nascent polypeptide-associated complex (NAC), alpha subunit; The nascent polypeptide-associated complex (NAC) is a complex, conserved from archaea to human, that plays an important role in co translational targeting of nascent polypeptides to the endoplasmic reticulum (ER). In eukaryotes, under physiological conditions, the complex is a stable heterodimer of the NAC alpha subunit and the NAC beta subunit, also known as basal transcription factor 3b (BTF3b). An imbalance of the relative concentrations has been observed in diseases, like Alzheimer's, AIDS, and ulcerative colitis. NAC alpha consists of a NAC domain, also present in BTF3, and a unique C-terminal ubiquitin-associated (UBA) domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2014575467 268 GMKPVPGIMRVTVKKSKNILFVIAKPDVFKSPASDTYIIFGEAKIEDL 315
Cdd:cd22054     1 GLKPVPGVTRVTIKKSKNILFVINKPDVYKSPGSDTYIVFGEAKIEDL 48

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2014575467 355 EVDETGVEPKDVELVMSQAGVSRAKAVKALKIN 387
Cdd:cd14415     2 EVDETGVEVKDIELVMSQANVSRAKAVRALKNN 34

nascent polypeptide-associated complex (NAC), alpha subunit; The nascent polypeptide-associated complex (NAC) is a complex, conserved from archaea to human, that plays an important role in co translational targeting of nascent polypeptides to the endoplasmic reticulum (ER). In eukaryotes, under physiological conditions, the complex is a stable heterodimer of the NAC alpha subunit and the NAC beta subunit, also known as basal transcription factor 3b (BTF3b). An imbalance of the relative concentrations has been observed in diseases, like Alzheimer's, AIDS, and ulcerative colitis. NAC alpha consists of a NAC domain, also present in BTF3, and a unique C-terminal ubiquitin-associated (UBA) domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2014575467 268 GMKPVPGIMRVTVKKSKNILFVIAKPDVFKSPASDTYIIFGEAKIEDL 315
Cdd:cd22054     1 GLKPVPGVTRVTIKKSKNILFVINKPDVYKSPGSDTYIVFGEAKIEDL 48

hypothetical protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2014575467  91 WAPSEDEALRRLVASHGVRNWALVAT-ALATRNGKQCRERWHNALRPDICRSDWTIGED---VELwrRVVeLGTRWAQVS 166
Cdd:PLN03091   17 WSPEEDEKLLRHITKYGHGCWSSVPKqAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEEnliIEL--HAV-LGNRWSQIA 93

                          90       100
                  ....*....|....*....|...
gi 2014575467 167 AmHTPRRGVNDVKNRWNSLIRKQ 189
Cdd:PLN03091   94 A-QLPGRTDNEIKNLWNSCLKKK 115

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2014575467  91 WAPSEDEALRRLVASHGvRNWALVATALATRNGKQCRERWHNALRPDICRSDWTIGEDVEL 151
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQIAKELGRRTPKQCFDRWRRKLNPKISRGPWSKEEDQRL 60

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2014575467  90 AWAPSEDEALRRLVASHGVRNWALVATALATRNGKQCRERWHN 132
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRN 43

Transcription factor homologous to NACalpha-BTF3 [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2014575467 258 KKSRKAMQKLGMK--PVPGImRVTVK-KSKNIlfVIAKPDV--FKSPASDTYIIFGEAKIEDlsaqaqqaaaeqfkepvm 332
Cdd:COG1308     8 RKMKQMMKQMGIKveEIDAE-EVIIRtKDKEI--VFENPQVtvMKAQGQETYQIVGEPEEVE------------------ 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2014575467 333 tnkpemakvtkpviEEIGGEDGEVDETgvepkDVELVMSQAGVSRAKAVKALKINEG 389
Cdd:COG1308    67 --------------KGAEEAEVEIPEE-----DVELVAEQTGVSEEEAREALEEANG 104

HYPK UBA domain; This entry represents the UBA domain found at the C-terminus of the HYPK protein and its homologs. This domain in HYPK mediates a protein interaction with the Naa15 C-terminus.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 2014575467 359 TGVEPKDVELVMSQAGVSRAKAVKALKINEG 389
Cdd:pfam19026   1 VKVKKEDVELIMTELEVSKAKAERALREHGG 31

nascent polypeptide-associated complex (NAC), alpha subunit; The nascent polypeptide-associated complex (NAC) is a complex, conserved from archaea to human, that plays an important role in co translational targeting of nascent polypeptides to the endoplasmic reticulum (ER). In eukaryotes, under physiological conditions, the complex is a stable heterodimer of the NAC alpha subunit and the NAC beta subunit, also known as basal transcription factor 3b (BTF3b). An imbalance of the relative concentrations has been observed in diseases, like Alzheimer's, AIDS, and ulcerative colitis. NAC alpha consists of a NAC domain, also present in BTF3, and a unique C-terminal ubiquitin-associated (UBA) domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2014575467 268 GMKPVPGIMRVTVKKSKNILFVIAKPDVFKSPASDTYIIFGEAKIEDL 315
Cdd:cd22054     1 GLKPVPGVTRVTIKKSKNILFVINKPDVYKSPGSDTYIVFGEAKIEDL 48

hypothetical protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2014575467  91 WAPSEDEALRRLVASHGVRNWALVAT-ALATRNGKQCRERWHNALRPDICRSDWTIGED---VELwrRVVeLGTRWAQVS 166
Cdd:PLN03091   17 WSPEEDEKLLRHITKYGHGCWSSVPKqAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEEnliIEL--HAV-LGNRWSQIA 93

                          90       100
                  ....*....|....*....|...
gi 2014575467 167 AmHTPRRGVNDVKNRWNSLIRKQ 189
Cdd:PLN03091   94 A-QLPGRTDNEIKNLWNSCLKKK 115

Transcription repressor MYB5; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2014575467  64 CKGSGTVGVGDGSACGRVsdsGAKRRAWAPSEDEALRRLVASHGVRNW-ALVATALATRNGKQCRERWHNALRPDICRSD 142
Cdd:PLN03212    4 CGGKKPVSKKTTPCCTKM---GMKRGPWTVEEDEILVSFIKKEGEGRWrSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2014575467 143 WTIGEDVELWRRVVELGTRWAQVsAMHTPRRGVNDVKNRWNSLIRKQ 189
Cdd:PLN03212   81 ITSDEEDLILRLHRLLGNRWSLI-AGRIPGRTDNEIKNYWNTHLRKK 126

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2014575467   88 RRAWAPSEDEALRRLVASHGVRNWALVATALATRNGKQCRERWHNALRP 136
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWRNLLKP 49

Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2014575467  90 AWAPSEDEALRRLVASHGVRNWALVATALATRNGKQCRERWHNALRPDICRSDWTIGEDVELWRRVVELGTRWAQVsAMH 169
Cdd:COG5147    22 SWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWSTI-ADY 100

                          90
                  ....*....|....*...
gi 2014575467 170 TPRRGVNDVKNRWNSLIR 187
Cdd:COG5147   101 KDRRTAQQCVERYVNTLE 118

NAC domain; This family contains the NAC domain, named after the nascent polypeptide-associated complex (NAC) whose subunits contain NAC domains. In eukaryotes, the NAC complex, which plays an important role in co-translational targeting of nascent polypeptides to endoplasmic reticulum (ER), consists of 2 subunits: NAC alpha and a shortened splice variant of the basal transcription factor 3 (BTF3; also called BTF3b or NAC beta). The full length BTF3a protein excites transcription.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2014575467 272 VPGIMRVTVKKSKNILFVIAKPDVFKSPASDTYIIFGEAKIED 314
Cdd:cd21114     1 IPGIEEVTMVMEDGSVIVFTMPKVQASLASNVFVVTGEATREQ 43

UBA-like domain found in nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD); The subfamily includes a group of uncharacterized proteins mainly found in vertebrates. Their biological function remains unknown, but they show high sequence similarity to the nascent polypeptide-associated complex (NAC) subunit alpha (NACA) that exists as part of several protein complexes playing a role in proliferation, apoptosis, or degradation. Like NACA, NACAD contains an NAC domain and a C-terminal ubiquitin-associated (UBA) domain.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2014575467 357 DETGVEPKDVELVMSQAGVSRAKAVKALKINE 388
Cdd:cd14416     1 DETGLEVRDIELVMAQANVSRAKAVRALRHNN 32

UBA-like domain found in nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins; The family contains nascent polypeptide-associated complex subunit alpha (NACA), putative NACA-like protein (NACP1), nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD), and similar proteins found in archaea and bacteria. NACA, also called NAC-alpha or Alpha-NAC, together with BTF3, also called Beta-NAC, form the nascent polypeptide-associated complex (NAC) which is a cytosolic protein chaperone that contacts the nascent polypeptide chains as they emerge from the ribosome. Besides, NACA has a high affinity for nucleic acids and exists as part of several protein complexes playing a role in proliferation, apoptosis, or degradation. It is a cytokine-modulated specific transcript in the human TF-1 erythroleukemic cell line. It also acts as a transcriptional co-activator in osteoblasts by binding to phosphorylated c-Jun, a member of the activator-protein-1 (AP-1) family. Moreover, NACA binds to and regulates the adaptor protein Fas-associated death domain (FADD). In addition, NACA functions as a novel factor participating in the positive regulation of human erythroid-cell differentiation. The biological function of NACP1 (also called Alpha-NAC pseudogene 1 or NAC-alpha pseudogene 1) and NACAD remain unclear. The family also includes huntingtin-interacting protein K (HYPK), also called Huntingtin yeast partner K or Huntingtin yeast two-hybrid protein K. It is an intrinsically unstructured Huntingtin (HTT)-interacting protein with chaperone-like activity. It may be involved in regulating cell growth, cell cycle, unfolded protein response and cell death. All members in this family contain an ubiquitin-associated (UBA) domain.

                          10        20
                  ....*....|....*....|....*..
gi 2014575467 363 PKDVELVMSQAGVSRAKAVKALKINEG 389
Cdd:cd14278     1 EEDIELVMSQTGVSREEAIKALRENKG 27

UBA-like domain found in archaeal nascent polypeptide-associated complex homolog from Methanothermobacter marburgensis (AeNAC) and similar proteins; AeNAC is a functional archaeal homolog of eukaryotic nascent polypeptide-associated complex (NAC). Both AeNAC and eukaryotic NAC function as the cytosolic chaperone that can bind to ribosomal RNA, interact with the nascent polypeptide chains as they emerge from the ribosome, and assist in post-translational processes. They all contain a NAC domain and an ubiquitin-associated (UBA) domain in the C-terminus. However, unlike eukaryotic NAC, AeNAC forms a ribosome associated homodimer, but not heterodimer. The NAC domain of AeNAC is responsible for the homodimer formation.

                          10        20
                  ....*....|....*....|....*
gi 2014575467 365 DVELVMSQAGVSRAKAVKALKINEG 389
Cdd:cd14359     6 DIELVMEQTGVSREEARKALEESGG 30

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2014575467 140 RSDWTIGEDVELWRRVVELGTRWAQVsAMHTPRRGVNDVKNRWNSLI 186
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLGNRWKKI-AKLLPGRTDNQCKNRWQNYL 46

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2014575467  89 RAWAPSEDEALRRLVASHGVRNWALV---ATALATRNGKQCRERWHN 132
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKIlkdYFFVNNRTSVDLKDKWRN 47