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
                  ....*....|....*....|....*....|....*....|....*
gi 1913125841 258 IRGHRRKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYKA 302
Cdd:cd00024     6 ILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

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
                  ....*....|....*....|....*....|....*....|....*
gi 1913125841 258 IRGHRRKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYKA 302
Cdd:cd00024     6 ILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1913125841 258 IRGHR-RKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYKAK 303
Cdd:pfam00385   6 ILDHRkDKGGKEEYLVKWKGYPYDENTWEPEENLSKCPELIEEFKDR 52

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1913125841  11 VWRYHGIPKRIISDRGPQFASKFMESLCKALGIERNLSTAYHP 53
Cdd:pfam00665  56 IAFRGGVPLIIHSDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1913125841  15 HGIPKRIISDRGPQFASKFMESL------------CKALGIErnLSTAYHPQTDGQTERMNQ 64
Cdd:NF033594  185 HGKPVAFYSDKHSVFRVNEEELAgkgdgltqfgraLKELGIE--IICANSPQAKGRVERANQ 244

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
                  ....*....|....*....|....*....|....*....|....*
gi 1913125841 258 IRGHRRKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYKA 302
Cdd:cd00024     6 ILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

Chromatin organization modifier domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1913125841  258 IRGHRRKGRG-IQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYKAK 303
Cdd:smart00298   7 ILDHRWKKKGeLEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKK 53

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1913125841 258 IRGHR-RKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYKAK 303
Cdd:pfam00385   6 ILDHRkDKGGKEEYLVKWKGYPYDENTWEPEENLSKCPELIEEFKDR 52

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1913125841  12 WRYHGIPKRIISDRGPQFASKFMESLCKALGIERNLSTAYHPQTDGQTERMNQ---EIEIYLRAFINYRQ-----DDWTR 83
Cdd:COG2801   203 RRGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGtlkYELLYRRRFESLEEareaiEEYIE 282

                          90       100
                  ....*....|....*....|...
gi 1913125841  84 WlpmaefhYNDK-THAATG-QTP 104
Cdd:COG2801   283 F-------YNHErPHSSLGyLTP 298

chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1 (Tf2-1), and similar proteins. It belongs to the Ty3/gypsy family of long terminal repeat (LTR) retrotransposons. 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 1913125841 258 IRGHRRKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEY 300
Cdd:cd18973     6 ILDNKRRKGKWLYLVKWKGYGPEHNTWEPRENLEHAQKLLKKY 48

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
                  ....*....|....*....|....*....|....*....|
gi 1913125841 262 RRKGRGIQFLVHWKGYGNEDDSWIPRSSLENAEEALSEYK 301
Cdd:cd18633    11 KTEGGKVLYKVRWKGYTSDDDTWEPEVHLEDCKEVLLEFR 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
                  ....*....|....*....|....*....|...
gi 1913125841 270 FLVHWKGYGNEDDSWIPRSSLENAEEALSEYKA 302
Cdd:cd18980    24 YLVRWRGYGPSHDSWEPTSALENAQDLLREFWE 56

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
                  ....*....|....*....|....*....|....*....|....
gi 1913125841 258 IRGHRRKGRG-IQFLVHWKGYGNEDDSWIPRSSLENAEEALSEY 300
Cdd:cd18634     7 IVDKRKNKKGkTEYLVRWKGYDSEDDTWEPEQHLLNCEEFIHDF 50

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
                  ....*....|....*....|....*....|....*....|..
gi 1913125841 261 HRRKGRGI--QFLVHWKGYGNEDDSWIPRSSLENAEEALSEY 300
Cdd:cd18968    14 KDAESRKKgwKYLVKWAGYPDEENTWEPEESFDGCDDLLERF 55

IS3 family transposase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1913125841   9 EEVWRYHGIPKRII--SDRGPQFASKFMESLCKALGIERNLSTAYHPQTDGQTERMN----QEIeIYLRAFINYRQ---- 78
Cdd:NF033516  265 EMAIEWRGKPEGLIlhSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFgtlkREC-LYRRRFRTLEEarqa 343

                          90
                  ....*....|....*...
gi 1913125841  79 -DDWTRWlpmaefhYNDK 95
Cdd:NF033516  344 iEEYIEF-------YNHE 354

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
                  ....*....|....*....|....*....|....*..
gi 1913125841 264 KGRgIQFLVHWKGYGNEDDSWIPRSSLEnAEEALSEY 300
Cdd:cd18650    14 KGK-VEYLLKWKGFSDEDNTWEPEENLD-CPDLIAEF 48

chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, 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
                  ....*....|....*....|....*....|
gi 1913125841 262 RRKGRGIQFLVHWKGYGNEDDSWIPRSSLE 291
Cdd:cd18976    10 RKVRGQVQYLVKWRGFPRSEATWEPREELM 39

chromodomain 2 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 2 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1913125841 258 IRGHRRKGRGIQFLVHWKGYGneDDSWIPRSSLenAEEALSEYKA 302
Cdd:cd18629     8 ILESRGKGKDMEYLIEWKDGG--DCEWVKGVHV--AEDVASDYET 48