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Conserved domains on  [gi|1938941988|pdb|3JB9|c]
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Chain c, Pre-mRNA-splicing factor cwf19

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CwfJ_C_1 pfam04677
Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of ...
 399-523 1.46e-56

Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.


:

Pssm-ID: 428062  Cd Length: 122  Bit Score: 187.20  E-value: 1.46e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3JB9_c        399 GGDLKKINHVLDTCPLCLNYETQPLAPVISLSHRAYVSLPTQPeLAKYHCLIVPTGHRINTLSCDEDEWDEIRNFMKCIA 478
Cdd:pfam04677   1 GKDHKRIKILPDSCWFCLSNPNLEKHLIVSIGNKAYLALPKGP-LVSGHCLIIPIQHIPSTLSLDEEVWDEIRNFRKALT 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
3JB9_c        479 LMFDSMNLGVIFYENapSPQRYMHTAIECIPVSKRILSLAPAYFR 523
Cdd:pfam04677  80 LMYKSQGKDAVFFEI--ASQRRPHLHIQCIPVPKSIGKLAPLYFK 122
CwfJ_C_2 pfam04676
Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of ...
 532-634 2.92e-34

Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.


:

Pssm-ID: 461388  Cd Length: 96  Bit Score: 125.40  E-value: 2.92e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3JB9_c        532 EWSQHRKIIDTLEGSkkygkwAFRKMMVKELGYFHVWFSIDGGYGHVVEDEKAWGRhdQVPRQVFASMLNLPPEVIRRKG 611
Cdd:pfam04676   1 EWSQHKKLIDTSNKK------GFRRSIPKGFPYFHVEFGLDGGYAHVIEDEERFPL--QFGREVIAGMLDLPPRVWRKPC 72

                          90       100
                  ....*....|....*....|....
3JB9_c        612 SWTGKKD-PREDMFRSRFEKFDWT 634
Cdd:pfam04676  73 RQSKEEEeQRVEAFKKAWKKYDWT 96
DBD_XPA-like super family cl40444
DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA ...
 162-215 5.84e-03

DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14 and similar proteins; The family includes DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14, zinc transporter 9 (ZNT9) and similar proteins. XPA, also known as xeroderma pigmentosum group A-complementing protein (XPAC), is involved in DNA excision repair. It initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. Rad14 is involved in nucleotide excision repair. It binds specifically to damaged DNA and is required for the incision step. Rad14 is a component of the nucleotide excision repair factor 1 (NEF1) complex consisting of Rad1, Rad10 and Rad14. ZNT9, also known as solute carrier family 30 member 9 (SLC30A9), may act as a zinc transporter involved in intracellular zinc homeostasis and may also play a role as nuclear receptor coactivator. The model corresponds to the DNA-binding domain found in XPA and Rad14. It consists of a conserved N-terminal zinc-binding subdomain and a C-terminal alpha/beta fold subdomain. ZNT9 contains only C-terminal alpha/beta fold subdomain but lacks of N-terminal zinc-binding subdomain.


The actual alignment was detected with superfamily member cd21075:

Pssm-ID: 424075  Cd Length: 67  Bit Score: 35.64  E-value: 5.84e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
3JB9_c      162 SGINYKIGDN--GSRWRMMKLKRVFDmaqdqrrpVEEVALERYGSLKEFDFALEER 215
Cdd:cd21075  20 AGLPYEEKPNphGPSAAPMKLYLERE--------VERLAWRKHGGPEGLEAALEKR 67
 
Name Accession Description Interval E-value
CwfJ_C_1 pfam04677
Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of ...
 399-523 1.46e-56

Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.


Pssm-ID: 428062  Cd Length: 122  Bit Score: 187.20  E-value: 1.46e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3JB9_c        399 GGDLKKINHVLDTCPLCLNYETQPLAPVISLSHRAYVSLPTQPeLAKYHCLIVPTGHRINTLSCDEDEWDEIRNFMKCIA 478
Cdd:pfam04677   1 GKDHKRIKILPDSCWFCLSNPNLEKHLIVSIGNKAYLALPKGP-LVSGHCLIIPIQHIPSTLSLDEEVWDEIRNFRKALT 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
3JB9_c        479 LMFDSMNLGVIFYENapSPQRYMHTAIECIPVSKRILSLAPAYFR 523
Cdd:pfam04677  80 LMYKSQGKDAVFFEI--ASQRRPHLHIQCIPVPKSIGKLAPLYFK 122
CwfJ_C_2 pfam04676
Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of ...
 532-634 2.92e-34

Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.


Pssm-ID: 461388  Cd Length: 96  Bit Score: 125.40  E-value: 2.92e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3JB9_c        532 EWSQHRKIIDTLEGSkkygkwAFRKMMVKELGYFHVWFSIDGGYGHVVEDEKAWGRhdQVPRQVFASMLNLPPEVIRRKG 611
Cdd:pfam04676   1 EWSQHKKLIDTSNKK------GFRRSIPKGFPYFHVEFGLDGGYAHVIEDEERFPL--QFGREVIAGMLDLPPRVWRKPC 72

                          90       100
                  ....*....|....*....|....
3JB9_c        612 SWTGKKD-PREDMFRSRFEKFDWT 634
Cdd:pfam04676  73 RQSKEEEeQRVEAFKKAWKKYDWT 96
DBD_XPA-like cd21075
DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA ...
 162-215 5.84e-03

DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14 and similar proteins; The family includes DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14, zinc transporter 9 (ZNT9) and similar proteins. XPA, also known as xeroderma pigmentosum group A-complementing protein (XPAC), is involved in DNA excision repair. It initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. Rad14 is involved in nucleotide excision repair. It binds specifically to damaged DNA and is required for the incision step. Rad14 is a component of the nucleotide excision repair factor 1 (NEF1) complex consisting of Rad1, Rad10 and Rad14. ZNT9, also known as solute carrier family 30 member 9 (SLC30A9), may act as a zinc transporter involved in intracellular zinc homeostasis and may also play a role as nuclear receptor coactivator. The model corresponds to the DNA-binding domain found in XPA and Rad14. It consists of a conserved N-terminal zinc-binding subdomain and a C-terminal alpha/beta fold subdomain. ZNT9 contains only C-terminal alpha/beta fold subdomain but lacks of N-terminal zinc-binding subdomain.


Pssm-ID: 410961  Cd Length: 67  Bit Score: 35.64  E-value: 5.84e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
3JB9_c      162 SGINYKIGDN--GSRWRMMKLKRVFDmaqdqrrpVEEVALERYGSLKEFDFALEER 215
Cdd:cd21075  20 AGLPYEEKPNphGPSAAPMKLYLERE--------VERLAWRKHGGPEGLEAALEKR 67
 
Name Accession Description Interval E-value
CwfJ_C_1 pfam04677
Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of ...
 399-523 1.46e-56

Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.


Pssm-ID: 428062  Cd Length: 122  Bit Score: 187.20  E-value: 1.46e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3JB9_c        399 GGDLKKINHVLDTCPLCLNYETQPLAPVISLSHRAYVSLPTQPeLAKYHCLIVPTGHRINTLSCDEDEWDEIRNFMKCIA 478
Cdd:pfam04677   1 GKDHKRIKILPDSCWFCLSNPNLEKHLIVSIGNKAYLALPKGP-LVSGHCLIIPIQHIPSTLSLDEEVWDEIRNFRKALT 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
3JB9_c        479 LMFDSMNLGVIFYENapSPQRYMHTAIECIPVSKRILSLAPAYFR 523
Cdd:pfam04677  80 LMYKSQGKDAVFFEI--ASQRRPHLHIQCIPVPKSIGKLAPLYFK 122
CwfJ_C_2 pfam04676
Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of ...
 532-634 2.92e-34

Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.


Pssm-ID: 461388  Cd Length: 96  Bit Score: 125.40  E-value: 2.92e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3JB9_c        532 EWSQHRKIIDTLEGSkkygkwAFRKMMVKELGYFHVWFSIDGGYGHVVEDEKAWGRhdQVPRQVFASMLNLPPEVIRRKG 611
Cdd:pfam04676   1 EWSQHKKLIDTSNKK------GFRRSIPKGFPYFHVEFGLDGGYAHVIEDEERFPL--QFGREVIAGMLDLPPRVWRKPC 72

                          90       100
                  ....*....|....*....|....
3JB9_c        612 SWTGKKD-PREDMFRSRFEKFDWT 634
Cdd:pfam04676  73 RQSKEEEeQRVEAFKKAWKKYDWT 96
DBD_XPA-like cd21075
DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA ...
 162-215 5.84e-03

DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14 and similar proteins; The family includes DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14, zinc transporter 9 (ZNT9) and similar proteins. XPA, also known as xeroderma pigmentosum group A-complementing protein (XPAC), is involved in DNA excision repair. It initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. Rad14 is involved in nucleotide excision repair. It binds specifically to damaged DNA and is required for the incision step. Rad14 is a component of the nucleotide excision repair factor 1 (NEF1) complex consisting of Rad1, Rad10 and Rad14. ZNT9, also known as solute carrier family 30 member 9 (SLC30A9), may act as a zinc transporter involved in intracellular zinc homeostasis and may also play a role as nuclear receptor coactivator. The model corresponds to the DNA-binding domain found in XPA and Rad14. It consists of a conserved N-terminal zinc-binding subdomain and a C-terminal alpha/beta fold subdomain. ZNT9 contains only C-terminal alpha/beta fold subdomain but lacks of N-terminal zinc-binding subdomain.


Pssm-ID: 410961  Cd Length: 67  Bit Score: 35.64  E-value: 5.84e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
3JB9_c      162 SGINYKIGDN--GSRWRMMKLKRVFDmaqdqrrpVEEVALERYGSLKEFDFALEER 215
Cdd:cd21075  20 AGLPYEEKPNphGPSAAPMKLYLERE--------VERLAWRKHGGPEGLEAALEKR 67
 
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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