Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241   463 YALKMNSPSQSSPGMNPGQASSVLSPRQRmspgvaGSPRIPPSQFSPAGSLHSPVGV----CSSTGNSHSYTNSSLNALQ 538
Cdd:pfam16665    1 YGLNMNSPPQGSPGMTPPQQNLMMSPRHR------GSPKMPANQFSPGMGLHSPMGSvssgGSGGGGSRTYSSSSLNALQ 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 341942241   539 ALSEGHGVSLGSSLASPDLKMGNLQnspvNMNPPPLSKMGSLDSKDCFG 587
Cdd:pfam16665   75 AISEGVGNSLGSSLTSPVPKQDSSP----NINSTQQKKEGSSDSKSPSS 119

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241   268 ESFTTRQDLQGKITSLDTstmRAAMKPGWED--LVRRCIQKFHTQHEgesLSYAKRHHHEVL-RQGLAFSQIYRFSLSDG 344
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD---LRTAKSHLREIIqTRGRATSPSYRLRLRDG 75

                           90       100       110
                   ....*....|....*....|....*....|....
gi 341942241   345 TLVAAQTKSKLIRSQTTNEPQLVISLHMLHREQN 378
Cdd:pfam14598   76 DFLSVHTKSKLFLNQNSNQQPFIMCTHTILREEN 109

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 341942241  1279 GLPAAMSNPRIPQANAQQFPFPPNYGISQQPDPGFTGATTPQSPLMSPRMAHTQSPMM 1336
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNYGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 341942241    118 MMLEALDGFFFVVNLEGSVVFVSENVTQYLRYNQEELMNKSVYSILHVGDHTEFVKNL 175
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62

Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241   463 YALKMNSPSQSSPGMNPGQASSVLSPRQRmspgvaGSPRIPPSQFSPAGSLHSPVGV----CSSTGNSHSYTNSSLNALQ 538
Cdd:pfam16665    1 YGLNMNSPPQGSPGMTPPQQNLMMSPRHR------GSPKMPANQFSPGMGLHSPMGSvssgGSGGGGSRTYSSSSLNALQ 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 341942241   539 ALSEGHGVSLGSSLASPDLKMGNLQnspvNMNPPPLSKMGSLDSKDCFG 587
Cdd:pfam16665   75 AISEGVGNSLGSSLTSPVPKQDSSP----NINSTQQKKEGSSDSKSPSS 119

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241   268 ESFTTRQDLQGKITSLDTstmRAAMKPGWED--LVRRCIQKFHTQHEgesLSYAKRHHHEVL-RQGLAFSQIYRFSLSDG 344
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD---LRTAKSHLREIIqTRGRATSPSYRLRLRDG 75

                           90       100       110
                   ....*....|....*....|....*....|....
gi 341942241   345 TLVAAQTKSKLIRSQTTNEPQLVISLHMLHREQN 378
Cdd:pfam14598   76 DFLSVHTKSKLFLNQNSNQQPFIMCTHTILREEN 109

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 341942241  1279 GLPAAMSNPRIPQANAQQFPFPPNYGISQQPDPGFTGATTPQSPLMSPRMAHTQSPMM 1336
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNYGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 341942241    118 MMLEALDGFFFVVNLEGSVVFVSENVTQYLRYNQEELMNKSVYSILHVGDHTEFVKNL 175
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62

helix loop helix domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 341942241     35 EKRNREQENKYIEELAELIFANFNdidnfNFKPDKCAILKETVKQIRQIKEQEK 88
Cdd:smart00353    4 ERRRRRKINEAFDELRSLLPTLPK-----NKKLSKAEILRLAIEYIKSLQEELQ 52

PAS domain [Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241  119 MLEALDGFFFVVNLEGSVVFVSENVTQYLRYNQEELMNKSVySILHVGDHTEFVKNLLPKSMVNGGSWSGEPP--RRSSH 196
Cdd:COG2202    16 LVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTL-RDLLPPEDDDEFLELLRAALAGGGVWRGELRnrRKDGS 94

                          90
                  ....*....|....*..
gi 341942241  197 TFNCRMLVKPLPDSEEE 213
Cdd:COG2202    95 LFWVELSISPVRDEDGE 111

Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241   463 YALKMNSPSQSSPGMNPGQASSVLSPRQRmspgvaGSPRIPPSQFSPAGSLHSPVGV----CSSTGNSHSYTNSSLNALQ 538
Cdd:pfam16665    1 YGLNMNSPPQGSPGMTPPQQNLMMSPRHR------GSPKMPANQFSPGMGLHSPMGSvssgGSGGGGSRTYSSSSLNALQ 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 341942241   539 ALSEGHGVSLGSSLASPDLKMGNLQnspvNMNPPPLSKMGSLDSKDCFG 587
Cdd:pfam16665   75 AISEGVGNSLGSSLTSPVPKQDSSP----NINSTQQKKEGSSDSKSPSS 119

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 3 (NCoA-3) and similar proteins; NCoA-3, also termed ACTR, or amplified in breast cancer 1 protein (AIB-1), or CBP-interacting protein (pCIP), or Class E basic helix-loop-helix protein 42 (bHLHe42), or receptor-associated coactivator 3 (RAC-3), or steroid receptor coactivator protein 3 (SRC-3), or thyroid hormone receptor activator molecule 1 (TRAM-1), is a bHLH-PAS steroid/nuclear receptor-associated coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. It also plays a central role in creating a multisubunit coactivator complex, which probably acts via remodeling of chromatin.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 341942241   30 PKRSTEKRNREQENKYIEELAELIFANFNDIDNFNFKPDKCAILKETVKQIRQIKEQEKaAAANIDEVQKSDVS 103
Cdd:cd18949     1 LNCSGEKRRREQESKYIEELAELISANLSDIDNFNVKPDKCAILKETVRQIRQIKEQGK-SSSNDDDVQKADVS 73

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241   268 ESFTTRQDLQGKITSLDTstmRAAMKPGWED--LVRRCIQKFHTQHEgesLSYAKRHHHEVL-RQGLAFSQIYRFSLSDG 344
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD---LRTAKSHLREIIqTRGRATSPSYRLRLRDG 75

                           90       100       110
                   ....*....|....*....|....*....|....
gi 341942241   345 TLVAAQTKSKLIRSQTTNEPQLVISLHMLHREQN 378
Cdd:pfam14598   76 DFLSVHTKSKLFLNQNSNQQPFIMCTHTILREEN 109

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 (NCoA-1) and similar proteins; NCoA-1, also termed Class E basic helix-loop-helix protein 74 (bHLHe74), or protein Hin-2, or RIP160, or renal carcinoma antigen NY-REN-52, or steroid receptor coactivator 1 (SRC-1), is a bHLH-PAS nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 341942241   33 STEKRNREQENKYIEELAELIFANFNDIDNFNFKPDKCAILKETVKQIRQIK--EQEK 88
Cdd:cd18948     4 STEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVDQIQQMKrlEQEK 61

Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 341942241  1071 ESPSDEGALLDQLYLALRNFD--GLEEIDRALGIPELVSQSQAVDAE 1115
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDetGLEEIDRALGIPELVGQGQGLDPD 47

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341942241  123 LDGFFFVVNLEGSVVFVSENVTQYLRYNQEELMNKSVYSILHVGDHtEFVKNLLPKSMVNGGSWSGEP--PRRSSHTFNC 200
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDR-EELRERLENLLSGGEPVTLEVrlRRKDGSVIWV 79

                          90
                  ....*....|...
gi 341942241  201 RMLVKPLPDSEEE 213
Cdd:cd00130    80 LVSLTPIRDEGGE 92

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 341942241   119 MLEALDGFFFVVNLEGSVVFVSENVTQYLRYNQEELMNKSVYSILHVGDHTEFVKNLL 176
Cdd:pfam00989    6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63

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 341942241   35 EKRNREQENKYIEELAELifanfndIDNFNFKPDKCAILKETVKQIRQIKEqekAAAANIDEVQKS 100
Cdd:cd11398    15 ERRRRENINEGINELAAL-------VPGNAREKNKGAILARAVEYIQELQE---TEAKNIEKWTLE 70

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) family; The ARNT family of bHLH-PAS transcription regulators includes ARNT, ARNT-like proteins (ARNTL and ARNTL2), and Drosophila melanogaster protein cycle. They act as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor. ARNTL, also termed Basic-helix-loop-helix-PAS protein MOP3, or brain and muscle ARNT-like 1 (BMAL1), or Class E basic helix-loop-helix protein 5 (bHLHe5), or member of PAS protein 3, or PAS domain-containing protein 3 (PASD3), or bHLH-PAS protein JAP3, is a member of the bHLH-PAS transcription factor family that forms heterodimers with another bHLH-PAS protein, CLOCK (circadian locomotor output cycle kaput), which regulates circadian rhythm. ARNTL-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. ARNTL is highly homologous to ARNT. ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 341942241   34 TEKRNREQENKYIEELAELIFANFndidNFNFKPDKCAILKETVKQIRQIK 84
Cdd:cd11437     8 IEKRRRDKMNAYIQELSALVPACN----AMSRKLDKLTVLRMAVQHLKSLR 54

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found in a large group of bHLH transcription regulators that are involved in gene expression responding to environmental change and controlling aspects of neural development, including proteins from aryl hydrocarbon receptor nuclear translocator (ARNT) family, hypoxia-inducible factor (HIF) family, aryl hydrocarbon receptor (AhR) family, neuronal PAS domain-containing protein (NPAS) family, Circadian locomotor output cycles protein kaput (CLOCK)-like family, and single-minded (SIM) family. bHLH-PAS transcriptional regulatory factors have a bHLH DNA-binding domain followed by two PAS domains and a C-terminal activation or repression domain. bHLH-PAS family members can be divided into class I and class II based on their dimerization partner. bHLH-PAS class I factors include AhR, HIF and SIM. The best characterized bHLH-PAS Class II protein is the ubiquitous ARNT. Some members of bHLH-PAS family act as transcriptional coactivators (such as NCoA) that lack the ability to dimerize and bind DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 341942241   31 KRSTEKRNREQENKYIEELAELIFANFNDIDnfnfKPDKCAILKETVKQIR 81
Cdd:cd11391     4 SREAAKKRRDKENAEISELASLLPLPPAVGS----KLDKLSVLRLAVAYLR 50