basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2085060477  261 KVKEVKRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQRLQREL 333
Cdd:cd11394      1 PPKVEKRSAHNAIEKRYRSSINDRIIELKDLVVGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQENMALKKAL 73

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2085060477  261 KVKEVKRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQRLQREL 333
Cdd:cd11394      1 PPKVEKRSAHNAIEKRYRSSINDRIIELKDLVVGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQENMALKKAL 73

helix loop helix domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 2085060477   271 NAIERRYRTSINDKITELKNLVVGEQ--AKLNKSAVLRKSIDKIRDLQRQTHE 321
Cdd:smart00353    1 NARERRRRRKINEAFDELRSLLPTLPknKKLSKAEILRLAIEYIKSLQEELQK 53

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  116 VMQPTATIHHMDAQRMPPSAPLYSPSLGNGFVYQTVSPPTPPGDSSPhngnvqtmQTMAGQtaLPHVAPTPPyimcAQPP 195
Cdd:cd23959    100 AMAPDESLGPFRAARVPNPFSASSSTQRETHKTAQVAPPKAEPQTAP--------VTPFGQ--LPMFGQHPP----PAKP 165

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2085060477  196 LTPVAAMPALLKSPTtpMVASPKTSPSIAPQPRSSKGRVAQLAPTPAAAAGEIT 249
Cdd:cd23959    166 LPAAAAAQQSSASPG--EVASPFASGTVSASPFATATDTAPSSGAPDGFPAEAS 217

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2085060477  261 KVKEVKRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQRLQREL 333
Cdd:cd11394      1 PPKVEKRSAHNAIEKRYRSSINDRIIELKDLVVGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQENMALKKAL 73

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 2 (SREBP2) and similar proteins; SREBP2, also termed Class D basic helix-loop-helix protein 2 (bHLHd2), or sterol regulatory element-binding transcription factor 2 (SREBF2), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcription activator of cholesterol biosynthesis.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  266 KRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAE 325
Cdd:cd18922      6 RRTTHNIIEKRYRSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE 65

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family and similar proteins; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box. The family also includes Saccharomyces cerevisiae transcription factor HMS1 (also termed high-copy MEP suppressor protein 1) and serine-rich protein TYE7. HMS1 is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation. TYE7, also termed basic-helix-loop-helix protein SGC1, is a putative bHLHzip transcription activator required for Ty1-mediated glycolytic gene expression. TYE7 N-terminal is extremely rich in serine residues. It binds DNA on E-box motifs, 5'-CANNTG-3'. TYE7 is not essential for growth.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  264 EVKRSAHNAIERRYRTSINDKITELKNLV-----------------VGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAEL 326
Cdd:cd11395      1 PRKRLPHNAIEKRYRSNLNTKIERLRDAIpslrspegksddgglggLAPTTKLSKATILTKAIEYIRHLEQENERLEEEN 80

                   ....*..
gi 2085060477  327 QRLQREL 333
Cdd:cd11395     81 EELRQQV 87

Helix-loop-helix DNA-binding domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2085060477  266 KRSAHNAIERRYRTSINDKITELKNLV--VGEQAKLNKSAVLRKSIDKIRDLQ 316
Cdd:pfam00010    1 RREAHNERERRRRDRINDAFDELRELLptLPPDKKLSKAEILRLAIEYIKHLQ 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins; CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2085060477  265 VKRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHEL--KAELQRLQRE-LMAR 336
Cdd:cd11398      6 QRRDNHKEVERRRRENINEGINELAALVPGNAREKNKGAILARAVEYIQELQETEAKNieKWTLEKLLTDqAIAE 80

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins; MITF, also termed Class E basic helix-loop-helix protein 32 (bHLHe32), is a bHLHzip transcription factor that is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. It regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. It binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  256 SRAQPKVKEvKRSAHNAIERRYRTSINDKITELKNLVVGEQ---AKLNKSAVLRKSIDKIRDLQRQTHELKaELQRLQRE 332
Cdd:cd18926      4 ARALAKERQ-KKDNHNLIERRRRFNINDRIKELGTLIPKSNdpdMRWNKGTILKASVDYIRKLQREQQRAK-ELENRQKK 81

                   .
gi 2085060477  333 L 333
Cdd:cd18926     82 L 82

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like proteins (BIMs) and similar proteins; The family includes Arabidopsis thaliana BIM1 and its homologs (BIM2 and BIM3), which are bHLH transcription factors that interact with BES1 to regulate transcription of Brassinosteroid (BR)-induced gene. BR regulates many growth and developmental processes such as cell elongation, vascular development, senescence stress responses, and photomorphogenesis. BIM1 heterodimerize with BES1 and bind to E-box sequences present in many BR-induced promoters to regulated BR-induced genes.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2085060477  265 VKRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQRL 329
Cdd:cd11453      2 TPRSKHSATEQRRRSKINERLQALRDLIPHSDQKRDKASFLLEVIEYIQALQEKVAKLEEQVQGW 66

basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. Members of the bHLH superfamily have two highly conserved and functionally distinct regions. The basic part is at the amino end of the bHLH that may bind DNA to a consensus hexanucleotide sequence known as the E box (CANNTG). Different families of bHLH proteins recognize different E-box consensus sequences. At the carboxyl-terminal end of the region is the HLH region that interacts with other proteins to form homo- and heterodimers. bHLH proteins function as a diverse set of regulatory factors because they recognize different DNA sequences and dimerize with different proteins. The bHLH proteins can be divided to cell-type specific and widely expressed proteins. The cell-type specific members of bHLH superfamily are involved in cell-fate determination and act in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2085060477  274 ERRYRTSINDKITELKNLV--VGEQAKLNKSAVLRKSIDKIRDLQR 317
Cdd:cd00083      1 ERRRRDKINDAFEELKRLLpeLPDSKKLSKASILQKAVEYIRELQS 46

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription factors and similar proteins; bHLH proteins are the second largest class of plant transcription factors that regulate transcription of genes that are involve in many essential physiological and developmental process. bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. The Arabidopsis bHLH proteins that have been characterized so far have roles in regulation of fruit dehiscence, cell development (carpel, anther and epidermal), phytochrome signaling, flavonoid biosynthesis, hormone signaling and stress responses.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2085060477  270 HNAIERRYRTSINDKITELKNLVVGEQaKLNKSAVLRKSIDKIRDLQRQTHEL 322
Cdd:cd11393      1 HSIAERKRREKINERIRALRSLVPNGG-KTDKASILDEAIEYIKFLQEQVKVL 52

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2085060477  266 KRSAHNAIERRYRTSINDKITELKNLVVG-EQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQRLQR 331
Cdd:cd11404      2 RRLNHVRSEKKRRELIKKGYDELCALVPGlDPQKRTKADILQKAADWIQELKEENEKLEEQLDELKE 68

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, USF2 and similar proteins; Upstream stimulatory factor 1 and 2 (USF-1 and USF-2) are members of bHLHzip transcription factor family. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085060477  270 HNAIERRYRTSINDKITELKNLV-----VGEQAKLNKSAVLRKSIDKIRDLQRQTHE 321
Cdd:cd11396      2 HNEVERRRRDKINNWIVKLAKIVpdcekDNSKQGQSKGGILSKACDYIQELRSQNER 58

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae protein INO2 and similar proteins; INO2 is a positive regulatory factor required for depression of the co-regulated phospholipid biosynthetic enzymes in Saccharomyces cerevisiae. It is also involved in the expression of ITR1.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2085060477  264 EVKRSAHNAIERRYRTSINDKITELKNLVVGEQA----KLNKSAVLRKSIDKIRDLQRQTHELKAEL 326
Cdd:cd11388      1 PVKKWKHVEAEKKRRNQIKKGFEDLINLINYPRNnnekRISKSELLNKAVDDIRGLLKANEQLQEEI 67

basic helix-loop-helix-orange (bHLH-O) domain found in HERP/HES-like family; The HERP/HES-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. The HERP (HES-related repressor protein) subfamily proteins contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. Hairy and enhancer of split (HES)-related repressor protein (HERP) proteins (HEY1, HEY2 and HEYL) act as downstream effectors of Notch signaling. They are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. Hairy and enhancer of split-related protein HELT is a transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. Differentially expressed in chondrocytes proteins, DEC1 and DEC2, are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. Drosophila melanogaster protein clockwork orange (Cwo) is also included in this subfamily. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression. The HES subfamily proteins contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. They form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2085060477  273 IERRYRTSINDKITELKNLVV-----GEQAKLNKSAVLRKSIDKIRDLQR 317
Cdd:cd19685      1 SEKRRRQRINDKLNQLKELLPpnlskQSRSKLSKAEILEMAITELRRLQQ 50

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 (TT8) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as TT8, EGL1, and GL3. TT8, also termed AtbHLH42, or EN 32, is involved in the control of flavonoid pigmentation and plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). EGL1, also termed AtbHLH2, or EN 30, or AtMYC146, or protein enhancer of GLABRA 3, is involved in epidermal cell fate specification and regulates negatively stomata formation but promotes trichome formation. GL3, also termed AtbHLH1, or AtMYC6, or protein shapeshifter, or EN 31, is involved in epidermal cell fate specification. It regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2085060477  269 AHNAIERRYRTSINDKITELKNLVvGEQAKLNKSAVLRKSIDKIRDLQRQTHELKA 324
Cdd:cd11451      5 SHAMAERRRREKLNERFITLRSMV-PFVTKMDKVSILGDAIEYLKQLQRRVEELES 59

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins; USF3, also termed upstream transcription factor 3, is a bHLHzip protein that is involved in the negative regulation of epithelial-mesenchymal transition, the process by which epithelial cells lose their polarity and adhesion properties to become mesenchymal cells with enhanced migration and invasive properties.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2085060477  263 KEVKRSAHNAIERRYRTSINDKITELKNLvvgeqakLNKSAVLRKSIDKIRDlqrQTHELKAELQRLQRELMA 335
Cdd:cd18910      2 REKKRESHNEVERRRKDKINAGINKIGEL-------LPDRDAKKQSKNMILE---QAYKYIVELKKKNDKLLL 64

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2085060477  274 ERRYRTSINDKITELKNlVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQ 327
Cdd:cd11443      7 ERRRRKKLNDRLYMLRS-VVPKITKMDRASILGDAIDYVKELLQEINELQDELE 59

cell division protein DamX; Validated

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  154 PTPPGDSSPHNGNVQTMQTMAGQTAL------------------PH-VAPTPPYIMCAQPPLTPVAAMPALLKSPTTPMV 214
Cdd:PRK10905   124 PTEPATVAPVRNGNASRQTAKTQTAErpattrparkqaviepkkPQaTAKTEPKPVAQTPKRTEPAAPVASTKAPAATST 203

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  215 ASPKTSPSIAPQPRSskgrvAQLAPTPAAAAGEITNGKVAISRAQPkvkevkrSAHNAIERRYRTSIND-----KITELK 289
Cdd:PRK10905   204 PAPKETATTAPVQTA-----SPAQTTATPAAGGKTAGNVGSLKSAP-------SSHYTLQLSSSSNYDNlngwaKKENLK 271

                   ....*.
gi 2085060477  290 NLVVGE 295
Cdd:PRK10905   272 NYVVYE 277

basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins; MYC1, also termed AtbHLH12, or EN 58, acts as a transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2085060477  270 HNAIERRYRTSINDKITELKNLVvGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQR 328
Cdd:cd18918      1 LFATERERREKLNEKFSDLRNLI-PNPTKNDRASILSDAIKYINELQRTVEELKSLVEK 58

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  132 PPSAPLYSPSLGNGFVyqtvSPPTPPGDSSPHNGNVQTMQTMAGQTALPHVAPTPPYIMCAQPPLT----PVAAMPALLK 207
Cdd:PHA03247  2831 PTSAQPTAPPPPPGPP----PPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSrsteSFALPPDQPE 2906

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085060477  208 SPTTPMVASPKTS-------PSIAPQPRSSKGRVAQLAPTPAAAA-------------GEITNGKVAISRAQ 259
Cdd:PHA03247  2907 RPPQPQAPPPPQPqpqppppPQPQPPPPPPPRPQPPLAPTTDPAGagepsgavpqpwlGALVPGRVAVPRFR 2978

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor AP-4 (TFAP4) and similar proteins; TFAP4, also termed activating enhancer-binding protein 4, or Class C basic helix-loop-helix protein 41 (bHLHc41), is a bHLHzip transcription factor that activates both viral and cellular genes involved in the regulation of cellular proliferation, stemness, and epithelial-mesenchymal transition by binding to the symmetrical DNA sequence 5'-CAGCTG-3'.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2085060477  263 KEVKRSAHNAIERRYRTSINDKITELKNLV-VGEQAKLNKSAVLRKSIDKIRDLQRQTHEL 322
Cdd:cd11419      1 RRIRREIANSNERRRMQSINAGFQSLRTLLpHCDGEKLSKAAILQQTAEYIFSLEQEKTRL 61

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  116 VMQPTATIHHMDAQRMPPSAPLYSPSLGNGFVYQTVSPPTPPGDSSPhngnvqtmQTMAGQtaLPHVAPTPPyimcAQPP 195
Cdd:cd23959    100 AMAPDESLGPFRAARVPNPFSASSSTQRETHKTAQVAPPKAEPQTAP--------VTPFGQ--LPMFGQHPP----PAKP 165

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2085060477  196 LTPVAAMPALLKSPTtpMVASPKTSPSIAPQPRSSKGRVAQLAPTPAAAAGEIT 249
Cdd:cd23959    166 LPAAAAAQQSSASPG--EVASPFASGTVSASPFATATDTAPSSGAPDGFPAEAS 217

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  132 PPSAPLYSPSlgngfvyqtVSPPT--PP----GDSSPHNGNVQTMQTMAGQTALPHVA------PTPPYIMCAQPplTPv 199
Cdd:pfam03154  200 TPSAPSVPPQ---------GSPATsqPPnqtqSTAAPHTLIQQTPTLHPQRLPSPHPPlqpmtqPPPPSQVSPQP--LP- 267

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2085060477  200 aamPALLKSPTTPMVASPKTSPS-----IAPQPRSSKGRVAQ----LAPTPAAAAGEITNGKVAISRAQPKVKEVKR 267
Cdd:pfam03154  268 ---QPSLHGQMPPMPHSLQTGPShmqhpVPPQPFPLTPQSSQsqvpPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPR 341

biotin carboxyl carrier protein of acetyl-CoA carboxylase

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2085060477  178 ALPHVAPTPPYIMCAQPPLTPV--AAMPALLKSPTTPmVASPKTSPSIAPQPRSSK 231
Cdd:PLN02983   140 ALPQPPPPAPVVMMQPPPPHAMppASPPAAQPAPSAP-ASSPPPTPASPPPAKAPK 194

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster Circadian locomotor output cycles protein kaput (dCLOCK) and similar proteins; dCLOCK, also termed dPAS1, is a bHLH-PAS Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2085060477  265 VKRSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRD-----LQRQTHELKAE 325
Cdd:cd19735      9 IKRKSRNLSEKKRRDQFNVLINELCSMVSTSNRKMDKSTVLKSTIAFLKNhnevtMQSHQQEIQED 74

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477   44 ILDEMPLLLQTEDPMLKPVERPHVKSEHYS---PVHVKEEMLQQASLPLYNPdplmgsnyklpQQQPQPPPPQHVVMQPT 120
Cdd:pfam03154  166 ILQTQPPVLQAQSGAASPPSPPPPGTTQAAtagPTPSAPSVPPQGSPATSQP-----------PNQTQSTAAPHTLIQQT 234

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  121 ATIH-------HMDAQRMPPSAP--------LYSPSL-------------GNGFVYQTVSP--------------PTPPG 158
Cdd:pfam03154  235 PTLHpqrlpspHPPLQPMTQPPPpsqvspqpLPQPSLhgqmppmphslqtGPSHMQHPVPPqpfpltpqssqsqvPPGPS 314

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  159 DSSPHNGNvQTMQTMAGQTALPhvAPTPPyimcAQPPLTPVA-AMPALLKSPTTPMvaspktsPSIaPQPRSSKGRVAQL 237
Cdd:pfam03154  315 PAAPGQSQ-QRIHTPPSQSQLQ--SQQPP----REQPLPPAPlSMPHIKPPPTTPI-------PQL-PNPQSHKHPPHLS 379

                   ....
gi 2085060477  238 APTP 241
Cdd:pfam03154  380 GPSP 383

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085060477  274 ERRYRTSINDKITELKNlVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKAELQRLQ 330
Cdd:cd11450     11 ERNRRQKLNQRLFALRS-VVPNITKMDKASIIKDAISYIQELQYQEKKLEAEIRELE 66

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2085060477  267 RSAHNAIERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIR 313
Cdd:cd11441      1 RKSRNLSEKKRRDQFNVLINELASMLPGRGRKMDKSTVLKKTIAFLR 47

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  271 NAIERRYRTSINDKITELKNLvvgeQAKLNKSAVLRKSI---------DKIRDLQRQTHELKAELQRLQRELMARDGSKV 341
Cdd:pfam03938   25 EKKFKKRQAELEAKQKELQKL----YEELQKDGALLEEEreekeqelqKKEQELQQLQQKAQQELQKKQQELLQPIQDKI 100

                   ....*
gi 2085060477  342 KDLLQ 346
Cdd:pfam03938  101 NKAIK 105

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP) family; HERP (also called Hey/Hesr/HRT/CHF/gridlock) proteins corresponds to a family of bHLH-O transcriptional repressors that are related to the Drosophila hairy and Enhancer-of-split proteins and act as downstream effectors of Notch signaling. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2085060477  266 KRSAHNAIERRYRTSINDKITELKNLV---VGEQ--AKLNKSAVLRKSIDKIRDLQ 316
Cdd:cd11407      1 RKKRRGIIEKRRRDRINNSLAELRRLVptaFEKQgsAKLEKAEILQMTVDHLKMLH 56

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana ILI1-BINDING BHLH 1 (IBH1) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as IBH1, UPBEAT1, PAR1 and PAR2. IBH1, also termed bHLH zeta, or AtbHLH158, is an atypical and probable non DNA-binding bHLH transcription factor that acts as transcriptional repressor that negatively regulates cell and organ elongation in response to gibberellin (GA) and brassinosteroid (BR) signaling. IBH1 forms heterodimer with BHLH49, thus inhibiting DNA binding of BHLH49, which is a transcriptional activator that regulates the expression of a subset of genes involved in cell expansion by binding to the G-box motif. UPBEAT1, also termed AtbHLH151, or EN 146, is a bHLH transcription factor that modulates the balance between cellular proliferation and differentiation in root growth. It does not act through cytokinin and auxin signaling, but by repressing peroxidase expression in the elongation zone. PAR1 (also termed AtbHLH165, or protein helix-loop-helix 1, or protein phytochrome rapidly regulated 1) and PAR2 (also termed AtbHLH166, or protein helix-loop-helix 2, or protein phytochrome rapidly regulated 2) are two atypical bHLH transcription factors that act as negative regulators of a variety of shade avoidance syndrome (SAS) responses, including seedling elongation and photosynthetic pigment accumulation. They act as direct transcriptional repressor of two auxin-responsive genes, SAUR15 and SAUR68. They may function in integrating shade and hormone transcriptional networks in response to light and auxin changes.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2085060477  274 ERRYRTSINDKITELKNLVVGEQAKLNKSAVLRKSIDKIRDLQRQTHELKA 324
Cdd:cd11444      5 RRRGEEAIERRLRALRRLVPGGRESMEVEELLQETADYIMFLEMQVKVMKS 55

DNA polymerase III subunit gamma/tau;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085060477  154 PTPPGDSSPhNGNVQTMQtmAGQTALPHVAPTPPYIMCAQPPLTPVAAMPALLKSP--TTPMVASPKTSPSIAPQPRSSK 231
Cdd:PRK07003   360 PAVTGGGAP-GGGVPARV--AGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPkaAAAAAATRAEAPPAAPAPPATA 436

                           90       100
                   ....*....|....*....|....*....
gi 2085060477  232 GRVAQLAPTPAAAAGEITNGKVAISRAQP 260
Cdd:PRK07003   437 DRGDDAADGDAPVPAKANARASADSRCDE 465