chromodomain of the Chromodomain Y-like protein family; This group includes the chromodomain found in the mammalian chromodomain Y-like (CDY) protein family, and similar proteins. The human CDY family includes 6 proteins: the genes encoding four of these: two copies of CDY1 (CDY1a, CDY1a) and two copies of CDY2(CDY2a and CDY2b), are located on chromosome Y, and the genes encoding the other two members (CDYL and CDYL2) are located on autosomes. The chromosomal genes are only present in primates, whereas the CDYL and CDYL2 genes exist in most mammalian species. The CDY family proteins contain two functional domains: a chromodomain involved in chromatin binding and a catalytic domain found in many coenzyme A (CoA)- dependent acylation enzymes. CDYL is ubiquitously expressed, whereas CDYL2 shows selective expression in tissues of testis, prostate, spleen, and leukocyte. The CDYL genes are ubiquitously expressed, the CDY genes are only expressed in the testis. Deletion of the CDY1b gene has been shown to be a risk factor for male infertility. Impairments in CDY2 expression could be implicated in the pathogenesis of maturation arrest (a failure of germ cell development).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1491390975   6 LYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNR 57
Cdd:cd18634     1 LYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLLNCEEFIHDFNR 52

chromodomain of the Chromodomain Y-like protein family; This group includes the chromodomain found in the mammalian chromodomain Y-like (CDY) protein family, and similar proteins. The human CDY family includes 6 proteins: the genes encoding four of these: two copies of CDY1 (CDY1a, CDY1a) and two copies of CDY2(CDY2a and CDY2b), are located on chromosome Y, and the genes encoding the other two members (CDYL and CDYL2) are located on autosomes. The chromosomal genes are only present in primates, whereas the CDYL and CDYL2 genes exist in most mammalian species. The CDY family proteins contain two functional domains: a chromodomain involved in chromatin binding and a catalytic domain found in many coenzyme A (CoA)- dependent acylation enzymes. CDYL is ubiquitously expressed, whereas CDYL2 shows selective expression in tissues of testis, prostate, spleen, and leukocyte. The CDYL genes are ubiquitously expressed, the CDY genes are only expressed in the testis. Deletion of the CDY1b gene has been shown to be a risk factor for male infertility. Impairments in CDY2 expression could be implicated in the pathogenesis of maturation arrest (a failure of germ cell development).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1491390975   6 LYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNR 57
Cdd:cd18634     1 LYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLLNCEEFIHDFNR 52

enoyl-CoA hydratase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 300 RDIVVRKQDGFTHILLsTKSSENNSLNPEVMKEVQSALNTAAADDS-KLVLFSAVGSIFCCGLDfiyfIRRLTDDRKKES 378
Cdd:PRK06688    5 TDLLVELEDGVLTITI-NRPDKKNALTAAMYQALADALEAAATDPAvRVVVLTGAGRAFSAGGD----IKDFPKAPPKPP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1491390975 379 TKMAEAIRnFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSSLTFPRIMG 453
Cdd:PRK06688   80 DELAPVNR-FLRAIAALPKPVVAAVNGPAVGVGVSLALACDLVYASESAKFSLPFAKLGLCPDAGGSALLPRLIG 153

Chromatin organization modifier domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1491390975    7 YEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNRRHN 60
Cdd:smart00298   2 YEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKKER 55

fatty acid oxidation complex, alpha subunit, mitochondrial; Members represent alpha subunit of mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (EC 4.2.1.17) _ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35). Some characterization in human (SP:P40939), pig (SP:Q29554), and rat (SP:Q64428). The beta subunit has activity: acetyl-CoA C-acyltransferase (EC 2.3.1.16).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 302 IVVRKQDGFTHILLSTKSSENNSLNPEVMKEVQSALNTAAADDS--KLVLFSAVGSIFCCGLDfIYFIRrlTDDRKKEST 379
Cdd:TIGR02441  15 RHYEVKGDVAVVKIDSPNSKVNTLSKELFAEFKEVMNELWTNEAikSAVLISGKPGSFVAGAD-IQMIA--ACKTAQEVT 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491390975 380 KMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWA--NEKAWFQTPYTTFGQSPDGCSSLTFPRIMGL 454
Cdd:TIGR02441  92 QLSQEGQEMFERIEKSQKPIVAAISGSCLGGGLELALACHYRIAtkDRKTLLGLPEVMLGLLPGAGGTQRLPKLTGV 168

chromodomain of the Chromodomain Y-like protein family; This group includes the chromodomain found in the mammalian chromodomain Y-like (CDY) protein family, and similar proteins. The human CDY family includes 6 proteins: the genes encoding four of these: two copies of CDY1 (CDY1a, CDY1a) and two copies of CDY2(CDY2a and CDY2b), are located on chromosome Y, and the genes encoding the other two members (CDYL and CDYL2) are located on autosomes. The chromosomal genes are only present in primates, whereas the CDYL and CDYL2 genes exist in most mammalian species. The CDY family proteins contain two functional domains: a chromodomain involved in chromatin binding and a catalytic domain found in many coenzyme A (CoA)- dependent acylation enzymes. CDYL is ubiquitously expressed, whereas CDYL2 shows selective expression in tissues of testis, prostate, spleen, and leukocyte. The CDYL genes are ubiquitously expressed, the CDY genes are only expressed in the testis. Deletion of the CDY1b gene has been shown to be a risk factor for male infertility. Impairments in CDY2 expression could be implicated in the pathogenesis of maturation arrest (a failure of germ cell development).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1491390975   6 LYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNR 57
Cdd:cd18634     1 LYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLLNCEEFIHDFNR 52

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1491390975   7 YEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNR 57
Cdd:cd00024     1 YEVEKILDHRV-RKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1491390975   7 YEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNRR 58
Cdd:pfam00385   1 YEVERILDHRKDKGGKEEYLVKWKGYPYDENTWEPEENLSKCPELIEEFKDR 52

chromodomain of M-phase phosphoprotein 8; The chromodomain of M-phase phosphoprotein 8 (MPP8), a component of the RanBPM-containing large protein complex, binds methylated H3K9. This may in turn recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promoting tumor cell motility and invasion. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1491390975   6 LYEVERIVDKrKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNR 57
Cdd:cd18633     1 VFEVEKILDM-KTEGGKVLYKVRWKGYTSDDDTWEPEVHLEDCKEVLLEFRK 51

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1491390975   7 YEVE-----RIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEF 55
Cdd:cd18968     2 YEVEvilaaRVVKDAESRKKGWKYLVKWAGYPDEENTWEPEESFDGCDDLLERF 55

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1491390975   7 YEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLvNCEEYIHEF 55
Cdd:cd18631     2 YVVEKVLDRRV-VKGKVEYLLKWKGYPDEDNTWEPEENL-DCPDLIAEF 48

chromodomain of Rhizopus microsporus putative DDE transposases, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizopus microsporus putative DDE transposases, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1491390975   4 EELYEVERIVDKRKNKKGkTEYLVRWKGYDSEDDTWEPeQHLVNCEEYIHEFNR 57
Cdd:cd18978     1 DESYEVEKIINHRGEKNR-RKYLVKWKGYDDTDNSWVT-QEDFNDKDMIDEYEN 52

crotonase/enoyl-CoA hydratase family protein;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 323 NSLNPEVMKEVQSALNTAAADDS-KLVLFSAVGSIFCCGLDFIYFIRRLTDDrkkesTKMAEAIRNFVNTFIQFKKPIIV 401
Cdd:PRK06023   28 NAITRAMYATMAKALKAADADDAiRAHVFLGTEGCFSAGNDMQDFLAAAMGG-----TSFGSEILDFLIALAEAEKPIVS 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1491390975 402 AVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSSLTFPRIMG 453
Cdd:PRK06023  103 GVDGLAIGIGTTIHLHCDLTFASPRSLFRTPFVDLALVPEAGSSLLAPRLMG 154

enoyl-CoA hydratase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 323 NSLNPEVMKEVQSALNTAAADDSKLVLFSAVGSIFCCGLDfiyfirrLTD---DRKKESTKMAEAIRNFVNTFIQ----F 395
Cdd:PRK08140   26 NSFTREMHRELREALDQVEDDGARALLLTGAGRGFCAGQD-------LADrdvTPGGAMPDLGESIETFYNPLVRrlraL 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 396 KKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSSLTFPRIMGLA 455
Cdd:PRK08140   99 PLPVIAAVNGVAAGAGANLALACDIVLAARSASFIQAFVKIGLVPDSGGTWFLPRLVGMA 158

chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1491390975   7 YEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLvNCEEYIHEF 55
Cdd:cd18650     2 YVVEKVLDRRV-VKGKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEF 48

chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1491390975   4 EELYEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLVNcEEYIHEFNRR 58
Cdd:cd18644     1 DLVYAAEKILKKRV-RKGKVEYLVKWKGWSNKHNTWEPEENILD-RRLIEIFERT 53

chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Penicillium solitum protein PENSOL_c198G03123 a putative polyprotein from a Ty3/Gypsy long terminal repeat (LTR) retroelement. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1491390975   7 YEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEFNR 57
Cdd:cd18974     1 WEVEEIVDEKM-IDDELHYLVKWKGWPAEYNQWEPEDDMENAPKAIQSYEK 50

chromodomain of a Tasahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Trichosporon asahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1491390975   7 YEVERIVDKRKNKKGKTE--YLVRWKGYDSEDDTWEPEQHLVNCEEYIHEF 55
Cdd:cd18980     4 YEVEAILDHKVDRRYRDPnfYLVRWRGYGPSHDSWEPTSALENAQDLLREF 54

chromodomain of Hypsizygus marmoreus TY3B-I_0 protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Hypsizygus marmoreus TY3B-I_0 protein, a putative TY3/gypsy retrotransposon polyprotein, and similar proteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1491390975   7 YEVERIVDKRKNKKGKtEYLVRWKGYDSEDDTWEPEQHLVNCE 49
Cdd:cd18970     1 FFVERILDERRRGRGW-QYLVRWLGYGPSDDSWLPRRELEECE 42

enoyl-CoA hydratase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 323 NSLNPEVMKEVQSALNTAAADDSKLVLFSAVGSIFCCGLDF---IY---FIRRLTDdrkkestkMAEAIrnfVNTFIqfk 396
Cdd:PRK07854   22 NALNAELCEELREAVRKAVDESARAIVLTGQGTVFCAGADLsgdVYaddFPDALIE--------MLHAI---DAAPV--- 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1491390975 397 kPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDG 442
Cdd:PRK07854   88 -PVIAAINGPAIGAGLQLAMACDLRVVAPEAYFQFPVAKYGIALDN 132

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1491390975   7 YEVERIVDKRKNKkGKTEYLVRWKGYDSEDDTWEPEQHL 45
Cdd:cd18966     1 YEVERILAERRDD-GGKRYLVKWEGYPLEEATWEPEENI 38

chromodomain of a Rhizoctonia solani AG-3 Rhs1AP polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Rhizoctonia solani AG-3 Rhs1AP, a putative Ty3/Gypsy polyprotein/retrotransposon which includes a protease, a reverse transcriptase, a ribonuclease H, and an integrase domain, in that order, with a chromodomain at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1491390975   7 YEVERIVD----KRKNKKGKtEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHEF 55
Cdd:cd18977     4 YEVEKIVGekwkKRKNRRVK-LYKVRFKGYGPEEDEWLTKEELKNAPEILAEW 55

chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier (chromo) domain of Polycomb and Polycomb-group (PcG) chromobox (CBX) family proteins such as CBX2, CBX4, CBX6, CBX7, and CBX8. These CBX proteins are components of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1491390975   7 YEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLVN 47
Cdd:cd18627     1 FAAECILKKRI-RKGKVEYLVKWKGWSQKYNTWEPEENILD 40

enoyl-CoA hydratase/isomerase family protein;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 323 NSLNPEVMKEVQSALNT-AAADDSKLVLFSAVGSIFCCGLDfiyfIRRLTDDRKKESTKMAEA--IRNFVNTFIQFKKPI 399
Cdd:PRK06495   25 NALSRELRDELIAVFDEiSERPDVRVVVLTGAGKVFCAGAD----LKGRPDVIKGPGDLRAHNrrTRECFHAIRECAKPV 100

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1491390975 400 IVAVNGPAIGLGASILPLCDVVWANEKAWFQTP 432
Cdd:PRK06495  101 IAAVNGPALGAGLGLVASCDIIVASENAVFGLP 133

enoyl-CoA hydratase

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 302 IVVRKQDGFTHILLSTKSSENnSLNPEVMKEVQSALNTAAADDS-KLVLFSAVGSIFCCGLDfiyfirrLT--DDRKKES 378
Cdd:PLN02888   12 LVPKSRNGIATITINRPKALN-ALTRPMMVELAAAFKRLDEDDSvKVIILTGSGRAFCSGVD-------LTaaEEVFKGD 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491390975 379 TKMAEAirnfvNTFIQF---KKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSSLTFPRIMG 453
Cdd:PLN02888   84 VKDVET-----DPVAQMercRKPIIGAINGFAITAGFEIALACDILVASRGAKFIDTHAKFGIFPSWGLSQKLSRIIG 156

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1491390975   7 YEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLvNCEEYIHEF 55
Cdd:cd18652     2 FVVEKVLDRRV-VNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 48

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1491390975   8 EVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQ 43
Cdd:cd18659     4 IVERIIAHREDDEGVTEYLVKWKGLPYDECTWESEE 39

enoyl-CoA hydratase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 302 IVVRKQDGFTHILLStKSSENNSLNPEVMKEVQSALNTAAADDSKLVLFSAVGSIFCCGLDfiyfIRRLTDDRKKESTKM 381
Cdd:PRK07659    8 VVVKYEGRVATIMLN-RPEALNALDEPMLKELLQALKEVAESSAHIVVLRGNGRGFSAGGD----IKMMLSSNDESKFDG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1491390975 382 A-EAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDG 442
Cdd:PRK07659   83 VmNTISEIVVTLYTMPKLTISAIHGPAAGLGLSIALTADYVIADISAKLAMNFIGIGLIPDG 144

chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1491390975   7 YEVERIVDKRkNKKGKTEYLVRWKGYDSEDDTWEPEQHlVNCEEYIHEFNR 57
Cdd:cd18975     1 YEVESILNSR-LHRGKLQYLIQWKGYPLEEASWELEDN-IKNPRLIEEFHK 49

chromodomain of chromobox homolog 7; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 7 (CBX7), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX7 has been shown to function as a tumor suppressor in lung carcinoma and an oncogene in gastric cancer and lymphoma.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1491390975   4 EELYEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLVN 47
Cdd:cd18646     2 EQVFAVESIRKKRV-RKGKVEYLVKWKGWPPKYSTWEPEEHILD 44

enoyl-CoA hydratase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 323 NSLNPEVMKEVQSALNTAAAD-DSKLVLFSAVGSIFCCGLDfiyfirrLTDDRKKESTKMAEAIRNFVNTFI---QFKKP 398
Cdd:PRK05870   25 NAVTAEMSAQLRAAVAAAEADpDVHALVVTGAGKAFCAGAD-------LTALGAAPGRPAEDGLRRIYDGFLavaSCPLP 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1491390975 399 IIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSSLTFPRIMG 453
Cdd:PRK05870   98 TIAAVNGAAVGAGLNLALAADVRIAGPKALFDARFQKLGLHPGGGATWMLQRAVG 152

short-chain-enoyl-CoA hydratase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 299 YRDIVVRKQDGFTHILLStKSSENNSLNPEVMKEVQSALNTAAADDS--KLVLFSAVGSIFCCGLDfiyfIRRLTDDRKK 376
Cdd:PRK05809    3 LKNVILEKEGHIAVVTIN-RPKALNALNSETLKELDTVLDDIENDDNvyAVILTGAGEKAFVAGAD----ISEMKDLNEE 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1491390975 377 ESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSSLTFPRIMGLA 455
Cdd:PRK05809   78 EGRKFGLLGNKVFRKLENLDKPVIAAINGFALGGGCELSMACDIRIASEKAKFGQPEVGLGITPGFGGTQRLARIVGPG 156

enoyl-CoA hydratase-isomerase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491390975 301 DIVVRKQDGFTHILLStKSSENNSLNPEVMKEVQSALNTAAADDS-KLVLFSAVGSIFCCGLDFIYFIRR-----LTDDR 374
Cdd:PRK09674    3 ELLVSRQQRVLLLTLN-RPEARNALNNALLTQLVNELEAAATDTSiGVCVITGNARFFAAGADLNEMAEKdlaatLNDPR 81