Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 423 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 502
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2223504951 503 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 533
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112

Ycf46; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 229 PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIvyvphihLWW-EI-- 304
Cdd:CHL00195  259 PRgLLLVGIQGTGKS--LTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCI-------LWIdEIdk 329

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2223504951 305 ----------VGPTLK--ATFTTLLQTIPSfaPVLLLATSEKPYSaLPEEVqeLFTHDYGEIFNVQLPDKEERTKFFE 370
Cdd:CHL00195  330 afsnseskgdSGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI--LRKGRFDEIFFLDLPSLEEREKIFK 402

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 423 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 502
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2223504951 503 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 533
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDwNPKPVDMFLEELAEHCVGYCGAD 80
Cdd:TIGR01243 306 MDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGAD 384

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2223504951  81 IKSICAEAALCALRRRYPQIYTTSEKLQLD---LSSITISAKDFEAALQKIRPASQRAV 136
Cdd:TIGR01243 385 LAALAKEAAMAALRRFIREGKINFEAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 38
Cdd:cd19517   133 MDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2223504951 445 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 501
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 438 IDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdrDPGDRLIRHRacal 517
Cdd:COG5076   162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA---- 234

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2223504951 518 rdtayAIIKEELDEDFEQLCEEIQESRKKRG 548
Cdd:COG5076   235 -----KELEKYFLKLIEEIPEEMLELSIKPG 260

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 423 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 502
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2223504951 503 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 533
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDwNPKPVDMFLEELAEHCVGYCGAD 80
Cdd:TIGR01243 306 MDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGAD 384

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2223504951  81 IKSICAEAALCALRRRYPQIYTTSEKLQLD---LSSITISAKDFEAALQKIRPASQRAV 136
Cdd:TIGR01243 385 LAALAKEAAMAALRRFIREGKINFEAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDWnPKPVDMFLEELAEHCVGYCGAD 80
Cdd:TIGR01243 582 MDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSM-PLAEDVDLEELAEMTEGYTGAD 660

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2223504951  81 IKSICAEAALCALRRRYPQIytTSEKLQLDLSSIT----ISAKDFEAALQKIRPA 131
Cdd:TIGR01243 661 IEAVCREAAMAALRESIGSP--AKEKLEVGEEEFLkdlkVEMRHFLEALKKVKPS 713

26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an internal

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGAD 80
Cdd:TIGR01242 253 LDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAE-DVDLEAIAKMTEGASGAD 331

                          90
                  ....*....|....*.
gi 2223504951  81 IKSICAEAALCALRRR 96
Cdd:TIGR01242 332 LKAICTEAGMFAIREE 347

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLdsRGEIVVIGATNRLDSIDPALRRpgRFDREFLFSLPDKNARKEILKIHTRDwNPKPVDMFLEELAEHCVGYCGAD 80
Cdd:COG0464   285 MEEL--RSDVVVIAATNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIHLRK-RPLDEDVDLEELAEATEGLSGAD 359

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2223504951  81 IKSICAEAALCALRrrypqiyttseklqldLSSITISAKDFEAALQKIRPASQR 134
Cdd:COG0464   360 IRNVVRRAALQALR----------------LGREPVTTEDLLEALEREDIFLKR 397

26 proteosome regulatory subunit 4-like protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGAD 80
Cdd:PTZ00361  314 LDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAE-DVDLEEFIMAKDELSGAD 392

                          90       100
                  ....*....|....*....|
gi 2223504951  81 IKSICAEAALCALRRRYPQI 100
Cdd:PTZ00361  393 IKAICTEAGLLALRERRMKV 412

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 38
Cdd:cd19517   133 MDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170

ATP-dependent zinc metalloprotease FtsH;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDWnPKPVDMFLEELAEHCVGYCGAD 80
Cdd:PRK10733  282 MDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV-PLAPDIDAAIIARGTPGFSGAD 360

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2223504951  81 IKSICAEAALCALR--RRypqiyttseklqldlssiTISAKDFEAALQKIRPASQR 134
Cdd:PRK10733  361 LANLVNEAALFAARgnKR------------------VVSMVEFEKAKDKIMMGAER 398

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 425 LRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpDRD 504
Cdd:cd05512     2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80

                          90       100
                  ....*....|....*....|..
gi 2223504951 505 PgdrlIRHRACA-LRDTAYAII 525
Cdd:cd05512    81 T----IFYRAAVrLRDQGGAIL 98

Predicted ATPase, AAA+ superfamily [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951   1 MDGLDSrgEIVVIGATNRLDSIDPALRRpgRFDREFLFSLPDKNARKEILKIHTRDWnPKPVDMFLEELAEHCVGYCGAD 80
Cdd:COG1223   129 LDGLPS--GSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEILELNLKKF-PLPFELDLKKLAKKLEGLSGAD 203

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2223504951  81 IKSICAEaalcALRRrypQIYTTSEKlqldlssitISAKDFEAALQKIR 129
Cdd:COG1223   204 IEKVLKT----ALKK---AILEDREK---------VTKEDLEEALKQRK 236

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2223504951 445 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 500
Cdd:cd05511    21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76

first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDRE 35
Cdd:cd19519   128 MDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDRE 162

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2223504951 435 RLAIDKRFRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 501
Cdd:cd05506    11 KLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNP 79

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 443 RVFTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 500
Cdd:cd05500    23 RPFLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19502   134 LDGFDPRGNIKVIMATNRPDILDPALLRPGRFDR 167

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2223504951 444 VFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 505
Cdd:cd05499    23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 445 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRD 504
Cdd:cd05504    33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2223504951 445 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 500
Cdd:cd05513    22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19529   122 LDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2223504951 445 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 505
Cdd:cd05503    21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2223504951 445 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 500
Cdd:cd05505    21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 434 HRLAIdkrfrVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN-PD 502
Cdd:cd05515    21 RRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNePD 85

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2223504951   1 MDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 40
Cdd:pfam00004  92 LDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19528   124 MDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 438 IDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdrDPGDRLIRHRacal 517
Cdd:COG5076   162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA---- 234

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2223504951 518 rdtayAIIKEELDEDFEQLCEEIQESRKKRG 548
Cdd:COG5076   235 -----KELEKYFLKLIEEIPEEMLELSIKPG 260

Ycf46; Provisional

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2223504951  12 VIGATNRLDSIDPALRRPGRFDREFLFSLPDKNARKEILKIHTRDWNPKPVDMF-LEELAEHCVGYCGADIKSICAEA 88
Cdd:CHL00195  363 VVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYdIKKLSKLSNKFSGAEIEQSIIEA 440

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 441 RFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 500
Cdd:cd05522    24 LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2223504951   1 MDGLDSRGE-IVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19527   122 LDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223504951 406 LTAEEVKRLEeqeedtfrelRIFLRNVTHRLAIDkrfrvFTKPVDPdEVPDYVTVIKQPMDLSSVISKIDL---HKYLTV 482
Cdd:cd05502     1 LSPIDQRKCE----------RLLLELYCHELSLP-----FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPkspQHYSSP 64

                          90       100
                  ....*....|....*....|
gi 2223504951 483 KDYLKDIDLICSNALEYNPD 502
Cdd:cd05502    65 EEFVADVRLMFKNCYKFNEE 84

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2223504951   1 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19526   121 LDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154

Ycf46; Provisional