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Conserved domains on  [gi|1829230040|gb|KAF3973528|]
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hypothetical protein CMV_003064 [Castanea mollissima]

Protein Classification

SWIB-MDM2_like domain-containing protein( domain architecture ID 12970674)

SWIB-MDM2_like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SWIB-MDM2_like cd10567
SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes ...
 170-240 1.93e-40

SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes Schizosaccharomyces pombe upstream activation factor subunit spp27, Saccharomyces cerevisiae upstream activation factor subunit UAF30, Chlamydiae DNA topoisomerase/SWIB domain fusion protein, Arabidopsis thaliana zinc finger CCCH domain-containing proteins, AtC3H19 and AtC3H44, and similar proteins. S. pombe spp27, also termed upstream activation factor 27 KDa subunit (p27), or upstream activation factor 30 KDa subunit (p30), or upstream activation factor subunit uaf30, is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. S. cerevisiae UAF30, also termed upstream activation factor 30 KDa subunit (p30), is a non-essential component of the UAF. It seems to play a role in silencing transcription by RNA polymerase II. The SWIB domain found in Chlamydiae DNA topoisomerase may play a role in chromatin condensation-decondensation, which is characteristic of the chlamydial developmental cycle and not found in any other types of bacteria. AtC3H19, also termed protein needed for RDR2-independent DNA methylation (NERD), is a plant-specific GW repeat- and PHD finger-containing protein that plays a central role in integrating RNA silencing and chromatin signals in 21 nt small-interfering RNA (siRNA)-dependent DNA methylation on the cytosine pathway, leading to transcriptional gene silencing of specific sequences. This family also includes many uncharacterized proteins containing two copies of SWIB/MDM2 domain.


:

Pssm-ID: 349489 [Multi-domain]  Cd Length: 71  Bit Score: 136.52  E-value: 1.93e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829230040 170 CGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:cd10567     1 YKLSPELAAFLGVSELSRTEVVKKLWAYIKENNLQDPKNKREILCDEKLKKVFGKDEVVMFEMNKLLSKHL 71
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 272-313 5.78e-12

SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.


:

Pssm-ID: 460488 [Multi-domain]  Cd Length: 73  Bit Score: 60.57  E-value: 5.78e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1829230040 272 PVVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:pfam02201   2 PFKLSPELAELLGE--EELSRPEVVKALWEYIKENNLQDPED 41
 
Name Accession Description Interval E-value
SWIB-MDM2_like cd10567
SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes ...
 170-240 1.93e-40

SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes Schizosaccharomyces pombe upstream activation factor subunit spp27, Saccharomyces cerevisiae upstream activation factor subunit UAF30, Chlamydiae DNA topoisomerase/SWIB domain fusion protein, Arabidopsis thaliana zinc finger CCCH domain-containing proteins, AtC3H19 and AtC3H44, and similar proteins. S. pombe spp27, also termed upstream activation factor 27 KDa subunit (p27), or upstream activation factor 30 KDa subunit (p30), or upstream activation factor subunit uaf30, is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. S. cerevisiae UAF30, also termed upstream activation factor 30 KDa subunit (p30), is a non-essential component of the UAF. It seems to play a role in silencing transcription by RNA polymerase II. The SWIB domain found in Chlamydiae DNA topoisomerase may play a role in chromatin condensation-decondensation, which is characteristic of the chlamydial developmental cycle and not found in any other types of bacteria. AtC3H19, also termed protein needed for RDR2-independent DNA methylation (NERD), is a plant-specific GW repeat- and PHD finger-containing protein that plays a central role in integrating RNA silencing and chromatin signals in 21 nt small-interfering RNA (siRNA)-dependent DNA methylation on the cytosine pathway, leading to transcriptional gene silencing of specific sequences. This family also includes many uncharacterized proteins containing two copies of SWIB/MDM2 domain.


Pssm-ID: 349489 [Multi-domain]  Cd Length: 71  Bit Score: 136.52  E-value: 1.93e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829230040 170 CGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:cd10567     1 YKLSPELAAFLGVSELSRTEVVKKLWAYIKENNLQDPKNKREILCDEKLKKVFGKDEVVMFEMNKLLSKHL 71
SWIB smart00151
SWI complex, BAF60b domains;
166-241 1.06e-37

SWI complex, BAF60b domains;


Pssm-ID: 128456 [Multi-domain]  Cd Length: 77  Bit Score: 129.35  E-value: 1.06e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1829230040  166 LNKVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHII 241
Cdd:smart00151   1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLI 76
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 168-240 5.06e-35

SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.


Pssm-ID: 460488 [Multi-domain]  Cd Length: 73  Bit Score: 122.21  E-value: 5.06e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1829230040 168 KVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:pfam02201   1 KPFKLSPELAELLGEEELSRPEVVKALWEYIKENNLQDPEDKREIICDEKLKKLFGGDRVKFFEMPKLLSPHL 73
Rsc6 COG5531
DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];
158-240 3.86e-30

DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];


Pssm-ID: 444282 [Multi-domain]  Cd Length: 85  Bit Score: 110.03  E-value: 3.86e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829230040 158 KRRGGPGGLNKVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFE-TDCTDMFKMNKLL 236
Cdd:COG5531     1 AKRKKNAAFMKPLTPSAELAAVVGAKPLPRTEVTKKVWDYIKKNNLQDPANKRNINADAKLKKVFGgKDQVSMFEMTKLV 80


                  ....
gi 1829230040 237 AKHI 240
Cdd:COG5531    81 SKHL 84
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 145-241 9.53e-17

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 81.41  E-value: 9.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829230040 145 TPHTPKESAPVGAKR-RGGPgglnkVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFE 223
Cdd:PRK06319  767 TVKKKSKAKSKKTTKkRAGP-----LYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIG 841

                          90
                  ....*....|....*...
gi 1829230040 224 TDCTDMFKMNKLLAKHII 241
Cdd:PRK06319  842 PDPIDMFQLSKKLSQHLI 859
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 272-313 5.78e-12

SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.


Pssm-ID: 460488 [Multi-domain]  Cd Length: 73  Bit Score: 60.57  E-value: 5.78e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1829230040 272 PVVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:pfam02201   2 PFKLSPELAELLGE--EELSRPEVVKALWEYIKENNLQDPED 41
SWIB-MDM2_like cd10567
SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes ...
 273-313 4.44e-10

SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes Schizosaccharomyces pombe upstream activation factor subunit spp27, Saccharomyces cerevisiae upstream activation factor subunit UAF30, Chlamydiae DNA topoisomerase/SWIB domain fusion protein, Arabidopsis thaliana zinc finger CCCH domain-containing proteins, AtC3H19 and AtC3H44, and similar proteins. S. pombe spp27, also termed upstream activation factor 27 KDa subunit (p27), or upstream activation factor 30 KDa subunit (p30), or upstream activation factor subunit uaf30, is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. S. cerevisiae UAF30, also termed upstream activation factor 30 KDa subunit (p30), is a non-essential component of the UAF. It seems to play a role in silencing transcription by RNA polymerase II. The SWIB domain found in Chlamydiae DNA topoisomerase may play a role in chromatin condensation-decondensation, which is characteristic of the chlamydial developmental cycle and not found in any other types of bacteria. AtC3H19, also termed protein needed for RDR2-independent DNA methylation (NERD), is a plant-specific GW repeat- and PHD finger-containing protein that plays a central role in integrating RNA silencing and chromatin signals in 21 nt small-interfering RNA (siRNA)-dependent DNA methylation on the cytosine pathway, leading to transcriptional gene silencing of specific sequences. This family also includes many uncharacterized proteins containing two copies of SWIB/MDM2 domain.


Pssm-ID: 349489 [Multi-domain]  Cd Length: 71  Bit Score: 55.24  E-value: 4.44e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1829230040 273 VVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:cd10567     1 YKLSPELAAFLGV--SELSRTEVVKKLWAYIKENNLQDPKN 39
SWIB smart00151
SWI complex, BAF60b domains;
270-313 5.94e-10

SWI complex, BAF60b domains;


Pssm-ID: 128456 [Multi-domain]  Cd Length: 77  Bit Score: 55.01  E-value: 5.94e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1829230040  270 SSPVVISEALAKFLGTGgrEMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:smart00151   2 TKKVTLSPELAKVLGAP--EMTRTEIIKRLWEYIKEHNLQDPQN 43
Rsc6 COG5531
DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];
272-313 3.89e-08

DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];


Pssm-ID: 444282 [Multi-domain]  Cd Length: 85  Bit Score: 49.94  E-value: 3.89e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1829230040 272 PVVISEALAKFLGTGgrEMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:COG5531    12 PLTPSAELAAVVGAK--PLPRTEVTKKVWDYIKKNNLQDPAN 51
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 247-313 2.56e-03

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 39.81  E-value: 2.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829230040 247 KESSQAKRLKVDVESTTEsvQRGSSPVVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:PRK06319  764 AAKTVKKKSKAKSKKTTK--KRAGPLYTPSPALAAMIGA--EPVGRGEATKKVWDYIKEHGLQSPEN 826
 
Name Accession Description Interval E-value
SWIB-MDM2_like cd10567
SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes ...
 170-240 1.93e-40

SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes Schizosaccharomyces pombe upstream activation factor subunit spp27, Saccharomyces cerevisiae upstream activation factor subunit UAF30, Chlamydiae DNA topoisomerase/SWIB domain fusion protein, Arabidopsis thaliana zinc finger CCCH domain-containing proteins, AtC3H19 and AtC3H44, and similar proteins. S. pombe spp27, also termed upstream activation factor 27 KDa subunit (p27), or upstream activation factor 30 KDa subunit (p30), or upstream activation factor subunit uaf30, is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. S. cerevisiae UAF30, also termed upstream activation factor 30 KDa subunit (p30), is a non-essential component of the UAF. It seems to play a role in silencing transcription by RNA polymerase II. The SWIB domain found in Chlamydiae DNA topoisomerase may play a role in chromatin condensation-decondensation, which is characteristic of the chlamydial developmental cycle and not found in any other types of bacteria. AtC3H19, also termed protein needed for RDR2-independent DNA methylation (NERD), is a plant-specific GW repeat- and PHD finger-containing protein that plays a central role in integrating RNA silencing and chromatin signals in 21 nt small-interfering RNA (siRNA)-dependent DNA methylation on the cytosine pathway, leading to transcriptional gene silencing of specific sequences. This family also includes many uncharacterized proteins containing two copies of SWIB/MDM2 domain.


Pssm-ID: 349489 [Multi-domain]  Cd Length: 71  Bit Score: 136.52  E-value: 1.93e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829230040 170 CGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:cd10567     1 YKLSPELAAFLGVSELSRTEVVKKLWAYIKENNLQDPKNKREILCDEKLKKVFGKDEVVMFEMNKLLSKHL 71
SWIB smart00151
SWI complex, BAF60b domains;
166-241 1.06e-37

SWI complex, BAF60b domains;


Pssm-ID: 128456 [Multi-domain]  Cd Length: 77  Bit Score: 129.35  E-value: 1.06e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1829230040  166 LNKVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHII 241
Cdd:smart00151   1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLI 76
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 168-240 5.06e-35

SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.


Pssm-ID: 460488 [Multi-domain]  Cd Length: 73  Bit Score: 122.21  E-value: 5.06e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1829230040 168 KVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:pfam02201   1 KPFKLSPELAELLGEEELSRPEVVKALWEYIKENNLQDPEDKREIICDEKLKKLFGGDRVKFFEMPKLLSPHL 73
Rsc6 COG5531
DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];
158-240 3.86e-30

DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];


Pssm-ID: 444282 [Multi-domain]  Cd Length: 85  Bit Score: 110.03  E-value: 3.86e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829230040 158 KRRGGPGGLNKVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFE-TDCTDMFKMNKLL 236
Cdd:COG5531     1 AKRKKNAAFMKPLTPSAELAAVVGAKPLPRTEVTKKVWDYIKKNNLQDPANKRNINADAKLKKVFGgKDQVSMFEMTKLV 80


                  ....
gi 1829230040 237 AKHI 240
Cdd:COG5531    81 SKHL 84
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 145-241 9.53e-17

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 81.41  E-value: 9.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829230040 145 TPHTPKESAPVGAKR-RGGPgglnkVCGVSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFE 223
Cdd:PRK06319  767 TVKKKSKAKSKKTTKkRAGP-----LYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIG 841

                          90
                  ....*....|....*...
gi 1829230040 224 TDCTDMFKMNKLLAKHII 241
Cdd:PRK06319  842 PDPIDMFQLSKKLSQHLI 859
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 136-240 6.90e-16

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 78.84  E-value: 6.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829230040 136 KPEAFAQNATPHTP-KESAPVGAKRRGGPGGLNKVcgvSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIIC 214
Cdd:PRK14724  884 KKAAAKKVAAKTAAaKTPRKAAKKKAAPPAAGLKP---SAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINA 960

                          90       100
                  ....*....|....*....|....*.
gi 1829230040 215 DDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:PRK14724  961 DAKLRPVFGKDQVTMFELAGIVGKHL 986
SWIB_like cd10568
SWIB domain found in the 60 kda subunit of the ATP-dependent SWI/SNF chromatin-remodeling ...
 172-240 2.10e-14

SWIB domain found in the 60 kda subunit of the ATP-dependent SWI/SNF chromatin-remodeling complexes and similar proteins; SWIB domain is a conserved region found within proteins in the SWI/SNF family of complexes. SWI/SNF complex proteins display helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors), among which the BAF60 subunit serves as a key link between the core complexes and specific transcriptional factors. The BAF60 subunit have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. The family also includes Saccharomyces cerevisiae transcription regulatory protein SNF12 and remodel the structure of chromatin complex subunit 6 (RSC6), and Schizosaccharomyces pombe SWI/SNF and RSC complexes subunit SSR3. SNF12, also termed 73-kDa subunit of the SWI/SNF transcriptional regulatory complex, or SWI/SNF complex component SWP73, is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). RSC6 and SSR3 are components of the RSC, which is involved in transcription regulation and nucleosome positioning. RSC6 is essential for mitotic growth and suppresses formamide sensitivity of the RSC8 mutants.


Pssm-ID: 349490 [Multi-domain]  Cd Length: 69  Bit Score: 67.17  E-value: 2.10e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1829230040 172 VSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 240
Cdd:cd10568     1 LSPALAQLLGIKEGTRPNIIYALWQYIKLNKLQDPEDRRLINCDEALKQLFGVERFKFSELPELLNPHL 69
SWIB-MDM2 cd00855
SWIB/MDM2 domain family; The SWIB/MDM2 protein domain, short for SWI/SNF complex B/MDM2, has ...
 172-225 8.16e-14

SWIB/MDM2 domain family; The SWIB/MDM2 protein domain, short for SWI/SNF complex B/MDM2, has been found in both SWI/SNF complex B (SWIB) and the negative regulator of the p53 tumor suppressor MDM2, which are homologous and share a common fold. The SWIB domain is a conserved region found within proteins in the SWI/SNF (SWItch/Sucrose Non-Fermentable) family of complexes. SWI/SNF complex proteins display helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). MDM2 is an inhibitor of p53 tumor repressor. It binds to the transactivation domain and down-regulates the ability of p53 to activate transcription. This family corresponds to the SWIB domain and the p53 binding domain of MDM2.


Pssm-ID: 349487 [Multi-domain]  Cd Length: 69  Bit Score: 65.71  E-value: 8.16e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1829230040 172 VSPELQAVVG-EPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETD 225
Cdd:cd00855     1 LSPELEALLKsYETFTLKEILQALWQYIKKKNLMDPDDPSIVVCDERLRQLFEVP 55
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 272-313 5.78e-12

SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.


Pssm-ID: 460488 [Multi-domain]  Cd Length: 73  Bit Score: 60.57  E-value: 5.78e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1829230040 272 PVVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:pfam02201   2 PFKLSPELAELLGE--EELSRPEVVKALWEYIKENNLQDPED 41
SWIB-MDM2_like cd10567
SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes ...
 273-313 4.44e-10

SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes Schizosaccharomyces pombe upstream activation factor subunit spp27, Saccharomyces cerevisiae upstream activation factor subunit UAF30, Chlamydiae DNA topoisomerase/SWIB domain fusion protein, Arabidopsis thaliana zinc finger CCCH domain-containing proteins, AtC3H19 and AtC3H44, and similar proteins. S. pombe spp27, also termed upstream activation factor 27 KDa subunit (p27), or upstream activation factor 30 KDa subunit (p30), or upstream activation factor subunit uaf30, is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. S. cerevisiae UAF30, also termed upstream activation factor 30 KDa subunit (p30), is a non-essential component of the UAF. It seems to play a role in silencing transcription by RNA polymerase II. The SWIB domain found in Chlamydiae DNA topoisomerase may play a role in chromatin condensation-decondensation, which is characteristic of the chlamydial developmental cycle and not found in any other types of bacteria. AtC3H19, also termed protein needed for RDR2-independent DNA methylation (NERD), is a plant-specific GW repeat- and PHD finger-containing protein that plays a central role in integrating RNA silencing and chromatin signals in 21 nt small-interfering RNA (siRNA)-dependent DNA methylation on the cytosine pathway, leading to transcriptional gene silencing of specific sequences. This family also includes many uncharacterized proteins containing two copies of SWIB/MDM2 domain.


Pssm-ID: 349489 [Multi-domain]  Cd Length: 71  Bit Score: 55.24  E-value: 4.44e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1829230040 273 VVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:cd10567     1 YKLSPELAAFLGV--SELSRTEVVKKLWAYIKENNLQDPKN 39
SWIB smart00151
SWI complex, BAF60b domains;
270-313 5.94e-10

SWI complex, BAF60b domains;


Pssm-ID: 128456 [Multi-domain]  Cd Length: 77  Bit Score: 55.01  E-value: 5.94e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1829230040  270 SSPVVISEALAKFLGTGgrEMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:smart00151   2 TKKVTLSPELAKVLGAP--EMTRTEIIKRLWEYIKEHNLQDPQN 43
Rsc6 COG5531
DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];
272-313 3.89e-08

DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics];


Pssm-ID: 444282 [Multi-domain]  Cd Length: 85  Bit Score: 49.94  E-value: 3.89e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1829230040 272 PVVISEALAKFLGTGgrEMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:COG5531    12 PLTPSAELAAVVGAK--PLPRTEVTKKVWDYIKKNNLQDPAN 51
SWIB_like cd10568
SWIB domain found in the 60 kda subunit of the ATP-dependent SWI/SNF chromatin-remodeling ...
 275-311 5.78e-06

SWIB domain found in the 60 kda subunit of the ATP-dependent SWI/SNF chromatin-remodeling complexes and similar proteins; SWIB domain is a conserved region found within proteins in the SWI/SNF family of complexes. SWI/SNF complex proteins display helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors), among which the BAF60 subunit serves as a key link between the core complexes and specific transcriptional factors. The BAF60 subunit have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. The family also includes Saccharomyces cerevisiae transcription regulatory protein SNF12 and remodel the structure of chromatin complex subunit 6 (RSC6), and Schizosaccharomyces pombe SWI/SNF and RSC complexes subunit SSR3. SNF12, also termed 73-kDa subunit of the SWI/SNF transcriptional regulatory complex, or SWI/SNF complex component SWP73, is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). RSC6 and SSR3 are components of the RSC, which is involved in transcription regulation and nucleosome positioning. RSC6 is essential for mitotic growth and suppresses formamide sensitivity of the RSC8 mutants.


Pssm-ID: 349490 [Multi-domain]  Cd Length: 69  Bit Score: 43.29  E-value: 5.78e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1829230040 275 ISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDP 311
Cdd:cd10568     1 LSPALAQLLGI--KEGTRPNIIYALWQYIKLNKLQDP 35
SWIB_BAF60C cd17676
SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins; BAF60C, also ...
 172-226 8.36e-06

SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins; BAF60C, also termed SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 (SMARCD3), or 60 kDa BRG-1/Brm-associated factor subunit C, is a core subunit of the SWI/SNF chromatin-remodeling complex that activates the transcription of fatty acid oxidation genes during fasting. It is involved in chromatin remodeling and hepatic lipid metabolism. It is also essential for cardiomyocyte differentiation at the early heart development. Moreover, BAF60C drives glycolytic metabolism in the muscle and improves systemic glucose homeostasis through Deptor-mediated Akt activation. Furthermore, BAF60C epigenetically regulates epithelial-mesenchymal transition (EMT) by activating WNT signaling pathways.


Pssm-ID: 349495  Cd Length: 74  Bit Score: 43.05  E-value: 8.36e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1829230040 172 VSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFetDC 226
Cdd:cd17676     1 LDPRLARLLGIHTQTRSAIIQALWQYIKTNKLQDSHDKEYINCDKYFQQIF--DC 53
SWIB_BAF60A cd17674
SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins; BAF60A, also ...
 174-229 3.69e-05

SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins; BAF60A, also termed SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 (SMARCD1), or 60 kDa BRG-1/Brm-associated factor subunit A, or SWI/SNF complex 60 kDa subunit, is a core subunit of the SWI/SNF chromatin-remodeling complex that activates the transcription of fatty acid oxidation genes during fasting. BAF60A is involved in chromatin remodeling and hepatic lipid metabolism. It mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. It is also a key component of the transcriptional control in cardiac progenitors. Moreover, BAF60A interacts with p53 to recruit the SWI/SNF complex, suggesting that the SWI/SNF chromatin remodeling complex is involved in the suppression of tumors.


Pssm-ID: 349493  Cd Length: 77  Bit Score: 41.34  E-value: 3.69e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1829230040 174 PELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFEtdCTDM 229
Cdd:cd17674     6 PRLARLLGIHTQTRPVIINALWQYIKTHKLQDPHEREYINCDKYLQQIFE--CQRM 59
SWIB_BAF60B cd17675
SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins; BAF60B, also ...
 172-229 4.80e-05

SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins; BAF60B, also termed SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 (SMARCD2), or 60 kDa BRG-1/Brm-associated factor subunit B, is a component of the BAF complex. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It plays a role in the ATM-p53 pathway in sensing chromatin opening by facilitating ATM recruitment to the SWI/SNF complex, as well as ATM activation. It also regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Thus, it acts as a key factor controlling myelopoiesis and is a potential tumor suppressor in leukemia.


Pssm-ID: 349494  Cd Length: 80  Bit Score: 41.11  E-value: 4.80e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1829230040 172 VSPELQAVVGEPALPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFetDCTDM 229
Cdd:cd17675     7 LDPRLARLLGVHTQTRANIMQALWLYIKHNKLQDSHEKEYINCNRYFRQIF--NCLRM 62
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 247-313 2.56e-03

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 39.81  E-value: 2.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829230040 247 KESSQAKRLKVDVESTTEsvQRGSSPVVISEALAKFLGTggREMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:PRK06319  764 AAKTVKKKSKAKSKKTTK--KRAGPLYTPSPALAAMIGA--EPVGRGEATKKVWDYIKEHGLQSPEN 826
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 237-313 4.09e-03

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 39.17  E-value: 4.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829230040 237 AKHIIALEPTKESSQAKRLKVDVESTTESVQRGSSPvviSEALAKFLGTGgrEMPQSEAITRVWEYIKANRLEDPLN 313
Cdd:PRK14724  883 AKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLKP---SAALAAVIGAE--PVARPEVIKKLWDYIKANNLQDPAD 954
 
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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