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Conserved domains on  [gi|1704664484|pdb|6E1F|C]
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Chain C, Lysine-specific histone demethylase 1A

Protein Classification

SWIRM domain-containing protein( domain architecture ID 10516817)

SWIRM domain-containing protein similar to Schizosaccharomyces pombe SWIRM domain-containing proteins laf1 and laf2, which are components of the RPD3C(L) histone deacetylase complex (HDAC) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SWIRM pfam04433
SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid ...
 8-86 1.31e-25

SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.


:

Pssm-ID: 461307 [Multi-domain]  Cd Length: 78  Bit Score: 90.31  E-value: 1.31e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
6E1F_C         8 DRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEapynSDTVLVHRVHSYLERHGLINF 86
Cdd:pfam04433  4 DKLHPIEKRLLPEFFNGKSKTPEVYLEIRNFILNLWRENPKEYLTKTDARRALK----GDVNLISRIHEFLERWGLINF 78
 
Name Accession Description Interval E-value
SWIRM pfam04433
SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid ...
 8-86 1.31e-25

SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.


Pssm-ID: 461307 [Multi-domain]  Cd Length: 78  Bit Score: 90.31  E-value: 1.31e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
6E1F_C         8 DRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEapynSDTVLVHRVHSYLERHGLINF 86
Cdd:pfam04433  4 DKLHPIEKRLLPEFFNGKSKTPEVYLEIRNFILNLWRENPKEYLTKTDARRALK----GDVNLISRIHEFLERWGLINF 78
PLN02328 PLN02328
lysine-specific histone demethylase 1 homolog
 5-88 1.45e-07

lysine-specific histone demethylase 1 homolog


Pssm-ID: 215187 [Multi-domain]  Cd Length: 808  Bit Score: 46.91  E-value: 1.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6E1F_C         5 LPHDRMTSQE-AACFPDIISGPQQTQkvFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSdtvLVHRVHSYLERHGL 83
Cdd:PLN02328 142 FPVDSLTEEEiEANVVSTIGGTEQAN--YIVVRNHILARWRSNVSNWLTRDHALESIRAEHKN---LVDSAYNFLLEHGY 216


                 ....*
6E1F_C        84 INFGI 88
Cdd:PLN02328 217 INFGV 221
RSC8 COG5259
RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / ...
 25-88 3.48e-03

RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227584 [Multi-domain]  Cd Length: 531  Bit Score: 34.48  E-value: 3.48e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
6E1F_C       25 PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEApynsDTVLVHRVHSYLERHGLINFGI 88
Cdd:COG5259  83 PSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAG----DVAAIVRVHRFLEKWGLINYQV 142
 
Name Accession Description Interval E-value
SWIRM pfam04433
SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid ...
 8-86 1.31e-25

SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.


Pssm-ID: 461307 [Multi-domain]  Cd Length: 78  Bit Score: 90.31  E-value: 1.31e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
6E1F_C         8 DRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEapynSDTVLVHRVHSYLERHGLINF 86
Cdd:pfam04433  4 DKLHPIEKRLLPEFFNGKSKTPEVYLEIRNFILNLWRENPKEYLTKTDARRALK----GDVNLISRIHEFLERWGLINF 78
PLN02328 PLN02328
lysine-specific histone demethylase 1 homolog
 5-88 1.45e-07

lysine-specific histone demethylase 1 homolog


Pssm-ID: 215187 [Multi-domain]  Cd Length: 808  Bit Score: 46.91  E-value: 1.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6E1F_C         5 LPHDRMTSQE-AACFPDIISGPQQTQkvFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSdtvLVHRVHSYLERHGL 83
Cdd:PLN02328 142 FPVDSLTEEEiEANVVSTIGGTEQAN--YIVVRNHILARWRSNVSNWLTRDHALESIRAEHKN---LVDSAYNFLLEHGY 216


                 ....*
6E1F_C        84 INFGI 88
Cdd:PLN02328 217 INFGV 221
PLN03000 PLN03000
amine oxidase
 5-88 4.09e-05

amine oxidase


Pssm-ID: 178578 [Multi-domain]  Cd Length: 881  Bit Score: 40.00  E-value: 4.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6E1F_C         5 LPHDRMTSQE--AACFPdIISGPQQTQkvFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSdtvLVHRVHSYLERHG 82
Cdd:PLN03000  91 FPADSLTEEEieFGVVP-IVGGIEQVN--YILIRNHIISKWRENISSWVTKEMFLGSIPKHCSS---LLDSAYNYLVTHG 164


                 ....*.
6E1F_C        83 LINFGI 88
Cdd:PLN03000 165 YINFGI 170
RSC8 COG5259
RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / ...
 25-88 3.48e-03

RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227584 [Multi-domain]  Cd Length: 531  Bit Score: 34.48  E-value: 3.48e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
6E1F_C       25 PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEApynsDTVLVHRVHSYLERHGLINFGI 88
Cdd:COG5259  83 PSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAG----DVAAIVRVHRFLEKWGLINYQV 142
 
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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