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 2462522544  65 RTHGDLVSGLYQHILLSLQKILADPVRPLCCHYGAVVGLHALGWKAVERVLYPHLSTYWTNLQAVLDDySVSNAQVKADG 144
Cdd:cd08050   128 KKYSTSYPTLQPRITKTLLKALLDPSKPLTTHYGAIVGLAALGPEAVRALLLPNLKAYLERLESELED-SSSNALKRIEA 206

                          90
                  ....*....|
gi 2462522544 145 HKVYGAILVA 154
Cdd:cd08050   207 EKVYGALLKA 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 2462522544  65 RTHGDLVSGLYQHILLSLQKILADPVRPLCCHYGAVVGLHALGWKAVERVLYPHLSTYWTNLQAVLDDySVSNAQVKADG 144
Cdd:cd08050   128 KKYSTSYPTLQPRITKTLLKALLDPSKPLTTHYGAIVGLAALGPEAVRALLLPNLKAYLERLESELED-SSSNALKRIEA 206

                          90
                  ....*....|
gi 2462522544 145 HKVYGAILVA 154
Cdd:cd08050   207 EKVYGALLKA 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 2462522544  65 RTHGDLVSGLYQHILLSLQKILADPVRPLCCHYGAVVGLHALGWKAVERVLYPHLSTYWTNLQAVLDDySVSNAQVKADG 144
Cdd:cd08050   128 KKYSTSYPTLQPRITKTLLKALLDPSKPLTTHYGAIVGLAALGPEAVRALLLPNLKAYLERLESELED-SSSNALKRIEA 206

                          90
                  ....*....|
gi 2462522544 145 HKVYGAILVA 154
Cdd:cd08050   207 EKVYGALLKA 216

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 2462522544 101 VGLHALGWKAVERVL--YPHLSTYWTNLQAVLD-DYSVSNAQVKADGHKVYGAILVAVERLLKMKAQAAE 167
Cdd:cd08925    12 VDVDEVGAEALARLLivYPWTQRYFSSFGDLSSaAAIAGNPKVAAHGKKVLGALGEAIKHLDDIKATFAD 81