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Conserved domains on  [gi|14318535|ref|NP_116668|]
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Ioc3p [Saccharomyces cerevisiae S288C]

Protein Classification

WHIM1 domain-containing protein( domain architecture ID 10634769)

WHIM1 (WSTF, HB1, Itc1p, MBD9 motif 1) domain-containing protein similar to Saccharomyces cerevisiae ISWI one complex protein 3 that functions as a component of the ISW1A complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
 365-411 4.94e-07

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


:

Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 46.72  E-value: 4.94e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 14318535   365 LESNPLYNREMDKNGILALKPMDRVVLLRALTDWCAShSSAIHDEIY 411
Cdd:pfam15612   1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLS-SSAIRDEIE 46
PRK13808 super family cl31642
adenylate kinase; Provisional
 74-134 7.53e-03

adenylate kinase; Provisional


The actual alignment was detected with superfamily member PRK13808:

Pssm-ID: 172341 [Multi-domain]  Cd Length: 333  Bit Score: 39.49  E-value: 7.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 14318535   74 KERANKPKRKRPAPPKKKAPSTQNS-KSNDKVEKKKTTSIAKDGKPTLKTNDKKVAPKPKPA 134
Cdd:PRK13808 213 KKASAKAKSAAKKVSKKKAAKTAVSaKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKA 274
 
Name Accession Description Interval E-value
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
 365-411 4.94e-07

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 46.72  E-value: 4.94e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 14318535   365 LESNPLYNREMDKNGILALKPMDRVVLLRALTDWCAShSSAIHDEIY 411
Cdd:pfam15612   1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLS-SSAIRDEIE 46
PRK13808 PRK13808
adenylate kinase; Provisional
 74-134 7.53e-03

adenylate kinase; Provisional


Pssm-ID: 172341 [Multi-domain]  Cd Length: 333  Bit Score: 39.49  E-value: 7.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 14318535   74 KERANKPKRKRPAPPKKKAPSTQNS-KSNDKVEKKKTTSIAKDGKPTLKTNDKKVAPKPKPA 134
Cdd:PRK13808 213 KKASAKAKSAAKKVSKKKAAKTAVSaKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKA 274
 
Name Accession Description Interval E-value
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
 365-411 4.94e-07

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 46.72  E-value: 4.94e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 14318535   365 LESNPLYNREMDKNGILALKPMDRVVLLRALTDWCAShSSAIHDEIY 411
Cdd:pfam15612   1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLS-SSAIRDEIE 46
PRK13808 PRK13808
adenylate kinase; Provisional
 74-134 7.53e-03

adenylate kinase; Provisional


Pssm-ID: 172341 [Multi-domain]  Cd Length: 333  Bit Score: 39.49  E-value: 7.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 14318535   74 KERANKPKRKRPAPPKKKAPSTQNS-KSNDKVEKKKTTSIAKDGKPTLKTNDKKVAPKPKPA 134
Cdd:PRK13808 213 KKASAKAKSAAKKVSKKKAAKTAVSaKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKA 274
 
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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