C-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6); This model characterizes the carboxy (C)-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6), which is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. This C-terminal HEAT repeat domain of TAF6 (TAF6C) is proposed to form a homodimer that effectively bridges the downstream promoter-interacting TAFs (TAF1, -2, and -7) with lobe B of TFIID. This domain influences the TAF6-TAF9 complex, is thus important for TFIID assembly, and may trigger signals from transcriptional effectors. The HEAT domain motif is generally involved in protein/protein interactions, and in A. locustae, the conserved TAF6C domain is formed by five HEAT repeats, tightly packed against each other, defining a single structural domain. TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays a key role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions such as serving as activator-binding sites, core-promoter recognition, or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription, as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold domain (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. The N-terminal HFD of TAF6, interacts with the HFD of TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 160 LTDDLLKYYQQVTRAVLGDDPQLMKVALQDLQTNSKIAALLPYFVYVVS-GVKSVSHDLEQLHRLLQVARSLIRNPHLCL 238
Cdd:cd08050    4 LSKELQLYFEKITEALLGDDEELRKAALASLRTDPGLQPLLPYFVQFIAeGVTKNLRNLALLIYLLRMVRALLDNPHLFL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 239 GPYVRSLVGSVLYCVLEPLAASINPLNDHWTLRDGAALLLSHIFWTHGDLVSGLYQQILLSLQKVLTDPVRPLCSHYGAV 318
Cdd:cd08050   84 EPYLHQLLPSVLTCLLAKQLGSRPPTDNHWALRDFAASLLAQICKKYSTSYPTLQPRITKTLLKALLDPSKPLTTHYGAI 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 295317363 319 VGLHALGWKAVERVLYPHLPTYWTNLQAVLDDySVSNAQVKADGHKVYGAILVA 372
Cdd:cd08050  164 VGLAALGPEAVRALLLPNLKAYLERLESELED-SSSNALKRIEAEKVYGALLKA 216

C-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6); This model characterizes the carboxy (C)-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6), which is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. This C-terminal HEAT repeat domain of TAF6 (TAF6C) is proposed to form a homodimer that effectively bridges the downstream promoter-interacting TAFs (TAF1, -2, and -7) with lobe B of TFIID. This domain influences the TAF6-TAF9 complex, is thus important for TFIID assembly, and may trigger signals from transcriptional effectors. The HEAT domain motif is generally involved in protein/protein interactions, and in A. locustae, the conserved TAF6C domain is formed by five HEAT repeats, tightly packed against each other, defining a single structural domain. TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays a key role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions such as serving as activator-binding sites, core-promoter recognition, or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription, as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold domain (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. The N-terminal HFD of TAF6, interacts with the HFD of TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 160 LTDDLLKYYQQVTRAVLGDDPQLMKVALQDLQTNSKIAALLPYFVYVVS-GVKSVSHDLEQLHRLLQVARSLIRNPHLCL 238
Cdd:cd08050    4 LSKELQLYFEKITEALLGDDEELRKAALASLRTDPGLQPLLPYFVQFIAeGVTKNLRNLALLIYLLRMVRALLDNPHLFL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 239 GPYVRSLVGSVLYCVLEPLAASINPLNDHWTLRDGAALLLSHIFWTHGDLVSGLYQQILLSLQKVLTDPVRPLCSHYGAV 318
Cdd:cd08050   84 EPYLHQLLPSVLTCLLAKQLGSRPPTDNHWALRDFAASLLAQICKKYSTSYPTLQPRITKTLLKALLDPSKPLTTHYGAI 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 295317363 319 VGLHALGWKAVERVLYPHLPTYWTNLQAVLDDySVSNAQVKADGHKVYGAILVA 372
Cdd:cd08050  164 VGLAALGPEAVRALLLPNLKAYLERLESELED-SSSNALKRIEAEKVYGALLKA 216

histone-fold domain found in TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L) and similar proteins; TAF6L, also called PCAF-associated factor 65-alpha (PAF65-alpha), is a component of the PCAF complex, which can efficiently acetylate histones in a nucleosomal context. The PCAF complex is composed of several TBP-associated factors (TAFs) and PCAF-associated factors (PAFs). It might be the human version of the yeast SAGA complex. With TAF5L, TAF6L acts as an epigenetic regulator essential for somatic reprogramming. It also regulates target genes through H3K9ac deposition and MYC recruitment, which trigger the MYC regulatory network to orchestrate gene expression programs to control embryonic stem cell state.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 295317363  19 IPRESVRLMAESTGL-ELSDEVAALLAEDVCYRLREATQNSSQFMKHTKRRKLTVEDFNRALRWSSVEAVCG 89
Cdd:cd22932    1 LSTESIRLMAESLGIsELSEDVAKLLAEDVSYRLREVIQNASQFMRHSKRRKLTTEDVNRALKWSDVEPVYG 72

TATA box binding protein associated factor; TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 295317363    17 VEIPRESVRLMAESTGL-ELSDEVAALLAEDVCYRLREATQNSSQFMKHTKRRKLTVEDFNRALR 80
Cdd:smart00803   1 SWLPKETIKDVAESLGIgNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65

C-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6); This model characterizes the carboxy (C)-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6), which is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. This C-terminal HEAT repeat domain of TAF6 (TAF6C) is proposed to form a homodimer that effectively bridges the downstream promoter-interacting TAFs (TAF1, -2, and -7) with lobe B of TFIID. This domain influences the TAF6-TAF9 complex, is thus important for TFIID assembly, and may trigger signals from transcriptional effectors. The HEAT domain motif is generally involved in protein/protein interactions, and in A. locustae, the conserved TAF6C domain is formed by five HEAT repeats, tightly packed against each other, defining a single structural domain. TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays a key role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions such as serving as activator-binding sites, core-promoter recognition, or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription, as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold domain (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. The N-terminal HFD of TAF6, interacts with the HFD of TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 160 LTDDLLKYYQQVTRAVLGDDPQLMKVALQDLQTNSKIAALLPYFVYVVS-GVKSVSHDLEQLHRLLQVARSLIRNPHLCL 238
Cdd:cd08050    4 LSKELQLYFEKITEALLGDDEELRKAALASLRTDPGLQPLLPYFVQFIAeGVTKNLRNLALLIYLLRMVRALLDNPHLFL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 239 GPYVRSLVGSVLYCVLEPLAASINPLNDHWTLRDGAALLLSHIFWTHGDLVSGLYQQILLSLQKVLTDPVRPLCSHYGAV 318
Cdd:cd08050   84 EPYLHQLLPSVLTCLLAKQLGSRPPTDNHWALRDFAASLLAQICKKYSTSYPTLQPRITKTLLKALLDPSKPLTTHYGAI 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 295317363 319 VGLHALGWKAVERVLYPHLPTYWTNLQAVLDDySVSNAQVKADGHKVYGAILVA 372
Cdd:cd08050  164 VGLAALGPEAVRALLLPNLKAYLERLESELED-SSSNALKRIEAEKVYGALLKA 216

histone-fold domain found in TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L) and similar proteins; TAF6L, also called PCAF-associated factor 65-alpha (PAF65-alpha), is a component of the PCAF complex, which can efficiently acetylate histones in a nucleosomal context. The PCAF complex is composed of several TBP-associated factors (TAFs) and PCAF-associated factors (PAFs). It might be the human version of the yeast SAGA complex. With TAF5L, TAF6L acts as an epigenetic regulator essential for somatic reprogramming. It also regulates target genes through H3K9ac deposition and MYC recruitment, which trigger the MYC regulatory network to orchestrate gene expression programs to control embryonic stem cell state.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 295317363  19 IPRESVRLMAESTGL-ELSDEVAALLAEDVCYRLREATQNSSQFMKHTKRRKLTVEDFNRALRWSSVEAVCG 89
Cdd:cd22932    1 LSTESIRLMAESLGIsELSEDVAKLLAEDVSYRLREVIQNASQFMRHSKRRKLTTEDVNRALKWSDVEPVYG 72

TATA box binding protein associated factor; TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 295317363    17 VEIPRESVRLMAESTGL-ELSDEVAALLAEDVCYRLREATQNSSQFMKHTKRRKLTVEDFNRALR 80
Cdd:smart00803   1 SWLPKETIKDVAESLGIgNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65

histone-fold domain found in transcription initiation factor TFIID subunit 6 (TAF6) and similar proteins; This subfamily includes TAF6 and TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L). TAF6, also called TATA Binding Protein (TBP) associated factor 6, RNA polymerase II TBP-associated factor subunit E, transcription initiation factor TFIID 70 kDa subunit (TAF(II)70, TAFII-70, TAFII70), or transcription initiation factor TFIID 80 kDa subunit, (TAF(II)80, TAFII-80, TAFII80), is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAF6L, also called PCAF-associated factor 65-alpha (PAF65-alpha), is a component of the PCAF complex, which can efficiently acetylate histones in a nucleosomal context. The PCAF complex is composed of several TAFs and PCAF-associated factors (PAFs). It might be the human version of the yeast SAGA complex. With TAF5L, TAF6L acts as an epigenetic regulator essential for somatic reprogramming. It also regulates target genes through H3K9ac deposition and MYC recruitment, which trigger the MYC regulatory network to orchestrate gene expression programs to control embryonic stem cell state.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 295317363  19 IPRESVRLMAESTGL-ELSDEVAALLAEDVCYRLREATQNSSQFMKHTKRRKLTVEDFNRALRW 81
Cdd:cd22917    1 FPNDTVKLIAESLGIvNLSEEVAQLLAEDAEYRILEVIQNAKKFAHHSKRKKLTADDINNALRL 64

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 295317363  18 EIPRESV-RLMAESTGLELSDEVAALLAEDVCYRLREATQNSSQFMKHTKRRKLTVEDFNRALR 80
Cdd:cd22909    1 ELPKAPVkRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64

Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary hemoglobin throughout most of gestation. These Hbs types have differences in O2 affinity and in their interactions with allosteric effectors.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295317363 319 VGLHALGWKAVERVL--YPHLPTYWTNLQAVLD-DYSVSNAQVKADGHKVYGAILVAVERLLKMKAQAAE 385
Cdd:cd08925   12 VDVDEVGAEALARLLivYPWTQRYFSSFGDLSSaAAIAGNPKVAAHGKKVLGALGEAIKHLDDIKATFAD 81