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Conserved domains on  [gi|22328791|ref|NP_193654|]
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zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana]

Protein Classification

CIR N-terminal domain-containing protein( domain architecture ID 10660961)

CIR N-terminal domain-containing protein such as CWC25 which is involved in pre-mRNA splicing as a component of the spliceosome, and CIR1 (corepressor interacting with RBPJ) which is a component of the Notch corepressor complex and the histone deacetylase complex, and plays a role in splicing regulation and in RBPJ-mediated repression of transcription

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cir_N smart01083
N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region ...
 48-83 2.31e-07

N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex.


:

Pssm-ID: 198151 [Multi-domain]  Cd Length: 37  Bit Score: 47.15  E-value: 2.31e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 22328791     48 WHPLSYPNQRRKWIAEQTHAQHDRRAEEVAREFAQE 83
Cdd:smart01083   2 WHPGNKKNQKRVWKAEQKAEEEKKKIEERRKEIEKE 37
MSCRAMM_ClfA super family cl41352
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 337-567 5.24e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


The actual alignment was detected with superfamily member NF033609:

Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 5.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791  337 TDESSTGSEDSREKRGSKKRKKLKKKSKKQYDSDSLSFEGSGSDSYRLSRRRHTKHVDPSASLKSEVYHQGNSHREKHYY 416
Cdd:NF033609 614 SDSDSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 693

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791  417 DEKHQKRKEIVDRPSASSDDSDyyrSNSSRKKRSEDDYKSHHRERKQVHSNDPVSEKSQKQHYSESGKIQRVEKEHRYDE 496
Cdd:NF033609 694 SDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 770

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22328791  497 RRHRYVDMESENRNRSEKKPRYD---DRDSEKHHRSVKGKEKHVYEASDDPEEFSDRYRSTKKTESDSESNRRS 567
Cdd:NF033609 771 DSDSDSDSDSDSDSDSDSDSDSDsdsDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 844
 
Name Accession Description Interval E-value
Cir_N smart01083
N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region ...
 48-83 2.31e-07

N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex.


Pssm-ID: 198151 [Multi-domain]  Cd Length: 37  Bit Score: 47.15  E-value: 2.31e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 22328791     48 WHPLSYPNQRRKWIAEQTHAQHDRRAEEVAREFAQE 83
Cdd:smart01083   2 WHPGNKKNQKRVWKAEQKAEEEKKKIEERRKEIEKE 37
Cir_N pfam10197
N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region ...
 48-83 4.50e-07

N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex.


Pssm-ID: 462992 [Multi-domain]  Cd Length: 37  Bit Score: 46.25  E-value: 4.50e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 22328791    48 WHPLSYPNQRRKWIAEQTHAQHDRRAEEVAREFAQE 83
Cdd:pfam10197   2 WHPGLKKNQEKVWKAEQKALEERKKIEERKKEIEEE 37
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 337-567 5.24e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 5.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791  337 TDESSTGSEDSREKRGSKKRKKLKKKSKKQYDSDSLSFEGSGSDSYRLSRRRHTKHVDPSASLKSEVYHQGNSHREKHYY 416
Cdd:NF033609 614 SDSDSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 693

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791  417 DEKHQKRKEIVDRPSASSDDSDyyrSNSSRKKRSEDDYKSHHRERKQVHSNDPVSEKSQKQHYSESGKIQRVEKEHRYDE 496
Cdd:NF033609 694 SDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 770

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22328791  497 RRHRYVDMESENRNRSEKKPRYD---DRDSEKHHRSVKGKEKHVYEASDDPEEFSDRYRSTKKTESDSESNRRS 567
Cdd:NF033609 771 DSDSDSDSDSDSDSDSDSDSDSDsdsDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 844
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 438-528 9.22e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 38.72  E-value: 9.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791   438 DYYRSNSSRKKRSEDDYKSHHRERKQVHSNDPVSEKSQKQHYSESGKIQRVEKEHRYDERRHRYVDMESENRNRSEKKPR 517
Cdd:TIGR01642   2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRR 81

                          90
                  ....*....|.
gi 22328791   518 YDDRDSEKHHR 528
Cdd:TIGR01642  82 SRSVRSIEQHR 92
 
Name Accession Description Interval E-value
Cir_N smart01083
N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region ...
 48-83 2.31e-07

N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex.


Pssm-ID: 198151 [Multi-domain]  Cd Length: 37  Bit Score: 47.15  E-value: 2.31e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 22328791     48 WHPLSYPNQRRKWIAEQTHAQHDRRAEEVAREFAQE 83
Cdd:smart01083   2 WHPGNKKNQKRVWKAEQKAEEEKKKIEERRKEIEKE 37
Cir_N pfam10197
N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region ...
 48-83 4.50e-07

N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex.


Pssm-ID: 462992 [Multi-domain]  Cd Length: 37  Bit Score: 46.25  E-value: 4.50e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 22328791    48 WHPLSYPNQRRKWIAEQTHAQHDRRAEEVAREFAQE 83
Cdd:pfam10197   2 WHPGLKKNQEKVWKAEQKALEERKKIEERKKEIEEE 37
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 337-567 5.24e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 5.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791  337 TDESSTGSEDSREKRGSKKRKKLKKKSKKQYDSDSLSFEGSGSDSYRLSRRRHTKHVDPSASLKSEVYHQGNSHREKHYY 416
Cdd:NF033609 614 SDSDSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 693

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791  417 DEKHQKRKEIVDRPSASSDDSDyyrSNSSRKKRSEDDYKSHHRERKQVHSNDPVSEKSQKQHYSESGKIQRVEKEHRYDE 496
Cdd:NF033609 694 SDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 770

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22328791  497 RRHRYVDMESENRNRSEKKPRYD---DRDSEKHHRSVKGKEKHVYEASDDPEEFSDRYRSTKKTESDSESNRRS 567
Cdd:NF033609 771 DSDSDSDSDSDSDSDSDSDSDSDsdsDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 844
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 438-528 9.22e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 38.72  E-value: 9.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22328791   438 DYYRSNSSRKKRSEDDYKSHHRERKQVHSNDPVSEKSQKQHYSESGKIQRVEKEHRYDERRHRYVDMESENRNRSEKKPR 517
Cdd:TIGR01642   2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRR 81

                          90
                  ....*....|.
gi 22328791   518 YDDRDSEKHHR 528
Cdd:TIGR01642  82 SRSVRSIEQHR 92
 
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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