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Conserved domains on  [gi|40738418|gb|EAA57608|]
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hypothetical protein AN6966.2 [Aspergillus nidulans FGSC A4]

Protein Classification

transposase( domain architecture ID 1753654)

transposase binds to the end of a transposon and catalyzes the movement of the transposon to another part of the genome

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CD_CSD super family cl28914
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 283-331 3.17e-10

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.


The actual alignment was detected with superfamily member cd18971:

Pssm-ID: 475127  Cd Length: 50  Bit Score: 55.09  E-value: 3.17e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 40738418 283 YMVEKILDERRRRYRRGHRlEYLVKWSGYAQPTWEAATALEEVQALDEW 331
Cdd:cd18971   1 YEVEEILAARRRRIRGKGR-EVLVKWVGYAEPTWEPLDNLADTAALDRF 48
transpos_IS481 super family cl41329
IS481 family transposase; null
 17-99 6.71e-10

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.14  E-value: 6.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   17 SETdSESVAWALVRVlISKHGIP-KAITLDRGSQFTSDT--WARICTLTGINRRLSTAYHPQTDGSTERMNSTVET---Y 90
Cdd:NF033577 167 DET-AETAADFLRRA-FAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDefaY 244


                 ....*....
gi 40738418   91 LRMYTCYDQ 99
Cdd:NF033577 245 ARPYESLAE 253
 
Name Accession Description Interval E-value
CD_POL_like cd18971
chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar ...
 283-331 3.17e-10

chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Magnaporthe grisea putative retrotransposon polyprotein which includes 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.


Pssm-ID: 349327  Cd Length: 50  Bit Score: 55.09  E-value: 3.17e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 40738418 283 YMVEKILDERRRRYRRGHRlEYLVKWSGYAQPTWEAATALEEVQALDEW 331
Cdd:cd18971   1 YEVEEILAARRRRIRGKGR-EVLVKWVGYAEPTWEPLDNLADTAALDRF 48
transpos_IS481 NF033577
IS481 family transposase; null
 17-99 6.71e-10

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.14  E-value: 6.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   17 SETdSESVAWALVRVlISKHGIP-KAITLDRGSQFTSDT--WARICTLTGINRRLSTAYHPQTDGSTERMNSTVET---Y 90
Cdd:NF033577 167 DET-AETAADFLRRA-FAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDefaY 244


                 ....*....
gi 40738418   91 LRMYTCYDQ 99
Cdd:NF033577 245 ARPYESLAE 253
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
2-116 1.51e-08

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 55.27  E-value: 1.51e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   2 VITDRLTKGVILEGMSETDSESVAWALVRvLISKHGIP--KAITLDRGSQFTSdtWARICTLTGINRRLSTAYHPQTDGS 79
Cdd:COG2826 191 TLVERKSRFVILLKLPDKTAESVADALIR-LLRKLPAFlrKSITTDNGKEFAD--HKEIEAALGIKVYFADPYSPWQRGT 267

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 40738418  80 TERMNSTVETYLRMYTCYDQKDWNRLLPLAELaINSR 116
Cdd:COG2826 268 NENTNGLLRQYFPKGTDFSTVTQEELDAIADR-LNNR 303
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 2-74 1.08e-07

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.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 49.23  E-value: 1.08e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40738418     2 VITDRLTKGVILEGMS-ETDSESVAWALVRVLISKHGIPKAITLDRGSQFTSDTWARICTLTGINRRLSTAYHP 74
Cdd:pfam00665  25 VIVDDFSREILAWALSsEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
283-334 2.06e-05

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 41.41  E-value: 2.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 40738418   283 YMVEKILDERRRRYRRGhrlEYLVKWSGYAQP--TWEAATALEEVQAL-DEWLDH 334
Cdd:pfam00385   1 YEVERILDHRKDKGGKE---EYLVKWKGYPYDenTWEPEENLSKCPELiEEFKDR 52
transpos_IS3 NF033516
IS3 family transposase;
16-98 3.24e-04

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 42.17  E-value: 3.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   16 MSET-DSESVAWALVRvLISKHGIPKAITL--DRGSQFTSDTWARICTLTGINRRLSTAYHPQTDGSTERMNSTVET-YL 91
Cdd:NF033516 251 VSTSmSAELVLDALEM-AIEWRGKPEGLILhsDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKReCL 329


                 ....*..
gi 40738418   92 RMYTCYD 98
Cdd:NF033516 330 YRRRFRT 336
CHROMO smart00298
Chromatin organization modifier domain;
282-334 6.68e-04

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 37.19  E-value: 6.68e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 40738418    282 EYMVEKILDerrRRYRRGHRLEYLVKWSGY--AQPTWEAATALEEVQA-LDEWLDH 334
Cdd:smart00298   1 EYEVEKILD---HRWKKKGELEYLVKWKGYsySEDTWEPEENLLNCSKkLDNYKKK 53
 
Name Accession Description Interval E-value
CD_POL_like cd18971
chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar ...
 283-331 3.17e-10

chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Magnaporthe grisea putative retrotransposon polyprotein which includes 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.


Pssm-ID: 349327  Cd Length: 50  Bit Score: 55.09  E-value: 3.17e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 40738418 283 YMVEKILDERRRRYRRGHRlEYLVKWSGYAQPTWEAATALEEVQALDEW 331
Cdd:cd18971   1 YEVEEILAARRRRIRGKGR-EVLVKWVGYAEPTWEPLDNLADTAALDRF 48
transpos_IS481 NF033577
IS481 family transposase; null
 17-99 6.71e-10

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.14  E-value: 6.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   17 SETdSESVAWALVRVlISKHGIP-KAITLDRGSQFTSDT--WARICTLTGINRRLSTAYHPQTDGSTERMNSTVET---Y 90
Cdd:NF033577 167 DET-AETAADFLRRA-FAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDefaY 244


                 ....*....
gi 40738418   91 LRMYTCYDQ 99
Cdd:NF033577 245 ARPYESLAE 253
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
2-116 1.51e-08

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 55.27  E-value: 1.51e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   2 VITDRLTKGVILEGMSETDSESVAWALVRvLISKHGIP--KAITLDRGSQFTSdtWARICTLTGINRRLSTAYHPQTDGS 79
Cdd:COG2826 191 TLVERKSRFVILLKLPDKTAESVADALIR-LLRKLPAFlrKSITTDNGKEFAD--HKEIEAALGIKVYFADPYSPWQRGT 267

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 40738418  80 TERMNSTVETYLRMYTCYDQKDWNRLLPLAELaINSR 116
Cdd:COG2826 268 NENTNGLLRQYFPKGTDFSTVTQEELDAIADR-LNNR 303
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 2-74 1.08e-07

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.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 49.23  E-value: 1.08e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40738418     2 VITDRLTKGVILEGMS-ETDSESVAWALVRVLISKHGIPKAITLDRGSQFTSDTWARICTLTGINRRLSTAYHP 74
Cdd:pfam00665  25 VIVDDFSREILAWALSsEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 283-333 6.06e-06

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.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 42.85  E-value: 6.06e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 40738418 283 YMVEKILDERRRRYRrghrLEYLVKWSGY--AQPTWEAATALEEVQ-ALDEWLD 333
Cdd:cd00024   1 YEVEKILDHRVRKGK----LEYLVKWKGYppEENTWEPEENLTNAPeLIKEYEK 50
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
16-99 7.94e-06

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 47.07  E-value: 7.94e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418  16 MSET-DSESVAWALVRvLISKHGIPKAITL--DRGSQFTSDTWARICTLTGINRRLSTAYHPQTDGSTERMNSTVET--- 89
Cdd:COG2801 184 VSDSmDAELVVDALEM-AIERRGPPKPLILhsDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYell 262

                        90
                ....*....|
gi 40738418  90 YLRMYTCYDQ 99
Cdd:COG2801 263 YRRRFESLEE 272
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
283-334 2.06e-05

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 41.41  E-value: 2.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 40738418   283 YMVEKILDERRRRYRRGhrlEYLVKWSGYAQP--TWEAATALEEVQAL-DEWLDH 334
Cdd:pfam00385   1 YEVERILDHRKDKGGKE---EYLVKWKGYPYDenTWEPEENLSKCPELiEEFKDR 52
CD_POL_like cd18970
chromodomain of Hypsizygus marmoreus TY3B-I_0 protein, and similar proteins; This subgroup ...
 283-332 1.37e-04

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.


Pssm-ID: 349326  Cd Length: 49  Bit Score: 38.96  E-value: 1.37e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 40738418 283 YMVEKILDERRRRYRRghrlEYLVKWSGYA--QPTWEAATALEEVQALDEWL 332
Cdd:cd18970   1 FFVERILDERRRGRGW----QYLVRWLGYGpsDDSWLPRRELEECEALDDWL 48
transpos_IS3 NF033516
IS3 family transposase;
16-98 3.24e-04

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 42.17  E-value: 3.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40738418   16 MSET-DSESVAWALVRvLISKHGIPKAITL--DRGSQFTSDTWARICTLTGINRRLSTAYHPQTDGSTERMNSTVET-YL 91
Cdd:NF033516 251 VSTSmSAELVLDALEM-AIEWRGKPEGLILhsDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKReCL 329


                 ....*..
gi 40738418   92 RMYTCYD 98
Cdd:NF033516 330 YRRRFRT 336
chromodomain cd18966
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 283-331 3.48e-04

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.


Pssm-ID: 349322  Cd Length: 49  Bit Score: 38.03  E-value: 3.48e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 40738418 283 YMVEKILDERRRRYRrghrLEYLVKWSGY--AQPTWEAATALEEVQALDEW 331
Cdd:cd18966   1 YEVERILAERRDDGG----KRYLVKWEGYplEEATWEPEENIGDEELLKEW 47
CHROMO smart00298
Chromatin organization modifier domain;
282-334 6.68e-04

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 37.19  E-value: 6.68e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 40738418    282 EYMVEKILDerrRRYRRGHRLEYLVKWSGY--AQPTWEAATALEEVQA-LDEWLDH 334
Cdd:smart00298   1 EYEVEKILD---HRWKKKGELEYLVKWKGYsySEDTWEPEENLLNCSKkLDNYKKK 53
chromodomain cd18967
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 304-331 1.19e-03

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.


Pssm-ID: 349323  Cd Length: 55  Bit Score: 36.84  E-value: 1.19e-03
                        10        20
                ....*....|....*....|....*...
gi 40738418 304 YLVKWSGYAQPTWEAATALEEVQALDEW 331
Cdd:cd18967  26 YLTKWEGFPDETWEPAESFDDRKILHDY 53
CD_NC-like cd18980
chromodomain of a Tasahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and ...
 280-328 1.58e-03

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.


Pssm-ID: 349336  Cd Length: 56  Bit Score: 36.40  E-value: 1.58e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 40738418 280 EEEYMVEKILDeRRRRYRRGHRLEYLVKWSGY--AQPTWEAATALEEVQAL 328
Cdd:cd18980   1 QPEYEVEAILD-HKVDRRYRDPNFYLVRWRGYgpSHDSWEPTSALENAQDL 50
CD_Clr4_like cd18632
N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar ...
 282-332 2.17e-03

N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of cryptic loci regulator 4 (Clr4), a histone H3 lysine methyltransferase which targets H3K9. Clr4 regulates silencing and switching at the mating-type loci and affects chromatin structure at centromeres. Clr4 is a catalytic component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. 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.


Pssm-ID: 349282  Cd Length: 55  Bit Score: 35.94  E-value: 2.17e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 40738418 282 EYMVEKILDERRRRYRRGHRleYLVKWSGYAQ--PTWEAATALEEVQA-LDEWL 332
Cdd:cd18632   1 EYEVEKIVDEKTDRNTAEPL--YLVRWKNYSKnhDTWEPAENLSGCQAvLEKWK 52
CD_HP1a_insect cd18653
chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. ...
 282-323 2.43e-03

chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. HP1a is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. 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. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CD of Drosophila melanogaster HP1a.


Pssm-ID: 349300  Cd Length: 50  Bit Score: 35.78  E-value: 2.43e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 40738418 282 EYMVEKILDERRRRYRrghrLEYLVKWSGYAQP--TWEAATALE 323
Cdd:cd18653   1 EYAVEKICDRRVRKGK----VEYYLKWKGYPETenTWEPEENLD 40
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
 282-339 4.19e-03

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.


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 34.86  E-value: 4.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 40738418 282 EYM-VEKILDERRRRYRRghrLEYLVKWSG--YAQPTWEAAtalEEVQalDEWLDHTKQYR 339
Cdd:cd18659   1 EYTiVERIIAHREDDEGV---TEYLVKWKGlpYDECTWESE---EDIS--DIFQEAIDEYK 53
CD_HP1alpha_Cbx5 cd18651
chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier ...
 282-332 4.57e-03

chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. 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, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349298  Cd Length: 50  Bit Score: 34.97  E-value: 4.57e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 40738418 282 EYMVEKILDERRRRYRrghrLEYLVKWSGYAQP--TWEAATALEEVQALDEWL 332
Cdd:cd18651   1 EYVVEKVLDRRVVKGQ----VEYLLKWKGFSEEhnTWEPEKNLDCPELISEFM 49
chromodomain cd18964
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 283-330 4.67e-03

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.


Pssm-ID: 349320  Cd Length: 54  Bit Score: 35.00  E-value: 4.67e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 40738418 283 YMVEKILDERRRRYRRGHRLEYLVKWSGY--AQPTWEAATALEEVQALDE 330
Cdd:cd18964   1 FFVERIIGRRPSARDGPGKFLWLVKWDGYpiEDATWEPPENLGEHAKLIE 50
CD_POL_like cd18976
chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup ...
 283-323 5.02e-03

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.


Pssm-ID: 349332  Cd Length: 51  Bit Score: 34.85  E-value: 5.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 40738418 283 YMVEKILDERRRRYRrghrLEYLVKWSGY--AQPTWEAATALE 323
Cdd:cd18976   1 YIVESLLDRRKVRGQ----VQYLVKWRGFprSEATWEPREELM 39
CD_HP1beta_Cbx1 cd18650
chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier ...
 282-332 5.80e-03

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).


Pssm-ID: 349297  Cd Length: 50  Bit Score: 34.53  E-value: 5.80e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 40738418 282 EYMVEKILDERRRRYRrghrLEYLVKWSGYAQP--TWEAATALEEVQALDEWL 332
Cdd:cd18650   1 EYVVEKVLDRRVVKGK----VEYLLKWKGFSDEdnTWEPEENLDCPDLIAEFL 49
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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