Domain of unknown function (DUF3371); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 amino acids in length.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2052811272 269 IQARAHGLPSMATS-LGPVELSNHLLKQQqhqpqgpqqpplypdelnggaeylprtPIMGAQPGGAAAVATSGGATSGMP 347
Cdd:pfam11851   1 MQARAHGLPVASSSgLCTAELAARVIKQE---------------------------PALPPCPPDLYDMSQPQPPTQAAV 53

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2052811272 348 SVPSSGatggagEPGDGSTTFSdplshFTDF---FSATLKEEHRLEEILMDDPLSPFG-TDPLLSAASPDASKGSSH 420
Cdd:pfam11851  54 SSSSTL------DLNDGLITFS-----FGDLsasFSDALKPGSKLDDILMDDTLSPLGpSDPLLSAMSPDASKDSSR 119

Domain of unknown function (DUF3371); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 amino acids in length.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2052811272 269 IQARAHGLPSMATS-LGPVELSNHLLKQQqhqpqgpqqpplypdelnggaeylprtPIMGAQPGGAAAVATSGGATSGMP 347
Cdd:pfam11851   1 MQARAHGLPVASSSgLCTAELAARVIKQE---------------------------PALPPCPPDLYDMSQPQPPTQAAV 53

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2052811272 348 SVPSSGatggagEPGDGSTTFSdplshFTDF---FSATLKEEHRLEEILMDDPLSPFG-TDPLLSAASPDASKGSSH 420
Cdd:pfam11851  54 SSSSTL------DLNDGLITFS-----FGDLsasFSDALKPGSKLDDILMDDTLSPLGpSDPLLSAMSPDASKDSSR 119

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2052811272  189 NLIERRRRYNINYRIKELGTLIPkSNDPDMRWNKGTILKASVEYIKWLQKEQQ 241
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLP-TLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

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 2052811272 172 EHDTRVMAKERQKKDNHNLIERRRRYNINYRIKELGTLIPKSNDPDMRWNKGTILKASVEYIKWLQKEQQHARELESRQK 251
Cdd:cd18926     1 ESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKELENRQK 80

                          90       100
                  ....*....|....*....|....
gi 2052811272 252 KLEQANRRLLLRIQELEIQARAHG 275
Cdd:cd18926    81 KLEHANRHLLLRIQELEMQARAHG 104

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins; TFEB, also termed Class E basic helix-loop-helix protein 35 (bHLHe35), is a bHLHzip transcription factor that is required for vascularization of the mouse placenta. It specifically recognizes and binds E-box sequences (5'-CANNTG-3'). Its efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFE3 or MITF.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2052811272 174 DTRVMAKERQKKDNHNLIERRRRYNINYRIKELGTLIPKSNDPDMRWNKGTILKASVEYIKWLQKEQQHARELESRQKKL 253
Cdd:cd18927     1 EARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKTNDLDVRWNKGTILKASVDYIKRMQKDLQRSRELENHSRRL 80

                          90
                  ....*....|.
gi 2052811272 254 EQANRRLLLRI 264
Cdd:cd18927    81 EMTNKQLWLRI 91

Domain of unknown function (DUF3371); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 amino acids in length.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2052811272 269 IQARAHGLPSMATS-LGPVELSNHLLKQQqhqpqgpqqpplypdelnggaeylprtPIMGAQPGGAAAVATSGGATSGMP 347
Cdd:pfam11851   1 MQARAHGLPVASSSgLCTAELAARVIKQE---------------------------PALPPCPPDLYDMSQPQPPTQAAV 53

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2052811272 348 SVPSSGatggagEPGDGSTTFSdplshFTDF---FSATLKEEHRLEEILMDDPLSPFG-TDPLLSAASPDASKGSSH 420
Cdd:pfam11851  54 SSSSTL------DLNDGLITFS-----FGDLsasFSDALKPGSKLDDILMDDTLSPLGpSDPLLSAMSPDASKDSSR 119

MITF/TFEB/TFEC/TFE3 N-terminus; This domain is found at the N-terminus of several transcription factors including microphthalmia-associated transcription factor, transcription factor EB, transcription factor EC and transcription factor E3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2052811272  18 EVQSHIENP-KYHLHQAQAQ----YL--TLSSKLAGQAHPGPHPHAGQP-LGTVPVMRNGHMPPQgdGSTPGSPIHLLTL 89
Cdd:pfam15951  61 KVQTHLENPtKYHIQQAQRQqvkqYLstTYGAKQALIPSASPPPPAQSPpPRTSPLMRGNQLPPG--NSAPNSPMAMLSI 138

                          90
                  ....*....|....*.
gi 2052811272  90 AtSSHDSEfpMDEVID 105
Cdd:pfam15951 139 G-SSEEKE--IDDVID 151

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the Myc family; The Myc family is a member of the bHLHzip family of transcription factors that play important roles in the control of normal cell proliferation, growth, survival and differentiation. All Myc isoforms contain two independently functioning polypeptide chain regions: N-terminal transactivating residues and a C-terminal bHLHzip segment. The bHLHzip family of bHLH transcription factors are characterized by a highly conserved N-terminal basic region that may bind DNA at a consensus hexanucleotide sequence known as the E-box (CANNTG) followed by HLH and leucine zipper motifs that may interact with other proteins to form homo- and heterodimers. Myc heterodimerizes with Max enabling specific binding to E-box DNA sequences in the promoters of target genes. The Myc proto-oncoprotein family includes at least five different functional members: c-, N-, L-, S- and B-Myc (which is lacking the bHLH domain).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2052811272 222 KGTILKASVEYIKWLQKEQqhaRELESRQKKLEQANRRLLLRIQEL 267
Cdd:cd11400    38 KVVILKKATEYIKQLQQEE---KKLEKEKDKLKARNEQLRKKLERL 80

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 1 (SREBP1) and similar proteins; SREBP1, also termed Class D basic helix-loop-helix protein 1 (bHLHd1), or sterol regulatory element-binding transcription factor 1 (SREBF1), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcriptional activator required for lipid homeostasis. It may control transcription of the low-density lipoprotein receptor gene as well as the fatty acid. SREBP1 has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2052811272 183 QKKDNHNLIERRRRYNINYRIKELGTLIPksnDPDMRWNKGTILKASVEYIKWLQKEQQharelesrqkKLEQANRRLLL 262
Cdd:cd18921     5 EKRTAHNAIEKRYRSSINDKIIELKDLVV---GTEAKLNKSAVLRKAIDYIRFLQQSNQ----------KLKQENMALKM 71

                  ....
gi 2052811272 263 RIQE 266
Cdd:cd18921    72 AVQK 75

UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2052811272 227 KASVEYIKWLQKEQQHA--RELESRQKKLEQANRRL 260
Cdd:cd22249    31 KASEELIRKLQEEEERQrkREREEQLKQDEELAKQL 66

Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily; Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2052811272 237 QKEQQHARELESRQKKLEQANRRLLLRIQELEIQAR 272
Cdd:cd14812    17 QRKKEEVEELEARVKELEAENRRLRQLLAQPEAEAS 52

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2052811272 205 ELGTLIPKSN-DPDMRWNKGTILKASVEYIKWLQKEQQHARElESRQKKLE 254
Cdd:cd11405    24 TLQSLIPSLGqNPNQKVSKAAMLQKAAEYIKSLKRERQQMQE-EAEQLRQE 73