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Conserved domains on  [gi|1109146858|ref|XP_019082932|]
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PREDICTED: protein FRIGIDA-ESSENTIAL 1-like isoform X1 [Camelina sativa]

Protein Classification

pre-mRNA-splicing factor CWC2( domain architecture ID 582806)

pre-mRNA-splicing factor CWC2 is involved in the first step of pre-mRNA splicing; it plays a role in the levels of the U1, U4, U5 and U6 snRNAs and the maintenance of the U4/U6 snRNA complex

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Torus super family cl24641
Torus domain; This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type ...
 78-132 2.65e-04

Torus domain; This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger.


The actual alignment was detected with superfamily member pfam16131:

Pssm-ID: 435160  Cd Length: 109  Bit Score: 40.66  E-value: 2.65e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1109146858  78 DNGTLSRFPAP---------GIT-----PNSFFpaagegnepeqkraahlCKFFAKGWCFNGVSCKFLH 132
Cdd:pfam16131  40 EDKYRSRTKAKtrcniardsGYTkadkeGGSYF-----------------CLYFARGCCPLGKKCEYLH 91
 
Name Accession Description Interval E-value
Torus pfam16131
Torus domain; This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type ...
 78-132 2.65e-04

Torus domain; This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger.


Pssm-ID: 435160  Cd Length: 109  Bit Score: 40.66  E-value: 2.65e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1109146858  78 DNGTLSRFPAP---------GIT-----PNSFFpaagegnepeqkraahlCKFFAKGWCFNGVSCKFLH 132
Cdd:pfam16131  40 EDKYRSRTKAKtrcniardsGYTkadkeGGSYF-----------------CLYFARGCCPLGKKCEYLH 91
ZnF_C3H1 smart00356
zinc finger;
113-134 9.98e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.84  E-value: 9.98e-04
                           10        20
                   ....*....|....*....|..
gi 1109146858  113 LCKFFAKGWCFNGVSCKFLHVK 134
Cdd:smart00356   6 LCKFFKRGYCPRGDRCKFAHPL 27
 
Name Accession Description Interval E-value
Torus pfam16131
Torus domain; This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type ...
 78-132 2.65e-04

Torus domain; This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger.


Pssm-ID: 435160  Cd Length: 109  Bit Score: 40.66  E-value: 2.65e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1109146858  78 DNGTLSRFPAP---------GIT-----PNSFFpaagegnepeqkraahlCKFFAKGWCFNGVSCKFLH 132
Cdd:pfam16131  40 EDKYRSRTKAKtrcniardsGYTkadkeGGSYF-----------------CLYFARGCCPLGKKCEYLH 91
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 114-132 5.29e-04

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 37.40  E-value: 5.29e-04
                          10
                  ....*....|....*....
gi 1109146858 114 CKFFAKGWCFNGVSCKFLH 132
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
113-134 9.98e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.84  E-value: 9.98e-04
                           10        20
                   ....*....|....*....|..
gi 1109146858  113 LCKFFAKGWCFNGVSCKFLHVK 134
Cdd:smart00356   6 LCKFFKRGYCPRGDRCKFAHPL 27
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
113-134 1.86e-03

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 36.02  E-value: 1.86e-03
                          10        20
                  ....*....|....*....|...
gi 1109146858 113 LCKFFAK-GWCFNGVSCKFLHVK 134
Cdd:pfam00642   5 LCRFFLRtGYCKYGDRCKFAHGQ 27
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 112-132 8.93e-03

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 34.10  E-value: 8.93e-03
                          10        20
                  ....*....|....*....|.
gi 1109146858 112 HLCKFFAKGWCFNGVSCKFLH 132
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
 
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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