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Conserved domains on  [gi|1958764296|ref|XP_038961898|]
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synaptonemal complex protein 2 isoform X4 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SYCP2_SLD pfam18584
Synaptonemal complex 2 Spt16M-like domain; Synaptonemal complex protein 2 (SYCP2) N-terminal ...
 53-164 8.27e-56

Synaptonemal complex 2 Spt16M-like domain; Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The SLD structure is highly similar to the middle domain of the histone chaperone FACT. It consists of a twisted ten-stranded beta-sheet flanked by two helices. Since the SLD domain structurally resembles Spt16M, which is known as the well-recognized histone protein H2A-H2B; it is speculated that the SLD may be involved in chromatin binding.


:

Pssm-ID: 465811  Cd Length: 111  Bit Score: 188.64  E-value: 8.27e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764296   53 VFTFPCLSAFLGKYELQIPSDEKLEEFWIDFNLGSHTLSFYIAgDDDDHQWEAVTVPEEKVDMYNIEVRESKKLLTLTLK 132
Cdd:pfam18584    1 VYSFPCLSAFLDKHELRKPADEKLEEFWIDFNLGSQSITFYID-NDESHLWETVRLPKEDVESYSLEEKDKKKLLTIYLK 79

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1958764296  133 NIVKISKKEGKELLLYFDAALEITNVTKKLFG 164
Cdd:pfam18584   80 NPITIGKKEGTKIEIHFDSQLEILDVTKKVLG 111
 
Name Accession Description Interval E-value
SYCP2_SLD pfam18584
Synaptonemal complex 2 Spt16M-like domain; Synaptonemal complex protein 2 (SYCP2) N-terminal ...
 53-164 8.27e-56

Synaptonemal complex 2 Spt16M-like domain; Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The SLD structure is highly similar to the middle domain of the histone chaperone FACT. It consists of a twisted ten-stranded beta-sheet flanked by two helices. Since the SLD domain structurally resembles Spt16M, which is known as the well-recognized histone protein H2A-H2B; it is speculated that the SLD may be involved in chromatin binding.


Pssm-ID: 465811  Cd Length: 111  Bit Score: 188.64  E-value: 8.27e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764296   53 VFTFPCLSAFLGKYELQIPSDEKLEEFWIDFNLGSHTLSFYIAgDDDDHQWEAVTVPEEKVDMYNIEVRESKKLLTLTLK 132
Cdd:pfam18584    1 VYSFPCLSAFLDKHELRKPADEKLEEFWIDFNLGSQSITFYID-NDESHLWETVRLPKEDVESYSLEEKDKKKLLTIYLK 79

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1958764296  133 NIVKISKKEGKELLLYFDAALEITNVTKKLFG 164
Cdd:pfam18584   80 NPITIGKKEGTKIEIHFDSQLEILDVTKKVLG 111
 
Name Accession Description Interval E-value
SYCP2_SLD pfam18584
Synaptonemal complex 2 Spt16M-like domain; Synaptonemal complex protein 2 (SYCP2) N-terminal ...
 53-164 8.27e-56

Synaptonemal complex 2 Spt16M-like domain; Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The SLD structure is highly similar to the middle domain of the histone chaperone FACT. It consists of a twisted ten-stranded beta-sheet flanked by two helices. Since the SLD domain structurally resembles Spt16M, which is known as the well-recognized histone protein H2A-H2B; it is speculated that the SLD may be involved in chromatin binding.


Pssm-ID: 465811  Cd Length: 111  Bit Score: 188.64  E-value: 8.27e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764296   53 VFTFPCLSAFLGKYELQIPSDEKLEEFWIDFNLGSHTLSFYIAgDDDDHQWEAVTVPEEKVDMYNIEVRESKKLLTLTLK 132
Cdd:pfam18584    1 VYSFPCLSAFLDKHELRKPADEKLEEFWIDFNLGSQSITFYID-NDESHLWETVRLPKEDVESYSLEEKDKKKLLTIYLK 79

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1958764296  133 NIVKISKKEGKELLLYFDAALEITNVTKKLFG 164
Cdd:pfam18584   80 NPITIGKKEGTKIEIHFDSQLEILDVTKKVLG 111
 
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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