GN=PIF3 PE=1 SV=1

 Score = 99.8 bits (247), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 52/101 (51%), Positives = 67/101 (66%), Gaps = 8/101 (7%)

Query: 31  QDEDHETKTGRSHS--------SKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNASKT 82
           +D + E+  GR  +        SKR R+A VHN SERRRRDRIN+KM+ALQ+L+PN +K 
Sbjct: 317 EDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKV 376

Query: 83  DKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGM 123
           DKASMLDE I+YLK L+ QVQ+M+          +M P GM
Sbjct: 377 DKASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMFPPGM 417

Transcription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3').

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GZM7|PIF1_ARATH Transcription factor PIF1 OS=Arabidopsis thaliana GN=PIF1 PE=1 SV=1

 Score = 95.9 bits (237), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/98 (54%), Positives = 69/98 (70%), Gaps = 11/98 (11%)

Query: 11  KSLKTKTTDEDSASHGRSENQDEDHETKTGR--SHSSKRRRTAAVHNQSERRRRDRINQK 68
           K  +  TTDE   +  RSE      ETK  R  + S+KR R A VHN SER+RRDRIN++
Sbjct: 253 KEREATTTDE---TESRSE------ETKQARVSTTSTKRSRAAEVHNLSERKRRDRINER 303

Query: 69  MKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMN 106
           MKALQ+L+P  +K+DKASMLDE I+Y+K L+ Q+QMM+
Sbjct: 304 MKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQMMS 341

Transcription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA).

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FUA4|SPT_ARATH Transcription factor SPATULA OS=Arabidopsis thaliana GN=SPT PE=1 SV=1

 Score = 95.1 bits (235), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 48/82 (58%), Positives = 61/82 (74%), Gaps = 1/82 (1%)

Query: 49  RTAAVHNQSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNV 108
           R A VHN SE+RRR RIN+KMKALQ L+PN++KTDKASMLDE I+YLKQL+ QVQM+  +
Sbjct: 197 RAAEVHNLSEKRRRSRINEKMKALQSLIPNSNKTDKASMLDEAIEYLKQLQLQVQML-TM 255

Query: 109 RNNMPQMNMMMPLGMQQQLQMS 130
           RN +    + +P      LQ+S
Sbjct: 256 RNGINLHPLCLPGTTLHPLQLS 277

Transcription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L5W8|PIL1_ARATH Transcription factor PIL1 OS=Arabidopsis thaliana GN=PIL1 PE=1 SV=1

 Score = 94.7 bits (234), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 63/167 (37%), Positives = 92/167 (55%), Gaps = 29/167 (17%)

Query: 9   SLKSLKTKTTD--EDSASHGRSENQDEDHETKT-----GRSHSSKRRRTAAVHNQSERRR 61
           S  SLK K  D  E+ +++  + + DE  + KT      R   +KR+R+  VH   ER+R
Sbjct: 182 SCCSLKRKYGDIEEEESTYLSNNSDDESDDAKTQVHARTRKPVTKRKRSTEVHKLYERKR 241

Query: 62  RDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPL 121
           RD  N+KM+ALQ L+PN  K DKAS+LDE I Y++ L+ QVQMM ++ N + +   M+P+
Sbjct: 242 RDEFNKKMRALQDLLPNCYKDDKASLLDEAIKYMRTLQLQVQMM-SMGNGLIRPPTMLPM 300

Query: 122 GMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLP 168
           G          + MG+G+ +G             AAAT  + PQ LP
Sbjct: 301 GH--------YSPMGLGMHMG-------------AAATPTSIPQFLP 326

Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHA2|ALC_ARATH Transcription factor ALC OS=Arabidopsis thaliana GN=ALC PE=2 SV=1

 Score = 89.4 bits (220), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 62/89 (69%), Gaps = 5/89 (5%)

Query: 22  SASHGRSENQDEDHETKTGRS-----HSSKRRRTAAVHNQSERRRRDRINQKMKALQKLV 76
           S  +G SE   + +  +  RS     +S KR   A  HN SE++RR +IN+KMKALQKL+
Sbjct: 61  SVGYGVSETGQDKYAFEHKRSGAKQRNSLKRNIDAQFHNLSEKKRRSKINEKMKALQKLI 120

Query: 77  PNASKTDKASMLDEVIDYLKQLKAQVQMM 105
           PN++KTDKASMLDE I+YLKQL+ QVQ +
Sbjct: 121 PNSNKTDKASMLDEAIEYLKQLQLQVQTL 149

Required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. Promotes the differentiation of a strip of labile nonlignified cells sandwiched between layers of lignified cells.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVU6|BH023_ARATH Transcription factor bHLH23 OS=Arabidopsis thaliana GN=BHLH23 PE=2 SV=1

 Score = 88.2 bits (217), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 58/125 (46%), Positives = 78/125 (62%), Gaps = 6/125 (4%)

Query: 14  KTKTTDEDSASHGRSENQDEDHETKTGR-SHSSKRRRTAAVHNQSERRRRDRINQKMKAL 72
           +T  TDE      R E   E+  T+  R S SSKR R A +H  SERRRR +IN+ MKAL
Sbjct: 242 ETDITDE-RKRKTREETNVENQGTEEARDSTSSKRSRAAIMHKLSERRRRQKINEMMKAL 300

Query: 73  QKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQMSLL 132
           Q+L+P  +KTD++SMLD+VI+Y+K L++Q+QM +     +P    MM  G  QQ  M  +
Sbjct: 301 QELLPRCTKTDRSSMLDDVIEYVKSLQSQIQMFSMGHVMIPP---MMYAGNIQQQYMPHM 357

Query: 133 ARMGM 137
           A MGM
Sbjct: 358 A-MGM 361

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVU7|BH056_ARATH Putative transcription factor bHLH056 OS=Arabidopsis thaliana GN=BHLH56 PE=4 SV=2

 Score = 87.0 bits (214), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 48/105 (45%), Positives = 70/105 (66%), Gaps = 8/105 (7%)

Query: 23  ASHGRSENQDEDHETKTGR-SHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNASK 81
           A+  + + ++E H T+  R S S KR RTA +HN +ERRRR++IN+KMK LQ+L+P  +K
Sbjct: 228 ATESKLKAREETHGTEEARGSTSRKRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNK 287

Query: 82  TDKASMLDEVIDYLKQLKAQVQ-----MMN--NVRNNMPQMNMMM 119
           + K S LD+ I+Y+K L++Q+Q     MMN  N +  MP M M M
Sbjct: 288 STKVSTLDDAIEYVKSLQSQIQGMMSPMMNAGNTQQFMPHMAMDM 332

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L5W7|PIF6_ARATH Transcription factor PIF6 OS=Arabidopsis thaliana GN=PIF6 PE=1 SV=1

 Score = 86.7 bits (213), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 57/149 (38%), Positives = 77/149 (51%), Gaps = 27/149 (18%)

Query: 46  KRRRTAAVHNQSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMM 105
           KR+R A  +N  ER +R+ IN+KM+ LQ L+PN+ K D  SMLDE I+Y+  L+ QVQMM
Sbjct: 185 KRKRNAEAYNSPERNQRNDINKKMRTLQNLLPNSHKDDNESMLDEAINYMTNLQLQVQMM 244

Query: 106 NNVRNNMPQMNMMMPLGMQQQLQMSLLARMGMGVG---------LGTGM----------- 145
             + N     +MMMPLG     QM L   +GM +G         LG G+           
Sbjct: 245 -TMGNRFVTPSMMMPLGPNYS-QMGLAMGVGMQMGEQQFLPAHVLGAGLPGINDSADMLR 302

Query: 146 -----GMLDMNTMAAAAATARTAPQSLPP 169
                G++ M   A    T   +PQS+PP
Sbjct: 303 FLNHPGLMPMQNSAPFIPTENCSPQSVPP 331

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	230
255547289	440	DNA binding protein, putative [Ricinus c	0.826	0.431	0.668	4e-68
449439645	458	PREDICTED: transcription factor UNE10-li	0.939	0.471	0.55	9e-60
225457285	423	PREDICTED: transcription factor UNE10-li	0.943	0.513	0.571	6e-54
297733906	385	unnamed protein product [Vitis vinifera]	0.943	0.563	0.571	8e-54
255541166	465	DNA binding protein, putative [Ricinus c	0.847	0.419	0.488	4e-40
147864191	367	hypothetical protein VITISV_041734 [Viti	0.847	0.531	0.496	2e-37
297814329	403	hypothetical protein ARALYDRAFT_912247 [	0.869	0.496	0.471	2e-34
297797077	406	hypothetical protein ARALYDRAFT_358332 [	0.973	0.551	0.425	2e-30
359489230	465	PREDICTED: transcription factor UNE10-li	0.821	0.406	0.490	7e-30
20127012	399	putative bHLH transcription factor [Arab	0.869	0.501	0.463	3e-29

>gi|255547289|ref|XP_002514702.1| DNA binding protein, putative [Ricinus communis] gi|223546306|gb|EEF47808.1| DNA binding protein, putative [Ricinus communis]

 Score =  263 bits (672), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 151/226 (66%), Positives = 162/226 (71%), Gaps = 36/226 (15%)

Query: 1   MMTWASYESLK-SLKTKTTDEDSASHGRSENQDEDHETKTG--RSHSSKRRRTAAVHNQS 57
           MMTWAS+ES   SLK KTTDEDSASHG SENQDED ETKT   RSHSS+R R AAVHNQS
Sbjct: 196 MMTWASFESPPPSLKAKTTDEDSASHGGSENQDEDRETKTETVRSHSSRRTRAAAVHNQS 255

Query: 58  ERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNM 117
           ERRRRDRINQKMKALQKLVPNASKTDKASMLDEVI+YLKQL+AQVQ M +VR NMPQ  M
Sbjct: 256 ERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIEYLKQLQAQVQAM-SVR-NMPQ--M 311

Query: 118 MMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAA-----------TARTAPQS 166
           MMPLGMQQQLQMSLLARMGMGV LG GMGMLDM+ MA +A             A +AP  
Sbjct: 312 MMPLGMQQQLQMSLLARMGMGVSLGMGMGMLDMSNMAHSAPQSLPPFIHPTQAAASAPTF 371

Query: 167 LPPPIYSPAA------------------SVTLPDPYYAFLAQSMNV 194
           +PPP   P+                   SV LPDPY + LAQ   V
Sbjct: 372 VPPPFVVPSMIPAHGSAPPASHDPATNNSVPLPDPYCSLLAQVCGV 417

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439645|ref|XP_004137596.1| PREDICTED: transcription factor UNE10-like [Cucumis sativus] gi|449487081|ref|XP_004157490.1| PREDICTED: transcription factor UNE10-like [Cucumis sativus]

 Score =  235 bits (600), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 143/260 (55%), Positives = 176/260 (67%), Gaps = 44/260 (16%)

Query: 1   MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETK--TGRSHSSKRRRTAAVHNQSE 58
           +MTWAS++S +SLKTK+ DEDSA H  SENQ+E+ +TK    RSHS++R R AA+HNQSE
Sbjct: 211 LMTWASFDSPRSLKTKSIDEDSACHVESENQEEEQDTKRVANRSHSARRSRAAAIHNQSE 270

Query: 59  RRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMM 118
           RRRRDRIN+KMKALQKLVPNASKTDKASMLDEVI+YLKQL+AQVQ M +VR+      M+
Sbjct: 271 RRRRDRINEKMKALQKLVPNASKTDKASMLDEVIEYLKQLQAQVQFM-SVRS---MQQMI 326

Query: 119 MPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPIYSPAASV 178
           MP+GMQQQLQMSLLARM      G G+G+     M   +  AR+A Q+LPP I+  +   
Sbjct: 327 MPIGMQQQLQMSLLARM------GMGVGLGMGMGMLDMSGMARSAQQTLPPLIHPTSVPT 380

Query: 179 TLP-----------------------------DPYYAFLAQSMNVELYNKMAALFRQQVK 209
           T P                             DP+ AFLAQ+MN+++YNKMAA +RQQV 
Sbjct: 381 TPPAFVPPHFLLPPSIPRQDPTQAKPATNGSVDPFCAFLAQTMNMDIYNKMAAFYRQQVN 440

Query: 210 QNTIQQAACSPSMQSNHMQG 229
           Q T   A  SP+ QSN+MQG
Sbjct: 441 QTT--NAMSSPT-QSNNMQG 457

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457285|ref|XP_002284441.1| PREDICTED: transcription factor UNE10-like [Vitis vinifera]

 Score =  216 bits (550), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 151/264 (57%), Positives = 170/264 (64%), Gaps = 47/264 (17%)

Query: 1   MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETKT--GRSHSSKRRRTAAVHNQSE 58
           MMTW S ES +SLK KTTDEDSA HG SENQDED ETKT  GRSHS++R R AA+HNQSE
Sbjct: 173 MMTWPSSESPRSLKAKTTDEDSACHGGSENQDEDRETKTQTGRSHSTRRSRAAAIHNQSE 232

Query: 59  RRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMM 118
           RRRRDRINQKMK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQVQMM +VRN    M  M
Sbjct: 233 RRRRDRINQKMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVQMM-SVRNMPQMMMPM 291

Query: 119 MPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPP-----PIYS 173
               MQQQLQMSLLARM      G G+G+     M   +A  R APQ+LP      P+ +
Sbjct: 292 G---MQQQLQMSLLARM------GMGVGLGMGMGMLDMSAVPRAAPQTLPSLLHANPVVA 342

Query: 174 PA---------------------------ASVTLPDPYYAFLAQSMNVELYNKMAALFRQ 206
                                        A+V L DPY AFLAQSMN++LY+KMAAL+RQ
Sbjct: 343 ATPTFVPPPFVVPPMMPSSSQPKSDAGANAAVPLQDPYCAFLAQSMNMDLYHKMAALYRQ 402

Query: 207 QVKQNTIQQAACSPSMQSNHMQGD 230
            V  N   Q   SP   SNH  GD
Sbjct: 403 HV--NHKAQPTSSPP-HSNHDLGD 423

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297733906|emb|CBI15153.3| unnamed protein product [Vitis vinifera]

 Score =  216 bits (549), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 151/264 (57%), Positives = 170/264 (64%), Gaps = 47/264 (17%)

Query: 1   MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETKT--GRSHSSKRRRTAAVHNQSE 58
           MMTW S ES +SLK KTTDEDSA HG SENQDED ETKT  GRSHS++R R AA+HNQSE
Sbjct: 135 MMTWPSSESPRSLKAKTTDEDSACHGGSENQDEDRETKTQTGRSHSTRRSRAAAIHNQSE 194

Query: 59  RRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMM 118
           RRRRDRINQKMK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQVQMM +VRN    M  M
Sbjct: 195 RRRRDRINQKMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVQMM-SVRNMPQMMMPM 253

Query: 119 MPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPP-----PIYS 173
               MQQQLQMSLLARM      G G+G+     M   +A  R APQ+LP      P+ +
Sbjct: 254 G---MQQQLQMSLLARM------GMGVGLGMGMGMLDMSAVPRAAPQTLPSLLHANPVVA 304

Query: 174 PA---------------------------ASVTLPDPYYAFLAQSMNVELYNKMAALFRQ 206
                                        A+V L DPY AFLAQSMN++LY+KMAAL+RQ
Sbjct: 305 ATPTFVPPPFVVPPMMPSSSQPKSDAGANAAVPLQDPYCAFLAQSMNMDLYHKMAALYRQ 364

Query: 207 QVKQNTIQQAACSPSMQSNHMQGD 230
            V  N   Q   SP   SNH  GD
Sbjct: 365 HV--NHKAQPTSSPP-HSNHDLGD 385

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541166|ref|XP_002511647.1| DNA binding protein, putative [Ricinus communis] gi|223548827|gb|EEF50316.1| DNA binding protein, putative [Ricinus communis]

 Score =  170 bits (431), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 111/227 (48%), Positives = 148/227 (65%), Gaps = 32/227 (14%)

Query: 2   MTWASYESLKSLKTKT-TDE-DSASHGRSENQDEDHETKTGRSH-SSKRRRTAAVHNQSE 58
            T  S+ S ++ KT T  DE DS  H    + D+D +   G+S  S+KR R AA+HNQSE
Sbjct: 237 FTSTSFGSQENTKTATAVDENDSVCH----SDDDDKQKANGKSSVSTKRSRAAAIHNQSE 292

Query: 59  RRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMM 118
           R+RRD+INQ+MK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQVQMM+ + N  P   +M
Sbjct: 293 RKRRDKINQRMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVQMMSRM-NIQP---VM 348

Query: 119 MPLGMQQQLQMSLLARMGMGVGL-GTGMGMLDMNTMAAAAATARTAPQSLPPPIYSP--- 174
           +P+ MQQQLQMS+LA M MG+GL G GM ++DMNT+ +    A  +P  L P  + P   
Sbjct: 349 LPMTMQQQLQMSMLAPMNMGMGLAGIGMNVMDMNTI-SRPNIAGISP-VLHPTAFMPMTS 406

Query: 175 ------------AASVTLPDPYYAFLA---QSMNVELYNKMAALFRQ 206
                       A+   + DP  AFLA   Q M ++ Y++MAA+++Q
Sbjct: 407 WDGSSGGDRLQTASPTVMHDPLAAFLACQTQPMTMDAYSRMAAIYQQ 453

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147864191|emb|CAN78817.1| hypothetical protein VITISV_041734 [Vitis vinifera]

 Score =  161 bits (408), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 131/264 (49%), Positives = 149/264 (56%), Gaps = 69/264 (26%)

Query: 1   MMTWASYESLKSLKTKTTDEDSASHGRSENQDEDHETK--TGRSHSSKRRRTAAVHNQSE 58
           MMTW S ES +SLK KTTDEDSA HG SENQDED ETK  TGRSHS++R R AA+HNQSE
Sbjct: 139 MMTWPSSESPRSLKAKTTDEDSACHGGSENQDEDRETKTQTGRSHSTRRSRAAAIHNQSE 198

Query: 59  RRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMM 118
           R                      TDKASMLDEVI+YLKQL+AQVQMM +VRN    M  M
Sbjct: 199 R----------------------TDKASMLDEVIEYLKQLQAQVQMM-SVRNMPQMMMPM 235

Query: 119 MPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPP-----PIYS 173
               MQQQLQMSLLARM      G G+G+     M   +A  R APQ+LP      P+ +
Sbjct: 236 G---MQQQLQMSLLARM------GMGVGLGMGMGMLDMSAVPRAAPQTLPSLLHANPVVA 286

Query: 174 PA---------------------------ASVTLPDPYYAFLAQSMNVELYNKMAALFRQ 206
                                        A+V L DPY AFLAQSMN++LY+KMAAL+RQ
Sbjct: 287 ATPTFVPPPFVVPPMMPSSSQPKSDAGANAAVPLQDPYCAFLAQSMNMDLYHKMAALYRQ 346

Query: 207 QVKQNTIQQAACSPSMQSNHMQGD 230
            V  N   Q   SP   SNH  GD
Sbjct: 347 HV--NHKAQPTSSPP-HSNHDLGD 367

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814329|ref|XP_002875048.1| hypothetical protein ARALYDRAFT_912247 [Arabidopsis lyrata subsp. lyrata] gi|297320885|gb|EFH51307.1| hypothetical protein ARALYDRAFT_912247 [Arabidopsis lyrata subsp. lyrata]

 Score =  151 bits (382), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 106/225 (47%), Positives = 140/225 (62%), Gaps = 25/225 (11%)

Query: 9   SLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSH-SSKRRRTAAVHNQSERRRRDRINQ 67
           S+ S      D DS  H R + +DE+ +   G+S  S+KR R AA+HNQSER+RRD+INQ
Sbjct: 174 SMGSQDNTIDDHDSVCHSRPQMEDEEEKKAGGKSSVSTKRSRAAAIHNQSERKRRDKINQ 233

Query: 68  KMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQL 127
           +MK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQV MM+  R NMP M + M +  QQQ 
Sbjct: 234 RMKILQKLVPNSSKTDKASMLDEVIEYLKQLQAQVSMMS--RMNMPSMMLPMAMQQQQQQ 291

Query: 128 QMSLLAR--MGMGVGLG-TGMGMLDMNTMAAAAAT-------ARTAPQSLPP---PIYSP 174
               L    MG+G+G+G  G+G+LD+N+M  AAA        A   P    P   P +  
Sbjct: 292 LQMSLMSNPMGLGIGMGMPGLGLLDLNSMNRAAAAATAPNIHANMMPNPFAPMTCPSWDA 351

Query: 175 AA------SVTLPDPYYAFLA---QSMNVELYNKMAALFRQQVKQ 210
           ++      S  +PDP  AFLA   Q   +E Y++MAAL++Q  +Q
Sbjct: 352 SSNDARFQSPLIPDPMAAFLACSTQPTTMEAYSRMAALYQQMQQQ 396

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297797077|ref|XP_002866423.1| hypothetical protein ARALYDRAFT_358332 [Arabidopsis lyrata subsp. lyrata] gi|297312258|gb|EFH42682.1| hypothetical protein ARALYDRAFT_358332 [Arabidopsis lyrata subsp. lyrata]

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 108/254 (42%), Positives = 146/254 (57%), Gaps = 30/254 (11%)

Query: 2   MTWASYESLKSLKT-KTTDEDSASHGRSENQD---EDHETK--TGRSHSSKRRRTAAVHN 55
           M+WAS+ES +SLKT +T D D    G SE QD   ++ ET+   GRS S +R R AA+HN
Sbjct: 158 MSWASFESARSLKTARTGDRDYIRSG-SETQDTEGDEQETRGEAGRS-SGRRGRAAAIHN 215

Query: 56  QSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQM 115
           +SERRRRDRINQ+M+ LQKL+P ASK DK S+LD+VI++LKQL+AQVQ M ++R N+PQ 
Sbjct: 216 ESERRRRDRINQRMRTLQKLLPTASKADKVSILDDVIEHLKQLQAQVQFM-SLRANLPQQ 274

Query: 116 NMMMPLGMQQQLQMSLLARMGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPPPI---- 171
            MM+P     Q  +S+  +               M+ +A  A        +    +    
Sbjct: 275 -MMIPQLPPPQSVLSIQHQQQQQQQQQQQQQQFQMSLLATMARMGMGGGGNGYGGLVPPP 333

Query: 172 --------------YSPAASVTLPDPYYAFLAQSMNVELYNKM-AALFRQQVKQNTIQQA 216
                          +  +S TL DPY AF AQ+MN++LYNKM AA++RQQ  Q+T    
Sbjct: 334 PPPPLMVPPMGNRDCTNGSSATLTDPYSAFFAQTMNMDLYNKMAAAIYRQQSDQSTKVNT 393

Query: 217 ACSPSMQSNHMQGD 230
              PS  SNH + D
Sbjct: 394 GM-PSSSSNHEKRD 406

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489230|ref|XP_002275629.2| PREDICTED: transcription factor UNE10-like [Vitis vinifera]

 Score =  136 bits (342), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 105/214 (49%), Positives = 133/214 (62%), Gaps = 25/214 (11%)

Query: 14  KTKTTDE-DSASHGRSENQDEDHETK---TGRSHSSKRRR-TAAVHNQSERRRRDRINQK 68
           KT T D+ DS  H R + +  D E K   TG+S  S +R   AA+HNQSER+RRD+INQ+
Sbjct: 242 KTITVDDHDSVCHSRPQRRAGDEEDKKRGTGKSSVSSKRSRAAAIHNQSERKRRDKINQR 301

Query: 69  MKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQLQ 128
           MK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQVQMMN +  +   M M     +QQQLQ
Sbjct: 302 MKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVQMMNRMNMSPMMMPMT----LQQQLQ 357

Query: 129 MSLLAR-MGMGVGLGTGMGMLDMNTMAAA-AATARTAPQSLPPPIYS-----------PA 175
           MSL+A+          GMG++DMNT+A    AT   +P   P P              PA
Sbjct: 358 MSLMAQMGMGMGMSPMGMGVVDMNTIARPNVATTGISPLLHPTPFLPLTSWDVSGDRLPA 417

Query: 176 ASVTLPDPYYAFLA---QSMNVELYNKMAALFRQ 206
           A   +PDP  AFLA   Q M ++ Y++MAAL++ 
Sbjct: 418 APTMVPDPLAAFLACQSQPMTMDAYSRMAALYQH 451

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|20127012|gb|AAM10933.1|AF488561_1 putative bHLH transcription factor [Arabidopsis thaliana]

 Score =  134 bits (337), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 103/222 (46%), Positives = 139/222 (62%), Gaps = 22/222 (9%)

Query: 9   SLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSH-SSKRRRTAAVHNQSERRRRDRINQ 67
           S+ S      D DS  H R + +DE+ +   G+S  S+KR R AA+HNQSER+RRD+INQ
Sbjct: 172 SMGSHDNTIDDHDSVCHSRPQMEDEEEKKAGGKSSVSTKRSRAAAIHNQSERKRRDKINQ 231

Query: 68  KMKALQKLVPNASKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGMQQQL 127
           +MK LQKLVPN+SKTDKASMLDEVI+YLKQL+AQV MM+  R NMP M + M +  QQQL
Sbjct: 232 RMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVSMMS--RMNMPSMMLPMAMQQQQQL 289

Query: 128 QMSLLAR--MGMGVGLGTGMGMLDMNTMAAAAATARTAPQSLPP----PIYSPAASVT-- 179
           QMSL++            G+G+LD+N+M  AAA+A     ++ P    P+  P+   +  
Sbjct: 290 QMSLMSNPMGLGMGMGMPGLGLLDLNSMNRAAASAPNIHANMMPNPFLPMNCPSWDASSN 349

Query: 180 --------LPDPYYAFLA---QSMNVELYNKMAALFRQQVKQ 210
                   +PDP  AFLA   Q   +E Y++MA L++Q  +Q
Sbjct: 350 DSRFQSPLIPDPMSAFLACSTQPTTMEAYSRMATLYQQMQRQ 391

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	230
TAIR|locus:2163163	366	PIF7 "AT5G61270" [Arabidopsis	0.421	0.265	0.580	1.3e-36
TAIR|locus:2126876	399	UNE10 "AT4G00050" [Arabidopsis	0.4	0.230	0.612	2.6e-30
TAIR|locus:2115080	373	SPT "AT4G36930" [Arabidopsis t	0.421	0.260	0.54	7.4e-19
UNIPROTKB|Q94LR3	191	OSJNBa0010C11.7 "Helix-loop-he	0.195	0.235	0.822	1e-18
TAIR|locus:2061634	478	PIL5 "phytochrome interacting	0.356	0.171	0.511	4.6e-18
UNIPROTKB|Q5VRS4	315	OSJNBa0015I14.14 "Basic helix-	0.339	0.247	0.594	5.8e-18
TAIR|locus:2077680	444	PIL6 "AT3G59060" [Arabidopsis	0.352	0.182	0.552	9.4e-18
TAIR|locus:2012345	524	PIF3 "AT1G09530" [Arabidopsis	0.382	0.167	0.537	1.1e-17
UNIPROTKB|Q948F6	298	OSJNBa0049O12.18 "Putative SPA	0.330	0.255	0.575	2e-17
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.369	0.150	0.558	2.2e-17

TAIR|locus:2163163 PIF7 "AT5G61270" [Arabidopsis thaliana (taxid:3702)]

 Score = 274 (101.5 bits), Expect = 1.3e-36, Sum P(2) = 1.3e-36
 Identities = 61/105 (58%), Positives = 80/105 (76%)

Query:     2 MTWASYESLKSLKT-KTTDEDSASHGRSENQD---EDHETK--TGRSHSSKRRRTAAVHN 55
             M+WAS+ES +SLKT +T D D    G SE QD   ++ ET+   GRS+  +R R AA+HN
Sbjct:   115 MSWASFESGRSLKTARTGDRDYFRSG-SETQDTEGDEQETRGEAGRSNG-RRGRAAAIHN 172

Query:    56 QSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKA 100
             +SERRRRDRINQ+M+ LQKL+P ASK DK S+LD+VI++LKQL+A
Sbjct:   173 ESERRRRDRINQRMRTLQKLLPTASKADKVSILDDVIEHLKQLQA 217

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0003690 "double-stranded DNA binding" evidence=IDA

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

GO:0009704 "de-etiolation" evidence=IMP

GO:0016607 "nuclear speck" evidence=IDA

TAIR|locus:2126876 UNE10 "AT4G00050" [Arabidopsis thaliana (taxid:3702)]

 Score = 281 (104.0 bits), Expect = 2.6e-30, Sum P(2) = 2.6e-30
 Identities = 57/93 (61%), Positives = 71/93 (76%)

Query:     9 SLKSLKTKTTDEDSASHGRSENQDEDHETKTGRSH-SSKRRRTAAVHNQSERRRRDRINQ 67
             S+ S      D DS  H R + +DE+ +   G+S  S+KR R AA+HNQSER+RRD+INQ
Sbjct:   172 SMGSHDNTIDDHDSVCHSRPQMEDEEEKKAGGKSSVSTKRSRAAAIHNQSERKRRDKINQ 231

Query:    68 KMKALQKLVPNASKTDKASMLDEVIDYLKQLKA 100
             +MK LQKLVPN+SKTDKASMLDEVI+YLKQL+A
Sbjct:   232 RMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQA 264

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009567 "double fertilization forming a zygote and endosperm" evidence=IMP

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2115080 SPT "AT4G36930" [Arabidopsis thaliana (taxid:3702)]

 Score = 229 (85.7 bits), Expect = 7.4e-19, P = 7.4e-19
 Identities = 54/100 (54%), Positives = 67/100 (67%)

Query:     3 TWASYESLKSLKTKTTDEDSASH-GRSENQDEDHETKTGRSH--SSKRRRTAAVHNQSER 59
             T  S  S+ +   +T + D  S  G     DE   +K+G S   SSKR R A VHN SE+
Sbjct:   148 TRVSSSSVGASGNETDEYDCESEEGGEAVVDEAPSSKSGPSSRSSSKRCRAAEVHNLSEK 207

Query:    60 RRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLK 99
             RRR RIN+KMKALQ L+PN++KTDKASMLDE I+YLKQL+
Sbjct:   208 RRRSRINEKMKALQSLIPNSNKTDKASMLDEAIEYLKQLQ 247

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009908 "flower development" evidence=NAS

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

GO:0009409 "response to cold" evidence=IMP

GO:0010114 "response to red light" evidence=IMP

GO:0010187 "negative regulation of seed germination" evidence=IMP

GO:0010154 "fruit development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=IEP

UNIPROTKB|Q94LR3 OSJNBa0010C11.7 "Helix-loop-helix DNA-binding domain containing protein, expressed" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 188 (71.2 bits), Expect = 1.0e-18, Sum P(2) = 1.0e-18
 Identities = 37/45 (82%), Positives = 42/45 (93%)

Query:    56 QSERRRRDRINQKMKALQKLVPNASKTDKASMLDEVIDYLKQLKA 100
             ++  +RRDRINQKMK LQKLVPN+SKTDKASMLDEVIDYLKQL+A
Sbjct:     8 KNNHKRRDRINQKMKTLQKLVPNSSKTDKASMLDEVIDYLKQLQA 52

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2061634 PIL5 "phytochrome interacting factor 3-like 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 4.6e-18, Sum P(2) = 4.6e-18
 Identities = 44/86 (51%), Positives = 63/86 (73%)

Query:    16 KTTDEDSASHGRSENQDEDHETKTGR--SHSSKRRRTAAVHNQSERRRRDRINQKMKALQ 73
             K  + ++ +   +E++ E  ETK  R  + S+KR R A VHN SER+RRDRIN++MKALQ
Sbjct:   251 KRKEREATTTDETESRSE--ETKQARVSTTSTKRSRAAEVHNLSERKRRDRINERMKALQ 308

Query:    74 KLVPNASKTDKASMLDEVIDYLKQLK 99
             +L+P  +K+DKASMLDE I+Y+K L+
Sbjct:   309 ELIPRCNKSDKASMLDEAIEYMKSLQ 334

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0015995 "chlorophyll biosynthetic process" evidence=IMP

GO:0010187 "negative regulation of seed germination" evidence=IGI;IMP

GO:0010313 "phytochrome binding" evidence=IDA

GO:0009959 "negative gravitropism" evidence=IMP;TAS

GO:0010029 "regulation of seed germination" evidence=TAS

GO:0010099 "regulation of photomorphogenesis" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

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

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=RCA;IMP

GO:0010100 "negative regulation of photomorphogenesis" evidence=IMP

GO:0010161 "red light signaling pathway" evidence=IDA

GO:0006783 "heme biosynthetic process" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

UNIPROTKB|Q5VRS4 OSJNBa0015I14.14 "Basic helix-loop-helix protein SPATULA-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 47/79 (59%), Positives = 57/79 (72%)

Query:    21 DSASHGRSENQDEDHETKTGRSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNAS 80
             DS + G SE +        G S  SKR R A VHN SE+RRR +IN+KMKALQ L+PN++
Sbjct:    76 DSEAGGSSEPEAAAGARPRGGS-GSKRSRAAEVHNLSEKRRRSKINEKMKALQSLIPNSN 134

Query:    81 KTDKASMLDEVIDYLKQLK 99
             KTDKASMLDE I+YLKQL+
Sbjct:   135 KTDKASMLDEAIEYLKQLQ 153

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2077680 PIL6 "AT3G59060" [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 9.4e-18, P = 9.4e-18
 Identities = 47/85 (55%), Positives = 62/85 (72%)

Query:    19 DEDSASH---GRSENQDEDHETKTG-RSHSSKRRRTAAVHNQSERRRRDRINQKMKALQK 74
             D++S S    G +   D+    K+  RS S++R R A VHN SERRRRDRIN++MKALQ+
Sbjct:   222 DQESVSQSDIGLTSTDDQTMGNKSSQRSGSTRRSRAAEVHNLSERRRRDRINERMKALQE 281

Query:    75 LVPNASKTDKASMLDEVIDYLKQLK 99
             L+P+ S+TDKAS+LDE IDYLK L+
Sbjct:   282 LIPHCSRTDKASILDEAIDYLKSLQ 306

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

GO:0009585 "red, far-red light phototransduction" evidence=IMP

GO:0009693 "ethylene biosynthetic process" evidence=IMP

GO:0010600 "regulation of auxin biosynthetic process" evidence=IDA

GO:0010928 "regulation of auxin mediated signaling pathway" evidence=IDA

GO:0000096 "sulfur amino acid metabolic process" evidence=RCA

GO:0006546 "glycine catabolic process" evidence=RCA

GO:0006636 "unsaturated fatty acid biosynthetic process" evidence=RCA

GO:0006733 "oxidoreduction coenzyme metabolic process" evidence=RCA

GO:0006766 "vitamin metabolic process" evidence=RCA

GO:0007623 "circadian rhythm" evidence=RCA

GO:0008652 "cellular amino acid biosynthetic process" evidence=RCA

GO:0009072 "aromatic amino acid family metabolic process" evidence=RCA

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0009106 "lipoate metabolic process" evidence=RCA

GO:0009108 "coenzyme biosynthetic process" evidence=RCA

GO:0009117 "nucleotide metabolic process" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009684 "indoleacetic acid biosynthetic process" evidence=RCA

GO:0009695 "jasmonic acid biosynthetic process" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010017 "red or far-red light signaling pathway" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0019344 "cysteine biosynthetic process" evidence=RCA

GO:0019748 "secondary metabolic process" evidence=RCA

GO:0019761 "glucosinolate biosynthetic process" evidence=RCA

GO:0030003 "cellular cation homeostasis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0044272 "sulfur compound biosynthetic process" evidence=RCA

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

TAIR|locus:2012345 PIF3 "AT1G09530" [Arabidopsis thaliana (taxid:3702)]

 Score = 223 (83.6 bits), Expect = 1.1e-17, P = 1.1e-17
 Identities = 50/93 (53%), Positives = 64/93 (68%)

Query:    12 SLKTKTTD-EDSASHGRS-ENQDEDHETKTGRSHS---SKRRRTAAVHNQSERRRRDRIN 66
             SLK K ++ +D   H    E +  D   + G S +   SKR R+A VHN SERRRRDRIN
Sbjct:   301 SLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRIN 360

Query:    67 QKMKALQKLVPNASKTDKASMLDEVIDYLKQLK 99
             +KM+ALQ+L+PN +K DKASMLDE I+YLK L+
Sbjct:   361 EKMRALQELIPNCNKVDKASMLDEAIEYLKSLQ 393

GO:0003677 "DNA binding" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009639 "response to red or far red light" evidence=IMP

GO:0010017 "red or far-red light signaling pathway" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0042802 "identical protein binding" evidence=IPI

GO:0031539 "positive regulation of anthocyanin metabolic process" evidence=IMP

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=IMP

GO:0009704 "de-etiolation" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0007165 "signal transduction" evidence=TAS

UNIPROTKB|Q948F6 OSJNBa0049O12.18 "Putative SPATULA" [Oryza sativa (taxid:4530)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 46/80 (57%), Positives = 57/80 (71%)

Query:    20 EDSASHGRSENQDEDHETKTGRSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA 79
             E   + G SE++     T+  R    KR R A VHN SE+RRR RIN+KMKALQ L+PN+
Sbjct:     7 ESEEALGSSESEQP---TRPARPRG-KRSRAAEVHNLSEKRRRSRINEKMKALQSLIPNS 62

Query:    80 SKTDKASMLDEVIDYLKQLK 99
             SKTDKASMLD+ I+YLKQL+
Sbjct:    63 SKTDKASMLDDAIEYLKQLQ 82

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q5NAE0 P0498A12.33 "Putative BP-5 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 221 (82.9 bits), Expect = 2.2e-17, P = 2.2e-17
 Identities = 48/86 (55%), Positives = 60/86 (69%)

Query:    14 KTKTTDEDSASHGRSENQDEDHETKTGRSHSSKRRRTAAVHNQSERRRRDRINQKMKALQ 73
             K +   E SAS    +  DE    +   + S+KR RTA VHN SERRRRDRIN+KM+ALQ
Sbjct:   278 KCQAQAECSASQD-DDLDDEPGVLRKSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQ 336

Query:    74 KLVPNASKTDKASMLDEVIDYLKQLK 99
             +L+PN +K DKASMLDE I+YLK L+
Sbjct:   337 ELIPNCNKIDKASMLDEAIEYLKTLQ 362

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

Your Input: GSVIVG00016258001 SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (365 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	230
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-15
smart00353	53	smart00353, HLH, helix loop helix domain	5e-14
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	1e-12

>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 = 67.6 bits (166), Expect = 2e-15
 Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 5/62 (8%)

Query: 45  SKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQ 101
            K RR A  HN  ERRRR+RIN     L+ L+P      K  KA +L + +DY+K L+  
Sbjct: 1   RKSRREA--HNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58

Query: 102 VQ 103
           +Q
Sbjct: 59  LQ 60

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|197674 smart00353, HLH, helix loop helix domain

 Score = 63.8 bits (156), Expect = 5e-14
 Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 55  NQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQVQ 103
           N  ERRRR +IN+    L+ L+P      K  KA +L   I+Y+K L+ ++Q
Sbjct: 1   NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

Length = 53

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

 Score = 60.6 bits (148), Expect = 1e-12
 Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 5/55 (9%)

Query: 47 RRRTAAVHNQSERRRRDRINQKMKALQKLVPNAS--KTDKASMLDEVIDYLKQLK 99
          RR+    HN+ ERRRRDRIN   + L++L+P     K  KA +L   I+Y+K L+
Sbjct: 1  RRKA---HNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	230
KOG1318	411	consensus Helix loop helix transcription factor EB	99.55
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.54
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.51
smart00353	53	HLH helix loop helix domain.	99.43
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.23
KOG4304	250	consensus Transcriptional repressors of the hairy/	99.15
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.77
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.73
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.67
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.24
KOG0561	373	consensus bHLH transcription factor [Transcription	98.08
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.0
KOG3910	632	consensus Helix loop helix transcription factor [T	97.83
PLN03217	93	transcription factor ATBS1; Provisional	97.65
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.69
KOG3898	254	consensus Transcription factor NeuroD and related	95.17
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	93.75
KOG4395	285	consensus Transcription factor Atonal, contains HT	93.17
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	91.88
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	90.75
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	85.8
KOG3582	856	consensus Mlx interactors and related transcriptio	85.5

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

Probab=99.55  E-value=1e-14  Score=137.00  Aligned_cols=82  Identities=29%  Similarity=0.560  Sum_probs=64.4

Q ss_pred             CCccchhhhhhccHHHHHHHHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHHHHHHHHHHHHH---hhcccCcc
Q 026943           43 HSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLKQLKAQVQMMNN---VRNNMPQM  115 (230)
Q Consensus        43 ~~~k~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk~Lq~~~~~Le~---~~~~~~~~  115 (230)
                      ...|.+++|+.||++|||||++||++|++|..|||.|    .|.+|..||..+|+||+.|++..++..+   ....+...
T Consensus       226 ~~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~rqk~le~~  305 (411)
T KOG1318|consen  226 ALERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRARELENRQKKLEST  305 (411)
T ss_pred             hhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHhH
Confidence            4556777799999999999999999999999999998    3677999999999999999998774443   23333343


Q ss_pred             cccCchhhh
Q 026943          116 NMMMPLGMQ  124 (230)
Q Consensus       116 ~~~lp~~~Q  124 (230)
                      +..|...++
T Consensus       306 n~~L~~rie  314 (411)
T KOG1318|consen  306 NQELALRIE  314 (411)
T ss_pred             HHHHHHHHH
Confidence            444544444

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

Probab=99.54  E-value=9.7e-15  Score=100.87  Aligned_cols=49  Identities=51%  Similarity=0.813  Sum_probs=46.4

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC-----CcchhhhhHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA-----SKTDKASMLDEVIDYLKQLK   99 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-----~K~dKasIL~~aI~YIk~Lq   99 (230)
                      +..||..||+||++||++|.+|+.+||.+     .|++|++||+.||+||++||
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            47899999999999999999999999987     68999999999999999997

; 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 ....

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

Probab=99.51  E-value=3.3e-14  Score=98.74  Aligned_cols=53  Identities=40%  Similarity=0.686  Sum_probs=49.8

Q ss_pred             hhhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHH
Q 026943           50 TAAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        50 ~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      .+..|+..||+||++||++|.+|+.+||..   .|++|++||..||+||++|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999988   78999999999999999999875

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

>smart00353 HLH helix loop helix domain

Probab=99.43  E-value=2.6e-13  Score=92.48  Aligned_cols=49  Identities=41%  Similarity=0.700  Sum_probs=45.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC---CCcchhhhhHHHHHHHHHHHHHHHH
Q 026943           55 NQSERRRRDRINQKMKALQKLVPN---ASKTDKASMLDEVIDYLKQLKAQVQ  103 (230)
Q Consensus        55 n~~ER~RR~~In~~~~~Lr~lvP~---~~K~dKasIL~~aI~YIk~Lq~~~~  103 (230)
                      |..||+||++||++|..|+.+||.   ..|++|++||..||+||++|+.+++
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            568999999999999999999995   5789999999999999999998875

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.23  E-value=8.3e-12  Score=106.41  Aligned_cols=68  Identities=31%  Similarity=0.514  Sum_probs=58.8

Q ss_pred             chhhhhhccHHHHHHHHHHHHHHHHHHhcCCCC-------CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCc
Q 026943           47 RRRTAAVHNQSERRRRDRINQKMKALQKLVPNA-------SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQ  114 (230)
Q Consensus        47 ~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-------~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~  114 (230)
                      +.|+|..|...|++||+.||.++..|++|||.|       .|+.||.||.++|+||.+|..+...-|++...+..
T Consensus        59 k~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k  133 (229)
T KOG1319|consen   59 KDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRK  133 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345578999999999999999999999999976       38999999999999999999988877766555544

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

Probab=99.15  E-value=3e-11  Score=107.75  Aligned_cols=56  Identities=34%  Similarity=0.524  Sum_probs=49.2

Q ss_pred             hhhhhhccHHHHHHHHHHHHHHHHHHhcCCCC--------CcchhhhhHHHHHHHHHHHHHHHH
Q 026943           48 RRTAAVHNQSERRRRDRINQKMKALQKLVPNA--------SKTDKASMLDEVIDYLKQLKAQVQ  103 (230)
Q Consensus        48 ~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--------~K~dKasIL~~aI~YIk~Lq~~~~  103 (230)
                      ..++..|-++|||||+|||+++.+|++||+.+        .|++||.||+.||+|++.|+....
T Consensus        30 ~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   30 QYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             HHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            33467889999999999999999999999954        578999999999999999997544

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

Probab=98.77  E-value=1.4e-08  Score=89.68  Aligned_cols=73  Identities=21%  Similarity=0.347  Sum_probs=60.3

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCCC--cch-hhhhHHHHHHHHHHHHHHHHHHHHhhcccCcccccCchhh
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNAS--KTD-KASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNMMMPLGM  123 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~~--K~d-KasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~~~~~lp~~~  123 (230)
                      +..||..||+||+.|++||..|+.+||..+  +.. .++||++|++||+.|+.+..+.+.+.+.+..+++.|-..+
T Consensus        60 R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl  135 (232)
T KOG2483|consen   60 RAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRKLKARL  135 (232)
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999873  333 6999999999999999988877776666655555554444

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

Probab=98.73  E-value=1.2e-08  Score=102.97  Aligned_cols=51  Identities=33%  Similarity=0.576  Sum_probs=48.3

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLKQLKAQ  101 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk~Lq~~  101 (230)
                      |++||.+|||||+++|.-|+||.+|||.|    .|+||.+||++||.+||.+++.
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            68999999999999999999999999988    4999999999999999999874

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.67  E-value=2.2e-08  Score=101.80  Aligned_cols=62  Identities=32%  Similarity=0.533  Sum_probs=55.5

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC-CcchhhhhHHHHHHHHHHHHHHHHHHHHhhccc
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNM  112 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~  112 (230)
                      |.+||++|||+|..||++|.+|+++||+. .|+.|..+|.+||+||++|+..++.+...+..+
T Consensus       277 RtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l  339 (953)
T KOG2588|consen  277 RTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL  339 (953)
T ss_pred             cchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence            58999999999999999999999999987 799999999999999999999888766544433

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

Probab=98.24  E-value=3.4e-06  Score=75.18  Aligned_cols=57  Identities=25%  Similarity=0.464  Sum_probs=49.0

Q ss_pred             ccHHHHHHHHHHHHHHHHHHh-cCCCC-CcchhhhhHHHHHHHHHHHHHHHHHHHHhhc
Q 026943           54 HNQSERRRRDRINQKMKALQK-LVPNA-SKTDKASMLDEVIDYLKQLKAQVQMMNNVRN  110 (230)
Q Consensus        54 Hn~~ER~RR~~In~~~~~Lr~-lvP~~-~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~  110 (230)
                      -.+.||||=.++|+.|++|+. -++|- .++-|+.||..||+||..||.-++++..+..
T Consensus       122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~  180 (284)
T KOG3960|consen  122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEK  180 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccch
Confidence            457899999999999999987 55655 5799999999999999999999988875443

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.08  E-value=5.8e-06  Score=75.44  Aligned_cols=57  Identities=35%  Similarity=0.598  Sum_probs=50.1

Q ss_pred             chhhhhhccHHHHHHHHHHHHHHHHHHhcCCC--CCcchhhhhHHHHHHHHHHHHHHHH
Q 026943           47 RRRTAAVHNQSERRRRDRINQKMKALQKLVPN--ASKTDKASMLDEVIDYLKQLKAQVQ  103 (230)
Q Consensus        47 ~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~--~~K~dKasIL~~aI~YIk~Lq~~~~  103 (230)
                      |+-+|+.-|..||||-.-||.+|..||.|||.  +.|++||.||+.+.+||..|+.+.-
T Consensus        57 rRmRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt  115 (373)
T KOG0561|consen   57 RRMRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKT  115 (373)
T ss_pred             HHHHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccc
Confidence            33447888999999999999999999999996  4899999999999999999987443

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

Probab=98.00  E-value=6.1e-06  Score=72.36  Aligned_cols=56  Identities=23%  Similarity=0.390  Sum_probs=50.0

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCC----CCcchhhhhHHHHHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPN----ASKTDKASMLDEVIDYLKQLKAQVQMMN  106 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~----~~K~dKasIL~~aI~YIk~Lq~~~~~Le  106 (230)
                      +..+|..||.|-..+|..|.+||.+||.    ..|++|+.+|..||.||++|+.-+..-+
T Consensus       110 ~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~  169 (228)
T KOG4029|consen  110 RQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE  169 (228)
T ss_pred             hhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence            5677888999999999999999999995    4689999999999999999997776555

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.83  E-value=1.9e-05  Score=76.13  Aligned_cols=56  Identities=25%  Similarity=0.325  Sum_probs=47.6

Q ss_pred             hhhhccHHHHHHHHHHHHHHHHHHhcCCCCCc----chhhhhHHHHHHHHHHHHHHHHHH
Q 026943           50 TAAVHNQSERRRRDRINQKMKALQKLVPNASK----TDKASMLDEVIDYLKQLKAQVQMM  105 (230)
Q Consensus        50 ~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~~K----~dKasIL~~aI~YIk~Lq~~~~~L  105 (230)
                      +|...|..||.|-..||+.|+||..++---.|    ..|..||..||..|-.|+++|++-
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            35788999999999999999999998654333    348999999999999999999853

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.65  E-value=0.00012  Score=55.54  Aligned_cols=48  Identities=27%  Similarity=0.502  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHhcCCCC------CcchhhhhHHHHHHHHHHHHHHHHHHHHhh
Q 026943           62 RDRINQKMKALQKLVPNA------SKTDKASMLDEVIDYLKQLKAQVQMMNNVR  109 (230)
Q Consensus        62 R~~In~~~~~Lr~lvP~~------~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~  109 (230)
                      -+.|++.+..|+.|+|..      .|.+.+-||++|+.||+.|+.+|..|.+.-
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerL   72 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERL   72 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            378999999999999953      467788899999999999999999998643

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.69  E-value=0.00088  Score=55.98  Aligned_cols=50  Identities=28%  Similarity=0.442  Sum_probs=46.7

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC--CcchhhhhHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA--SKTDKASMLDEVIDYLKQLKA  100 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--~K~dKasIL~~aI~YIk~Lq~  100 (230)
                      +..||+.||+|-..+|+.|..||.+||..  .|++|.--|+.|..||-+|=.
T Consensus        79 rv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~  130 (173)
T KOG4447|consen   79 RVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ  130 (173)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence            67899999999999999999999999976  899999999999999999864

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

Probab=95.17  E-value=0.02  Score=51.43  Aligned_cols=50  Identities=26%  Similarity=0.435  Sum_probs=43.5

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCC---CCcchhhhhHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPN---ASKTDKASMLDEVIDYLKQLKA  100 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~---~~K~dKasIL~~aI~YIk~Lq~  100 (230)
                      |..=|..||+|--.+|+.|+.||.+||.   ..|+.|...|..|-.||..|..
T Consensus        73 R~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   73 RLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             cccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            3445777999999999999999999994   3789999999999999999873

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=93.75  E-value=0.062  Score=53.08  Aligned_cols=39  Identities=41%  Similarity=0.680  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHH
Q 026943           58 ERRRRDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLK   96 (230)
Q Consensus        58 ER~RR~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk   96 (230)
                      -||-|+|+|.-++.|..|+|--    +|+||.+||.-+|.||+
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            5777999999999999999964    89999999999999986

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

Probab=93.17  E-value=0.37  Score=43.54  Aligned_cols=52  Identities=27%  Similarity=0.393  Sum_probs=45.9

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +..-|..||+|-..+|..|+.||..||..   .|++|-.-|..|-.||--|-...
T Consensus       175 r~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  175 RLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             hcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            46678999999999999999999999976   67999999999999998886444

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

Probab=91.88  E-value=0.32  Score=49.34  Aligned_cols=47  Identities=34%  Similarity=0.498  Sum_probs=39.4

Q ss_pred             hhccHHHHHHHHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHHHH
Q 026943           52 AVHNQSERRRRDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLKQL   98 (230)
Q Consensus        52 ~~Hn~~ER~RR~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk~L   98 (230)
                      +.-.-+.|.||-+-|+-|.+|..+||--    .-+|||+|+.-||.|++-=
T Consensus        48 EkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlr   98 (768)
T KOG3558|consen   48 EKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLR   98 (768)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHH
Confidence            3344568999999999999999999932    5699999999999998743

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=90.75  E-value=0.23  Score=47.84  Aligned_cols=42  Identities=40%  Similarity=0.549  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHHHH
Q 026943           57 SERRRRDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLKQL   98 (230)
Q Consensus        57 ~ER~RR~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk~L   98 (230)
                      ..|.||++-|.-|-+|.+++|-.    ..+||++|+.-|..|||--
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            47899999999999999999954    5699999999999999853

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=85.80  E-value=0.81  Score=47.33  Aligned_cols=11  Identities=9%  Similarity=0.220  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHH
Q 026943           90 EVIDYLKQLKA  100 (230)
Q Consensus        90 ~aI~YIk~Lq~  100 (230)
                      +|.+|=|.+.+
T Consensus       475 kA~e~~kk~~k  485 (1102)
T KOG1924|consen  475 KAAELEKKFDK  485 (1102)
T ss_pred             HHHHHHHHHHH
Confidence            45555444433

>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]

Probab=85.50  E-value=0.11  Score=52.48  Aligned_cols=59  Identities=20%  Similarity=0.331  Sum_probs=49.9

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC-----CcchhhhhHHHHHHHHHHHHHHHHHHHHhh
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA-----SKTDKASMLDEVIDYLKQLKAQVQMMNNVR  109 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-----~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~  109 (230)
                      ...|..+|.+||.+|+-+|..|-.++-+.     .|+.++.-|.++++||..++.+...+.++.
T Consensus       652 ~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~  715 (856)
T KOG3582|consen  652 PITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEA  715 (856)
T ss_pred             cccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhh
Confidence            47899999999999999999999999876     467788889999999998887766655443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	230
4f3l_A	361	Crystal Structure Of The Heterodimeric Clock:bmal1		2e-04
1an4_A	65	Structure And Function Of The BHLHZ DOMAIN OF USF L		6e-04

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 34/46 (73%), Gaps = 1/46 (2%)
Query: 55 NQSERRRRDRINQKMKALQKLVP-NASKTDKASMLDEVIDYLKQLK 99
          N+SE++RRD+ N  +K L  ++P NA K DK+++L + ID+L++ K
Sbjct: 17 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHK 62

>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF Length = 65

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 9/60 (15%)
Query: 46 KRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA------SKTDKASMLDEVIDYLKQLK 99
          KRR   A HN+ ERRRRD+IN  +  L K++P++      S   K  +L +  DY+++L+
Sbjct: 4  KRR---AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	230
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	4e-16
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	3e-15
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-13
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	1e-12
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	2e-12
4f3l_A	361	Mclock, circadian locomoter output cycles protein	4e-08
1a0a_A	63	BHLH, protein (phosphate system positive regulator	2e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	3e-07
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-07

>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 = 69.7 bits (171), Expect = 4e-16
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 46  KRRRTAAVHNQSERRRRDRINQKMKALQKLVPN-ASKTDKASMLDEVIDYLKQLKAQVQM 104
             +RTA  HN  E+R R  IN K+  L+ LV    +K +K+++L + IDY++ L+   Q 
Sbjct: 4   GEKRTA--HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 105 M 105
           +
Sbjct: 62  L 62

>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 = 67.0 bits (164), Expect = 3e-15
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 8/64 (12%)

Query: 46  KRRRTAAVHNQSERRRRDRINQKMKALQKLVP------NASKTDKASMLDEVIDYLKQLK 99
           ++RR    HN+ ERRRRD+IN  +  L K++P        S   K  +L +  DY+++L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 100 AQVQ 103
               
Sbjct: 61  QSNH 64

>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 = 61.6 bits (150), Expect = 4e-13
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 41  RSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVP--NASKTDKASMLDEVIDYLKQL 98
              S   +R    HN  ER+RRD I     +L+  VP     K  +A +LD+  +Y++ +
Sbjct: 5   EVESDADKRAH--HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYM 62

Query: 99  KAQVQMMNNVRNNMPQMN 116
           + +        +++ + N
Sbjct: 63  RRKNHTHQQDIDDLKRQN 80

>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 = 60.5 bits (147), Expect = 1e-12
 Identities = 20/85 (23%), Positives = 42/85 (49%), Gaps = 9/85 (10%)

Query: 47  RRRTAAVHNQSERRRRDRINQKMKALQKLVP--NASKTDKASMLDEVIDYLKQLKAQVQM 104
           +R     HN  ER+RRD I     +L+  VP     K  +A +LD+  +Y++ ++ +   
Sbjct: 2   KRAH---HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHT 58

Query: 105 MNNVRNNMPQMNMMMPLGMQQQLQM 129
                +++ + N +    ++QQ++ 
Sbjct: 59  HQQDIDDLKRQNAL----LEQQVRA 79

>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 = 60.4 bits (147), Expect = 2e-12
 Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 10/89 (11%)

Query: 43  HSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVP---NASKTDKASMLDEVIDYLKQLK 99
           H + +RRT   HN  ER+RR+ + +   AL+  +P   N  K  K  +L +   Y+  ++
Sbjct: 2   HMNVKRRT---HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58

Query: 100 AQVQMMNNVRNNMPQMNMMMPLGMQQQLQ 128
           A+ Q + +  + + +        ++ +L+
Sbjct: 59  AEEQKLISEEDLLRKRREQ----LKHKLE 83

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

 Score = 51.9 bits (124), Expect = 4e-08
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 42 SHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVP-NASKTDKASMLDEVIDYLKQLK 99
              K +      N+SE++RRD+ N  +K L  ++P NA K DK+++L + ID+L++ K
Sbjct: 4  EEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHK 62

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1 Length = 63

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 7/58 (12%)

Query: 52  AVHNQSERRRRDRINQKMKALQKLVPNASKTD-------KASMLDEVIDYLKQLKAQV 102
             H  +E+ RR+R+   +  L  L+P   K         KA+ ++    Y++ L+   
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

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

 Score = 46.0 bits (109), Expect = 3e-07
 Identities = 16/80 (20%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 52  AVHNQSERRRRDRINQKMKALQKLVP---NASKTDKASMLDEVIDYLKQLKAQVQMMNNV 108
           + HN+ E+ RR  +   ++ L+ LVP   ++S+    S+L +   ++K+L+   +   + 
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

Query: 109 RNNMPQMNMMMPLGMQQQLQ 128
            + + +        +++QL+
Sbjct: 63  IDQLQREQRH----LKRQLE 78

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

 Score = 48.5 bits (115), Expect = 5e-07
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 41  RSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVP----NASKTDKASMLDEVIDYLK 96
             H  + +     H+Q E+RRRD++N  +  L  LVP     + K DK ++L   + ++K
Sbjct: 4   AEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 63

Query: 97  QLKA 100
            L+ 
Sbjct: 64  TLRG 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	230
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.74
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.73
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.69
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.65
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.65
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.65
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.64
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.64
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.64
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.59
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.57
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.31
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.29
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.24
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.19
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.12
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.96
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.48

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

Probab=99.74  E-value=2e-18  Score=136.61  Aligned_cols=82  Identities=29%  Similarity=0.524  Sum_probs=52.1

Q ss_pred             CccchhhhhhccHHHHHHHHHHHHHHHHHHhcCCCCC----cchhhhhHHHHHHHHHHHHHHHHHHHHhh---cccCccc
Q 026943           44 SSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNAS----KTDKASMLDEVIDYLKQLKAQVQMMNNVR---NNMPQMN  116 (230)
Q Consensus        44 ~~k~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~~----K~dKasIL~~aI~YIk~Lq~~~~~Le~~~---~~~~~~~  116 (230)
                      ..|+.+++.+||++||+||++||++|.+|++|||++.    |++|++||++||+||++|+.+++.|+...   ..+...+
T Consensus        21 ~~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~~~~~l~~~n  100 (118)
T 4ati_A           21 LAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQKKLEHAN  100 (118)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC---------
T ss_pred             HhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556789999999999999999999999999884    67899999999999999999999998643   3455666


Q ss_pred             ccCchhhhh
Q 026943          117 MMMPLGMQQ  125 (230)
Q Consensus       117 ~~lp~~~Q~  125 (230)
                      ..|...+|+
T Consensus       101 ~~L~~riqe  109 (118)
T 4ati_A          101 RHLLLRVQE  109 (118)
T ss_dssp             ---------
T ss_pred             HHHHHHHHH
Confidence            677766663

>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=99.73  E-value=2.7e-18  Score=127.76  Aligned_cols=67  Identities=30%  Similarity=0.470  Sum_probs=60.4

Q ss_pred             chhhhhhccHHHHHHHHHHHHHHHHHHhcCCCC-CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccC
Q 026943           47 RRRTAAVHNQSERRRRDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMP  113 (230)
Q Consensus        47 ~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~  113 (230)
                      +..++..|+.+||+||++||++|.+|+++||++ .|+||++||.+||+||++|+.+++.|+.+...+.
T Consensus         3 ~~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~   70 (82)
T 1am9_A            3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344578999999999999999999999999998 8999999999999999999999999997664443

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

Probab=99.69  E-value=2.3e-17  Score=119.78  Aligned_cols=61  Identities=31%  Similarity=0.559  Sum_probs=54.8

Q ss_pred             cchhhhhhccHHHHHHHHHHHHHHHHHHhcCCCC-CcchhhhhHHHHHHHHHHHHHHHHHHH
Q 026943           46 KRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQLKAQVQMMN  106 (230)
Q Consensus        46 k~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-~K~dKasIL~~aI~YIk~Lq~~~~~Le  106 (230)
                      |.+.++.+||++||+||++||++|.+|+.|||.+ .|+||++||++||+||+.|+.++.=||
T Consensus         4 k~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            4 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            4455679999999999999999999999999975 699999999999999999998877654

>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=99.65  E-value=1.1e-16  Score=118.30  Aligned_cols=64  Identities=27%  Similarity=0.510  Sum_probs=58.6

Q ss_pred             hhhhccHHHHHHHHHHHHHHHHHHhcCCCC--CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccC
Q 026943           50 TAAVHNQSERRRRDRINQKMKALQKLVPNA--SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMP  113 (230)
Q Consensus        50 ~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~  113 (230)
                      .+..||.+||+||.+||++|.+|+.+||.+  .|++|++||..||+||++|+.++++|+.+...+.
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999986  6999999999999999999999999997665543

>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=99.65  E-value=2.2e-17  Score=117.40  Aligned_cols=52  Identities=38%  Similarity=0.677  Sum_probs=48.6

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCCC------cchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNAS------KTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~~------K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +.+||.+||+||++||++|.+|+.|||.+.      |++|++||++||+||++|+.++
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            588999999999999999999999999885      7899999999999999999764

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

Probab=99.65  E-value=4.3e-17  Score=119.02  Aligned_cols=56  Identities=32%  Similarity=0.559  Sum_probs=50.8

Q ss_pred             ccchhhhhhccHHHHHHHHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHHHHHH
Q 026943           45 SKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLKQLKA  100 (230)
Q Consensus        45 ~k~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk~Lq~  100 (230)
                      .|.++++.+|+.+||+||++||++|.+|+.|||.|    .|+|||+||+.||+||+.|+.
T Consensus         4 ~k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            4 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             -CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            35566689999999999999999999999999987    699999999999999999973

>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=99.64  E-value=1e-16  Score=119.07  Aligned_cols=67  Identities=27%  Similarity=0.505  Sum_probs=60.0

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC--CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCcccc
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA--SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNM  117 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~~~~  117 (230)
                      +.+||.+||+||++||++|.+|+.+||.+  .|++|++||.+||+||++|+.++++|+.+...+...+.
T Consensus         3 R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~   71 (83)
T 1nkp_B            3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNA   71 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999985  79999999999999999999999999977666655333

>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=99.64  E-value=1.1e-16  Score=120.59  Aligned_cols=67  Identities=22%  Similarity=0.372  Sum_probs=59.1

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCcccc
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQMNM  117 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~~~~  117 (230)
                      +..||.+||+||++||++|..|+++||.+   .|.+|++||.+||+||++|+.+++.|..+...+...+.
T Consensus         7 R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n~   76 (88)
T 1nkp_A            7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRRE   76 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            58899999999999999999999999975   59999999999999999999999998876555544333

>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=99.64  E-value=4.3e-17  Score=115.78  Aligned_cols=52  Identities=23%  Similarity=0.506  Sum_probs=47.8

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC-------CcchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA-------SKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-------~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +.+|+++||+||++||.+|.+|+.|||++       .|.+||+||+.||+||+.|++++
T Consensus         3 r~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999965       46779999999999999999765

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

Probab=99.59  E-value=9.1e-16  Score=113.75  Aligned_cols=64  Identities=22%  Similarity=0.344  Sum_probs=57.9

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCc
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQ  114 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~  114 (230)
                      +..||.+||+||+.||++|..|+++||.+   .|.+|++||.+|++||+.|+.+++.|..+...+..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999965   68999999999999999999999999977655544

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

Probab=99.57  E-value=1.1e-15  Score=112.41  Aligned_cols=56  Identities=30%  Similarity=0.456  Sum_probs=49.6

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCC---CCcc-hhhhhHHHHHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPN---ASKT-DKASMLDEVIDYLKQLKAQVQMMN  106 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~---~~K~-dKasIL~~aI~YIk~Lq~~~~~Le  106 (230)
                      +.+||.+||+||+.||++|.+|+.+||.   ..|. +|++||.+||+||++|+.++++++
T Consensus         6 R~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            6 RAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999995   3565 799999999999999999999887

>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=99.31  E-value=2.6e-12  Score=92.43  Aligned_cols=52  Identities=23%  Similarity=0.445  Sum_probs=48.2

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC--CcchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA--SKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +..||..||+|+..||+.|..||.+||..  .|++|+.||..||+||.+|+..+
T Consensus        13 R~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999975  68999999999999999999654

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

Probab=99.29  E-value=3.3e-12  Score=89.74  Aligned_cols=52  Identities=27%  Similarity=0.346  Sum_probs=47.7

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +..||..||+|+..||+.|..||.+||..   .|++|+.||..||+||.+|+..+
T Consensus         3 R~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L   57 (60)
T 2ql2_B            3 RMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL   57 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHT
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHH
Confidence            35699999999999999999999999975   58999999999999999999754

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

Probab=99.24  E-value=4.6e-12  Score=94.18  Aligned_cols=64  Identities=25%  Similarity=0.509  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHhcCCCC----CcchhhhhHHHHHHHHHHHHHHHHHHHHh---hcccCcccccCchhhhh
Q 026943           62 RDRINQKMKALQKLVPNA----SKTDKASMLDEVIDYLKQLKAQVQMMNNV---RNNMPQMNMMMPLGMQQ  125 (230)
Q Consensus        62 R~~In~~~~~Lr~lvP~~----~K~dKasIL~~aI~YIk~Lq~~~~~Le~~---~~~~~~~~~~lp~~~Q~  125 (230)
                      |.+||++|.+|++|||.+    .|.+|++||.+||+||++|+.+++.+..+   ...++..|..|+..+|+
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r~k~le~~n~~l~~riqE   74 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQKKLEHANRHLLLRVQE   74 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            899999999999999976    46899999999999999999988866653   33455666677777774

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

Probab=99.19  E-value=1.3e-11  Score=112.00  Aligned_cols=55  Identities=36%  Similarity=0.633  Sum_probs=42.5

Q ss_pred             chhhhhhccHHHHHHHHHHHHHHHHHHhcCC-CCCcchhhhhHHHHHHHHHHHHHH
Q 026943           47 RRRTAAVHNQSERRRRDRINQKMKALQKLVP-NASKTDKASMLDEVIDYLKQLKAQ  101 (230)
Q Consensus        47 ~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP-~~~K~dKasIL~~aI~YIk~Lq~~  101 (230)
                      ...++..||.+||+||++||+.|.+|+.||| +..|+||++||..||+|||.|+..
T Consensus         9 ~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A            9 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            3344688999999999999999999999999 557999999999999999999854

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

Probab=99.12  E-value=3.5e-11  Score=110.54  Aligned_cols=57  Identities=32%  Similarity=0.536  Sum_probs=49.6

Q ss_pred             ccchhhhhhccHHHHHHHHHHHHHHHHHHhcCC----CCCcchhhhhHHHHHHHHHHHHHH
Q 026943           45 SKRRRTAAVHNQSERRRRDRINQKMKALQKLVP----NASKTDKASMLDEVIDYLKQLKAQ  101 (230)
Q Consensus        45 ~k~~r~~~~Hn~~ER~RR~~In~~~~~Lr~lvP----~~~K~dKasIL~~aI~YIk~Lq~~  101 (230)
                      .|.+.++.+|+.+||+||++||+.|.+|+.|||    ...|+||++||..||+|||.|+..
T Consensus         8 ~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B            8 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             chhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            344555789999999999999999999999999    558999999999999999999843

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

Probab=98.96  E-value=1.6e-10  Score=82.84  Aligned_cols=45  Identities=27%  Similarity=0.476  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHH
Q 026943           56 QSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKA  100 (230)
Q Consensus        56 ~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~  100 (230)
                      ..||+|+..||++|..||.+||..   .|++|..||..||+||..||.
T Consensus        20 erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           20 EEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            349999999999999999999975   689999999999999999984

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

Probab=98.48  E-value=2.2e-07  Score=70.89  Aligned_cols=47  Identities=28%  Similarity=0.412  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHHHH
Q 026943           58 ERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQVQM  104 (230)
Q Consensus        58 ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~~~  104 (230)
                      ||.|-..||+.|..||.+||..   .|++|..+|..||+||.+|+.-+..
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            5778889999999999999965   6899999999999999999976654

---

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	230
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	4e-13
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	8e-13
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	3e-12
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	3e-12
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	5e-12
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	2e-11
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	2e-11
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	3e-11

>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 = 60.7 bits (147), Expect = 4e-13
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 8/84 (9%)

Query: 48  RRTAAVHNQSERRRRDRINQKMKALQKLVP--NASKTDKASMLDEVIDYLKQLKAQVQMM 105
           +R    HN  ER+RRD I     +L+  VP     K  +A +LD+  +Y++ ++ +    
Sbjct: 2   KRAH--HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH 59

Query: 106 NNVRNNMPQMNMMMPLGMQQQLQM 129
               +++ + N +    ++QQ++ 
Sbjct: 60  QQDIDDLKRQNAL----LEQQVRA 79

>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 = 59.4 bits (144), Expect = 8e-13
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 45  SKRRRTAAVHNQSERRRRDRINQKMKALQKLVP------NASKTDKASMLDEVIDYLKQL 98
            ++RR    HN+ ERRRRD+IN  +  L K++P        S   K  +L +  DY+++L
Sbjct: 2   DEKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

Query: 99  KAQVQ 103
           +    
Sbjct: 60  RQSNH 64

>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 = 58.4 bits (141), Expect = 3e-12
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 43  HSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVP---NASKTDKASMLDEVIDYLKQLK 99
           H + +RRT   HN  ER+RR+ + +   AL+  +P   N  K  K  +L +   Y+  ++
Sbjct: 2   HMNVKRRT---HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58

Query: 100 AQVQMMNNVRNNMPQMNMMM 119
           A+ Q + +  + + +    +
Sbjct: 59  AEEQKLISEEDLLRKRREQL 78

>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 = 58.0 bits (140), Expect = 3e-12
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 41  RSHSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNAS--KTDKASMLDEVIDYLKQL 98
           R  ++  RR A      ERRR  ++N+  + L++   +    +  K  +L   I Y++ L
Sbjct: 5   RKTTNADRRKA--ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGL 62

Query: 99  KAQVQ 103
           +A ++
Sbjct: 63  QALLR 67

>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 = 57.2 bits (138), Expect = 5e-12
 Identities = 13/63 (20%), Positives = 28/63 (44%), Gaps = 9/63 (14%)

Query: 48  RRTAAVHNQSERRRRDRINQKMKALQKLVPNA-------SKTDKASMLDEVIDYLKQLKA 100
           +R +  H  +E+ RR+R+   +  L  L+P         +   KA+ ++    Y++ L+ 
Sbjct: 2   KRES--HKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQ 59

Query: 101 QVQ 103
              
Sbjct: 60  NGS 62

>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 = 56.1 bits (135), Expect = 2e-11
 Identities = 14/77 (18%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 52  AVHNQSERRRRDRINQKMKALQKLVP---NASKTDKASMLDEVIDYLKQLKAQVQMMNNV 108
           + HN+ E+ RR  +   ++ L+ LVP   ++S+    S+L +   ++K+L+   +   + 
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

Query: 109 RNNMPQMNMMMPLGMQQ 125
            + + +    +   +++
Sbjct: 63  IDQLQREQRHLKRQLEK 79

>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 = 55.5 bits (134), Expect = 2e-11
 Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 62  RDRINQKMKALQKLVPN-ASKTDKASMLDEVIDYLKQLKAQVQMM 105
           R  IN K+  L+ LV    +K  K+ +L + IDY+K L+     +
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKL 45

>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 = 55.7 bits (134), Expect = 3e-11
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 44  SSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQLKAQV 102
           S   +RTA  HN  E+R R  IN K+  L+ LV    +K +K+++L + IDY++ L+   
Sbjct: 2   SRGEKRTA--HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSN 59

Query: 103 QMMNNVRNNMPQMNM 117
           Q +     ++     
Sbjct: 60  QKLKQENLSLRTAVH 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	230
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.63
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.6
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.6
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.55
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.44

>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=99.66  E-value=4e-17  Score=118.82  Aligned_cols=63  Identities=30%  Similarity=0.483  Sum_probs=57.4

Q ss_pred             hhhhccHHHHHHHHHHHHHHHHHHhcCCCC-CcchhhhhHHHHHHHHHHHHHHHHHHHHhhccc
Q 026943           50 TAAVHNQSERRRRDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNM  112 (230)
Q Consensus        50 ~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~-~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~  112 (230)
                      .+..||.+||+||++||++|.+|++|||++ .|++|++||..||+||++|+.+++.|+.+...+
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~l   69 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            368899999999999999999999999986 689999999999999999999999998665444

>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=99.64  E-value=7.5e-17  Score=116.87  Aligned_cols=64  Identities=22%  Similarity=0.344  Sum_probs=57.3

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCc
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQ  114 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~  114 (230)
                      +..||.+||+||++||++|.+|+++||.+   .|.+|++||..||+||+.|+.+++.|+.+...+..
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~   68 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999975   58999999999999999999999999876654443

>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=99.63  E-value=8.6e-17  Score=112.21  Aligned_cols=52  Identities=23%  Similarity=0.513  Sum_probs=47.8

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCC-------CCcchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPN-------ASKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~-------~~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +..||.+||+||++||++|.+|+.+||.       ..|++|++||+.||+||++|++++
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            4789999999999999999999999994       368999999999999999999754

>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=99.60  E-value=1.8e-16  Score=115.78  Aligned_cols=64  Identities=27%  Similarity=0.517  Sum_probs=57.4

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC--CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCc
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA--SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQ  114 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~  114 (230)
                      +.+||.+||+||++||++|.+|+++||++  .|++|++||..||+||+.|+.++..|+.+...+..
T Consensus         3 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   68 (83)
T d1nkpb_           3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999964  68999999999999999999999999876554433

>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=99.60  E-value=2.2e-16  Score=111.81  Aligned_cols=53  Identities=23%  Similarity=0.446  Sum_probs=49.1

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC--CcchhhhhHHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA--SKTDKASMLDEVIDYLKQLKAQVQ  103 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~--~K~dKasIL~~aI~YIk~Lq~~~~  103 (230)
                      +..||..||+||++||++|.+|+.+||.+  .|++|++||..||+||++|++.++
T Consensus        13 R~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            57899999999999999999999999986  578999999999999999997653

>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=99.60  E-value=2.2e-16  Score=116.56  Aligned_cols=65  Identities=23%  Similarity=0.402  Sum_probs=57.6

Q ss_pred             hhhhccHHHHHHHHHHHHHHHHHHhcCCCC---CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccCc
Q 026943           50 TAAVHNQSERRRRDRINQKMKALQKLVPNA---SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMPQ  114 (230)
Q Consensus        50 ~~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~---~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~~  114 (230)
                      ++..||.+||+||++||++|..|+++||++   .|.+|++||..||+||++|+.++..|+.+...+..
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   73 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK   73 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999965   57999999999999999999999999876554443

>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=99.55  E-value=4.8e-16  Score=108.98  Aligned_cols=52  Identities=38%  Similarity=0.677  Sum_probs=47.8

Q ss_pred             hhhccHHHHHHHHHHHHHHHHHHhcCCCC------CcchhhhhHHHHHHHHHHHHHHH
Q 026943           51 AAVHNQSERRRRDRINQKMKALQKLVPNA------SKTDKASMLDEVIDYLKQLKAQV  102 (230)
Q Consensus        51 ~~~Hn~~ER~RR~~In~~~~~Lr~lvP~~------~K~dKasIL~~aI~YIk~Lq~~~  102 (230)
                      +..||.+||+||++||++|.+|+++||.+      .|++|++||..||+||+.|++++
T Consensus         6 R~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            47899999999999999999999999975      38999999999999999998654

>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=99.44  E-value=1.5e-14  Score=100.12  Aligned_cols=52  Identities=29%  Similarity=0.430  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHhcCCCC-CcchhhhhHHHHHHHHHHHHHHHHHHHHhhcccC
Q 026943           62 RDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQLKAQVQMMNNVRNNMP  113 (230)
Q Consensus        62 R~~In~~~~~Lr~lvP~~-~K~dKasIL~~aI~YIk~Lq~~~~~Le~~~~~~~  113 (230)
                      |++||++|.+|+++||++ .|+|||+||.+||+||+.|+.+++.|+.+...+.
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            678999999999999987 5999999999999999999999999997665443