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 1924581578   87 LSGPQAAPSPlsPPQPAPTPLKMYPSMPafsPGPGIKeesvPLSILQT---PTPQPLPGALLPQSFPAPAPP-------Q 156
Cdd:pfam03154  366 LPNPQSHKHP--PHLSGPSPFQMNSNLP---PPPALK----PLSSLSThhpPSAHPPPLQLMPQSQQLPPPPaqppvltQ 436

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1924581578  157 FSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQVQSVVP 210
Cdd:pfam03154  437 SQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMP 490

Helix-loop-helix DNA-binding domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1924581578  324 KRTAHNAIEKRYRSSINDKIIELKDLV--------LNKSAVLRKAIDYIRFLQ 368
Cdd:pfam00010    1 RREAHNERERRRRDRINDAFDELRELLptlppdkkLSKAEILRLAIEYIKHLQ 53

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 1924581578   87 LSGPQAAPSPlsPPQPAPTPLKMYPSMPafsPGPGIKeesvPLSILQT---PTPQPLPGALLPQSFPAPAPP-------Q 156
Cdd:pfam03154  366 LPNPQSHKHP--PHLSGPSPFQMNSNLP---PPPALK----PLSSLSThhpPSAHPPPLQLMPQSQQLPPPPaqppvltQ 436

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1924581578  157 FSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQVQSVVP 210
Cdd:pfam03154  437 SQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMP 490

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   49 PPYAGSGAGGTdPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIkeeSVP 128
Cdd:pfam05109  476 PTPAGTTSGAS-PVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAV---TTP 551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  129 LSILQTPTP---QPLPGALLP---QSFPAPA---PPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPLpglpLASPPGVPPV 199
Cdd:pfam05109  552 TPNATSPTPavtTPTPNATIPtlgKTSPTSAvttPTPNATSPTVGETSPQANTTNHTLGGTSSTPV----VTSPPKNATS 627

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  200 SLHT---QVQSVVPQQLLTVTAAPTAAPVTTTVTSQIQQVPVLLQPHFIKADSLL-LTAMKTDGATVKAAGLSPLVSGTT 275
Cdd:pfam05109  628 AVTTgqhNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPLLTSAHPTGGENITqVTPASTSTHHVSTSSPAPRPGTTS 707

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 1924581578  276 VQTGPlptlvsGGTILATVPLVVDAEKLPINRLAAGSKAPASAQS 320
Cdd:pfam05109  708 QASGP------GNSSTSTKPGEVNVTKGTPPKNATSPQAPSGQKT 746

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  106 PLKMYPSMPaFSPGPGIKEESVPLSILQTPTPqplpgallPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPL 185
Cdd:cd21577      2 PVKTDMETS-FYSPSHSQLEPVDLSLSKRSSP--------PSSSSSSSSSSSSSSSPSSRASPPSPYSKSSPPSPPQQRP 72

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1924581578  186 PGLPLASPPGVPPVSLHT--------QVQSVVPQQL 213
Cdd:cd21577     73 LSPPLSLPPPVAPPPLSPgsvpgglpVISPVMVQPV 108

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 1924581578  319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLV------LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 384
Cdd:cd11394      1 PPKVEKRSAHNAIEKRYRSSINDRIIELKDLVvgpdakMNKSAVLRKAIDYIRYLQKVNQKLKQENMALKKA 72

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription factor HMS1 and similar proteins; HMS1, also termed high-copy MEP suppressor protein 1, is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  323 EKRTAHNAIEKRYRSSINDKIIELKDLV----------------------------LNKSAVLRKAIDYIRFLQHSNQKL 374
Cdd:cd11399      2 SKKTAHNMIEKRYRSNINDRIAELRDSVpalreayksargededeedlggltpatkLNKATILSKATEYIRHLEKKNKRL 81

                           90
                   ....*....|.
gi 1924581578  375 KQENLSLRTAV 385
Cdd:cd11399     82 SRENASLRERL 92

Helix-loop-helix DNA-binding domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1924581578  324 KRTAHNAIEKRYRSSINDKIIELKDLV--------LNKSAVLRKAIDYIRFLQ 368
Cdd:pfam00010    1 RREAHNERERRRRDRINDAFDELRELLptlppdkkLSKAEILRLAIEYIKHLQ 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream stimulatory factor)/MITF (microphthalmia-associated transcription factor) family includes two bHLHzip transcription factor subfamilies. 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. The MITF (also known as microphthalmia-TFE, or MiT) subfamily comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF subfamily proteins can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1924581578  328 HNAIEKRYRSSINDKIIELKDLV-----------LNKSAVLRKAIDYIRFLQHSNQ 372
Cdd:cd11387      2 HNAVERRRRDNINEKIQELGSLVppsrletkdlkPNKGSILSKAVEYIRELQNQNQ 57

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1924581578  323 EKRTAHNAIEKRYRSSINDKIIELKDLVL------NKSAVLRKAIDYIRFLQHSNQKLKQE 377
Cdd:cd11398      6 QRRDNHKEVERRRRENINEGINELAALVPgnarekNKGAILARAVEYIQELQETEAKNIEK 66

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max and similar proteins; Max, also termed Class D basic helix-loop-helix protein 4 (bHLHd4), or Myc-associated factor X, is a bHLHZip transcription regulator that forms a sequence-specific DNA-binding protein complex with MYC or MAD which recognizes the core sequence 5'-CAC[GA]TG-3'. The MYC:MAX complex is a transcriptional activator, whereas the MAD:MAX complex is a transcriptional repressor. Max homodimer bind DNA but is transcriptionally inactive. Targeted deletion of max results in early embryonic lethality in mice.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1924581578  324 KRTAHNAIEKRYRSSINDKIIELKDLV-------LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 383
Cdd:cd11406      1 KRAHHNALERKRRDHIKDSFHSLRDSVpslqgekASRAQILKKATEYIQYMRRKNHTHQQDIDDLKR 67

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 1924581578  312 SKAPASAQSRgEKRTAHNAIEKRYRSSINDKIIEL---------KDLVLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR 382
Cdd:cd18926      2 SEARALAKER-QKKDNHNLIERRRRFNINDRIKELgtlipksndPDMRWNKGTILKASVDYIRKLQREQQRAKELENRQK 80

                   ....*....
gi 1924581578  383 TAVHKSKSL 391
Cdd:cd18926     81 KLEHANRHL 89

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 1924581578  324 KRTAHNAIEKRYRSSINDKIIELKDLV-------LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAV 385
Cdd:cd11404      2 RRLNHVRSEKKRRELIKKGYDELCALVpgldpqkRTKADILQKAADWIQELKEENEKLEEQLDELKEAA 70

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) and similar proteins; USF2, also termed Class B basic helix-loop-helix protein 12 (bHLHb12), or major late transcription factor 2, or FOS-interacting protein (FIP), or upstream transcription factor 2, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  321 RGEKRTA-HNAIEKRYRSSINDKIIELKDLV-----------LNKSAVLRKAIDYIRFLQHSNQKLkQEN 378
Cdd:cd18923      4 RDERRRAqHNEVERRRRDKINNWIVQLSKIIpdcntdnsktgASKGGILSKACDYIRELRQTNQRM-QET 72

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 1924581578   87 LSGPQAAPSPlsPPQPAPTPLKMYPSMPafsPGPGIKeesvPLSILQT---PTPQPLPGALLPQSFPAPAPP-------Q 156
Cdd:pfam03154  366 LPNPQSHKHP--PHLSGPSPFQMNSNLP---PPPALK----PLSSLSThhpPSAHPPPLQLMPQSQQLPPPPaqppvltQ 436

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1924581578  157 FSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQVQSVVP 210
Cdd:pfam03154  437 SQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMP 490

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family; The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1924581578  325 RTAHNAIEKRYRSSINDKIIELKDLV-------LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR 382
Cdd:cd19682      1 RLRHKKRERERRSELRELFDKLKQLLgldsdekASKLAVLTEAIEEIQQLKREEDELQKEKARLT 65

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1924581578  320 SRGEKRTAHNAIEKRYRSSIN---DKIIEL--KDLVLNKSAV--LRKAIDYIRFLQHSNQKL 374
Cdd:cd18910      1 RREKKRESHNEVERRRKDKINagiNKIGELlpDRDAKKQSKNmiLEQAYKYIVELKKKNDKL 62

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 1924581578  328 HNAIEKRYRSSINDKIIELKDLV-----------LNKSAVLRKAIDYIRFLQHSNQK 373
Cdd:cd11396      2 HNEVERRRRDKINNWIVKLAKIVpdcekdnskqgQSKGGILSKACDYIQELRSQNER 58

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 1924581578   50 PYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIKEESVPL 129
Cdd:pfam03154  199 PTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQMPPM 278

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  130 SILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGS--PPGNTQ---------QPLPGLPLASPPGVPP 198
Cdd:pfam03154  279 PHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIhtPPSQSQlqsqqppreQPLPPAPLSMPHIKPP 358

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), MLX-interacting protein-like (MLXIPL) and similar proteins; The family includes MLXIP and MLXIPL. MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1924581578  324 KRTAHNAIEKRYRSSINDKIIELKDLV----------LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR 382
Cdd:cd11405      3 RRLSHISAEQKRRFNIKSGFDTLQSLIpslgqnpnqkVSKAAMLQKAAEYIKSLKRERQQMQEEAEQLR 71

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and similar proteins; TFEC, also termed Class E basic helix-loop-helix protein 34 (bHLHe34), or transcription factor EC-like (TFEC-L), is a bHLHzip transcriptional regulator that acts as a repressor or an activator and regulates gene expression in macrophages. It plays an important role in the niche to expand hematopoietic progenitors through the modulation of several cytokines.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1924581578  323 EKRTAHNAIEKRYRSSINDKIIEL---------KDLVLNKSAVLRKAIDYIRFLQHSNQKLKQ 376
Cdd:cd18925      4 QKKDNHNLIERRRRYNINYRIKELgtlipksndPDMRWNKGTILKASVEYIKWLQKEQQRARE 66

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   93 APSPLSPPQPAPTPLKMYPSMPAfSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPvlGYPSPPGGF 172
Cdd:PHA03247  2699 ADPPPPPPTPEPAPHALVSATPL-PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGP--PAPAPPAAP 2775

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1924581578  173 STGSPPGNTQQP-------LPGLPLASPPGVPPVSLHTQVQSVVPQQ 212
Cdd:PHA03247  2776 AAGPPRRLTRPAvaslsesRESLPSPWDPADPPAAVLAPAAALPPAA 2822

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins; spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1924581578  325 RTAHNAIEKRYRSSINDKIIELKDLV-------LNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR 382
Cdd:cd19690      1 RVSHKLAERKRRKEMKELFEDLRDALpqergtkASKWEILTKAISYIQQLKRHIRELRSEVNDLR 65

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP)-like family; The HERP-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split proteins. 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 (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 family. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1924581578  328 HNAIEKRYRSSINDKIIELKDLV-----------LNKSAVLRKAIDYIRFLQ 368
Cdd:cd11389      1 HKVIEKRRRDRINESLAELRRLVpearkskgsgkLEKAEILEMTLQHLKALQ 52

DNA polymerase III subunit gamma/tau;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   48 DPPYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIKEESV 127
Cdd:PRK12323   402 PPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPA 481

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  128 PLSILQTPTPQP--------LPGAL----LPQSFPAPAPPQFSSTPVLGYPSPPGGFSTgSPPGNTQQPLPGLPLASPPG 195
Cdd:PRK12323   482 RAAPAAAPAPADddpppweeLPPEFaspaPAQPDAAPAGWVAESIPDPATADPDDAFET-LAPAPAAAPAPRAAAATEPV 560

                   ....
gi 1924581578  196 VPPV 199
Cdd:PRK12323   561 VAPR 564

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in N-Myc and similar proteins; N-Myc, also termed Class E basic helix-loop-helix protein 37 (bHLHe37), is a bHLHZip proto-oncogene protein that positively regulates the transcription of MYCNOS in neuroblastoma cells. It is also essential during embryonic development. N-Myc has a critical role in regulating the switch between proliferation and differentiation of progenitor cells. It binds DNA as a heterodimer with MAX. The family also includes S-Myc, encoded by rat or mouse intronless myc gene, which has apoptosis-inducing activity.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1924581578  323 EKRTAHNAIEKRYRSSINDKIIELKD----LVLNKSA----VLRKAIDYIRFLQHSNQKLKQENLSLR 382
Cdd:cd11456      4 ERRRNHNILERQRRNDLRSSFLTLRDhvpeLVKNEKAakvvILKKATEYVHSLQAEEQKLLLEKEKLQ 71

Gametogenetin; GGN is a family of proteins largely found in mammals. It reacts with POG in the maturation of sperm and is expressed virtually only in the testis. It is found to be associated with the intracellular membrane, binds with GGNBP1 and may be involved in vesicular trafficking.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   88 SGPQAAPSPLSPPQPAPtPLKMYP-SMPAF---SP-------------GPGIKEESVPLSILQTP--TPQPLPGALLPQS 148
Cdd:pfam15685  326 SGGPAAPASHARALPPP-AYTTFPgSKPKFdwvSPpdgperhfrfngaGGGIGAPRRRAAALSGPwgSPPPPPGKAHPIP 404

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578  149 FPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPP-GVPPVSLHTQvQSVVPQQL-LTVTAAPTAAPVT 226
Cdd:pfam15685  405 GPRRPAPALLAPPMFIFPAPTNGEPVRPGPPAPQALLPRPPPPTPPaTPPPVPPPIP-QLPALQPMpLAAARPPTPRPCP 483

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1924581578  227 TTVTSQIQQVPVLLQPHFIKADSllltamktDGATVKAAGLSPLVSGTTVQTGPLP 282
Cdd:pfam15685  484 GHGESALAPAPTAPLPPALAADQ--------APAPALAAAPAPSPAPAPATADPLP 531

Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   94 PSPLSPPQPAPTPLKMYPSMpaFSPGPgikeESVPLSILQTPTPQPLPgaLLPQSFPAPAPPQF---SSTPVLGYP---- 166
Cdd:pfam15279  175 GKPQQHPPPSPLPAFMEPSS--MPPPF----LRPPPSIPQPNSPLSNP--MLPGIGPPPKPPRNlgpPSNPMHRPPfsph 246

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1924581578  167 -SPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVS 200
Cdd:pfam15279  247 hPPPPPTPPGPPPGLPPPPPRGFTPPFGPPFPPVN 281

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   88 SGPQAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPS 167
Cdd:PHA03247  2746 AGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPA 2825

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1924581578  168 PPggfstgSPPGNTQQPLPGlPLASPPGVPPVSL 201
Cdd:PHA03247  2826 GP------LPPPTSAQPTAP-PPPPGPPPPSLPL 2852

putative scaffolding protein

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924581578   83 LEAFLSGPQAAPSPLSPPQPAPTPLkMYPSMPAFSPGPGIKEEsvplsiLQTPTPQPLP---GALLPQSFP-APAPPQFS 158
Cdd:PHA01929     8 LPPGLAGLVANVPPAAAPTPQPNPV-IQPQAPVQPGQPGAPQQ------LAIPTQQPQPvptSAMTPHVVQqAPAQPAPA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1924581578  159 STPVLGYPSP----PGGFSTGSPPGNTQQPLPGLPLASPPGVPPVS 200
Cdd:PHA01929    81 APPAAGAALPealeVPPPPAFTPNGEIVGTLAGNLEGDPQLAPSVS 126

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 1924581578  324 KRTAHNAIEKRYRSSINDKIIELKDLV-----------LNKSAVLRKAIDYIRFLQ 368
Cdd:cd11407      1 RKKRRGIIEKRRRDRINNSLAELRRLVptafekqgsakLEKAEILQMTVDHLKMLH 56