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Conserved domains on  [gi|322510099|sp|O54772|]
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RecName: Full=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2; AltName: Full=60 kDa BRG-1/Brm-associated factor subunit B; AltName: Full=BRG1-associated factor 60B; Short=BAF60B

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SWIB_BAF60B cd17675
SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins; BAF60B, also ...
 307-386 1.02e-55

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: 181.33  E-value: 1.02e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099 307 QPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDP 386
Cdd:cd17675    1 QPPQYKLDPRLARLLGVHTQTRANIMQALWLYIKHNKLQDSHEKEYINCNRYFRQIFNCLRMRFSEIPMKLAGLLQHPDP 80
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 43-148 3.54e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 43.26  E-value: 3.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099   43 RGPGPSGGMGVPGAAAFRPMGPAGPAAQYQ-RPGMSPGSRMPMAGLQVGPPAGsPFGTAAPLRPGMPPTMmdpfRKRLLV 121
Cdd:TIGR01628 381 RMRQLPMGSPMGGAMGQPPYYGQGPQQQFNgQPLGWPRMSMMPTPMGPGGPLR-PNGLAPMNAVRAPSRN----AQNAAQ 455

                          90       100
                  ....*....|....*....|....*..
gi 322510099  122 PQAQPPMPAQRRGLKRRKMADKVLPQR 148
Cdd:TIGR01628 456 KPPMQPVMYPPNYQSLPLSQDLPQPQS 482
 
Name Accession Description Interval E-value
SWIB_BAF60B cd17675
SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins; BAF60B, also ...
 307-386 1.02e-55

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: 181.33  E-value: 1.02e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099 307 QPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDP 386
Cdd:cd17675    1 QPPQYKLDPRLARLLGVHTQTRANIMQALWLYIKHNKLQDSHEKEYINCNRYFRQIFNCLRMRFSEIPMKLAGLLQHPDP 80
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 310-381 3.15e-22

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: 90.23  E-value: 3.15e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 322510099  310 QYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLL 381
Cdd:pfam02201   2 PFKLSPELAELLGEEELSRPEVVKALWEYIKENNLQDPEDKREIICDEKLKKLFGGDRVKFFEMPKLLSPHL 73
SWIB smart00151
SWI complex, BAF60b domains;
307-382 6.85e-19

SWI complex, BAF60b domains;


Pssm-ID: 128456 [Multi-domain]  Cd Length: 77  Bit Score: 80.82  E-value: 6.85e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 322510099   307 QPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQ 382
Cdd:smart00151   1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLI 76
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 43-148 3.54e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 43.26  E-value: 3.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099   43 RGPGPSGGMGVPGAAAFRPMGPAGPAAQYQ-RPGMSPGSRMPMAGLQVGPPAGsPFGTAAPLRPGMPPTMmdpfRKRLLV 121
Cdd:TIGR01628 381 RMRQLPMGSPMGGAMGQPPYYGQGPQQQFNgQPLGWPRMSMMPTPMGPGGPLR-PNGLAPMNAVRAPSRN----AQNAAQ 455

                          90       100
                  ....*....|....*....|....*..
gi 322510099  122 PQAQPPMPAQRRGLKRRKMADKVLPQR 148
Cdd:TIGR01628 456 KPPMQPVMYPPNYQSLPLSQDLPQPQS 482
PHA03378 PHA03378
EBNA-3B; Provisional
 38-132 7.61e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 42.36  E-value: 7.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099  38 PNPALRGPGPSGGMGVPGAAAFRPMGPAGPAAQYQRPGMSPGSRMPMAGL--QVGPPAGSPFGTAAPLRPGMPPTMMDPf 115
Cdd:PHA03378 701 PTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAApgRARPPAAAPGRARPPAAAPGAPTPQPP- 779

                         90
                 ....*....|....*..
gi 322510099 116 rkrllvPQAqPPMPAQR 132
Cdd:PHA03378 780 ------PQA-PPAPQQR 789
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 309-363 3.37e-03

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 40.19  E-value: 3.37e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 322510099 309 PQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIF 363
Cdd:PRK06319 786 PLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI 840
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 44-131 8.08e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 38.84  E-value: 8.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099   44 GPGPSGGMGVPGAAAFRPMGPAGPAAQYQRPGMSPGSRMPMAGL---QVGPP-------AGSPFGTAAPLRPGMPPTMMD 113
Cdd:pfam09606 156 GGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMGGQmppQMGVPgmpgpadAGAQMGQQAQANGGMNPQQMG 235

                          90
                  ....*....|....*...
gi 322510099  114 PFRKRLLVPQAQPPMPAQ 131
Cdd:pfam09606 236 GAPNQVAMQQQQPQQQGQ 253
 
Name Accession Description Interval E-value
SWIB_BAF60B cd17675
SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins; BAF60B, also ...
 307-386 1.02e-55

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: 181.33  E-value: 1.02e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099 307 QPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDP 386
Cdd:cd17675    1 QPPQYKLDPRLARLLGVHTQTRANIMQALWLYIKHNKLQDSHEKEYINCNRYFRQIFNCLRMRFSEIPMKLAGLLQHPDP 80
SWIB_BAF60A cd17674
SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins; BAF60A, also ...
 310-386 2.42e-37

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: 132.25  E-value: 2.42e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 322510099 310 QYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDP 386
Cdd:cd17674    1 QFKLDPRLARLLGIHTQTRPVIINALWQYIKTHKLQDPHEREYINCDKYLQQIFECQRMKFSEIPQRLHPLLMPPDP 77
SWIB_BAF60C cd17676
SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins; BAF60C, also ...
 313-386 3.94e-34

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: 123.56  E-value: 3.94e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 322510099 313 LDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDP 386
Cdd:cd17676    1 LDPRLARLLGIHTQTRSAIIQALWQYIKTNKLQDSHDKEYINCDKYFQQIFDCPRLKFSEIPQRLTNLLLPPDP 74
SWIB_like cd10568
SWIB domain found in the 60 kda subunit of the ATP-dependent SWI/SNF chromatin-remodeling ...
 313-381 7.83e-27

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: 103.00  E-value: 7.83e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 322510099 313 LDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLL 381
Cdd:cd10568    1 LSPALAQLLGIKEGTRPNIIYALWQYIKLNKLQDPEDRRLINCDEALKQLFGVERFKFSELPELLNPHL 69
SWIB pfam02201
SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated ...
 310-381 3.15e-22

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: 90.23  E-value: 3.15e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 322510099  310 QYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLL 381
Cdd:pfam02201   2 PFKLSPELAELLGEEELSRPEVVKALWEYIKENNLQDPEDKREIICDEKLKKLFGGDRVKFFEMPKLLSPHL 73
SWIB smart00151
SWI complex, BAF60b domains;
307-382 6.85e-19

SWI complex, BAF60b domains;


Pssm-ID: 128456 [Multi-domain]  Cd Length: 77  Bit Score: 80.82  E-value: 6.85e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 322510099   307 QPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQ 382
Cdd:smart00151   1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLI 76
SWIB-MDM2 cd00855
SWIB/MDM2 domain family; The SWIB/MDM2 protein domain, short for SWI/SNF complex B/MDM2, has ...
 313-377 1.57e-13

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: 65.32  E-value: 1.57e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 322510099 313 LDPRLARLLGVH-TQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKL 377
Cdd:cd00855    1 LSPELEALLKSYeTFTLKEILQALWQYIKKKNLMDPDDPSIVVCDERLRQLFEVPSFPFSEIPKAL 66
SWIB-MDM2_like cd10567
SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins; This family includes ...
 311-383 7.29e-13

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: 63.72  E-value: 7.29e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 322510099 311 YKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIpMKLagLLQH 383
Cdd:cd10567    1 YKLSPELAAFLGVSELSRTEVVKKLWAYIKENNLQDPKNKREILCDEKLKKVFGKDEVVMFEM-NKL--LSKH 70
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 43-148 3.54e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 43.26  E-value: 3.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099   43 RGPGPSGGMGVPGAAAFRPMGPAGPAAQYQ-RPGMSPGSRMPMAGLQVGPPAGsPFGTAAPLRPGMPPTMmdpfRKRLLV 121
Cdd:TIGR01628 381 RMRQLPMGSPMGGAMGQPPYYGQGPQQQFNgQPLGWPRMSMMPTPMGPGGPLR-PNGLAPMNAVRAPSRN----AQNAAQ 455

                          90       100
                  ....*....|....*....|....*..
gi 322510099  122 PQAQPPMPAQRRGLKRRKMADKVLPQR 148
Cdd:TIGR01628 456 KPPMQPVMYPPNYQSLPLSQDLPQPQS 482
PHA03378 PHA03378
EBNA-3B; Provisional
 38-132 7.61e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 42.36  E-value: 7.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099  38 PNPALRGPGPSGGMGVPGAAAFRPMGPAGPAAQYQRPGMSPGSRMPMAGL--QVGPPAGSPFGTAAPLRPGMPPTMMDPf 115
Cdd:PHA03378 701 PTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAApgRARPPAAAPGRARPPAAAPGAPTPQPP- 779

                         90
                 ....*....|....*..
gi 322510099 116 rkrllvPQAqPPMPAQR 132
Cdd:PHA03378 780 ------PQA-PPAPQQR 789
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 309-363 3.37e-03

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 40.19  E-value: 3.37e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 322510099 309 PQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIF 363
Cdd:PRK06319 786 PLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI 840
PHA03201 PHA03201
uracil DNA glycosylase; Provisional
 38-148 3.39e-03

uracil DNA glycosylase; Provisional


Pssm-ID: 165468  Cd Length: 318  Bit Score: 39.88  E-value: 3.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099  38 PNPALRGPGPSGGMGVPGAAAFRPMGPAGPAAQyQRPGMSPGSRMPMAGLQvGPPAGSPFGTAAPLRPGM---------- 107
Cdd:PHA03201  11 PPRRPSPPRPTPPRSPDASPEETPPSPPGPGAE-PPPGRAAGPAAPRRRPR-GCPAGVTFSSSAPPRPPLglddapaatp 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 322510099 108 PPTMMDPFRKRLLVPQAQPPM-------PAQRRGL---KRRKMADKVLPQR 148
Cdd:PHA03201  89 PPLDWTEFRRRFLVGDAWRPLlepelanPLTARLMaeyERRCRTEEVLPPR 139
PHA03378 PHA03378
EBNA-3B; Provisional
 10-134 3.97e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 40.05  E-value: 3.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099  10 PLPPLSPGGGAVAAALGAPPPPAGPGMLPNPALRGPGPSGGMGVPGAAAFRPMGPAGPAAQYQRPGMSPGSRMPMAGLQV 89
Cdd:PHA03378 703 PMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQA 782

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 322510099  90 GP-PAGSPFGTAAPL-RPGMPPTMMdpfrkrllvpQAQPPMPAQRRG 134
Cdd:PHA03378 783 PPaPQQRPRGAPTPQpPPQAGPTSM----------QLMPRAAPGQQG 819
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 44-131 8.08e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 38.84  E-value: 8.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 322510099   44 GPGPSGGMGVPGAAAFRPMGPAGPAAQYQRPGMSPGSRMPMAGL---QVGPP-------AGSPFGTAAPLRPGMPPTMMD 113
Cdd:pfam09606 156 GGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMGGQmppQMGVPgmpgpadAGAQMGQQAQANGGMNPQQMG 235

                          90
                  ....*....|....*...
gi 322510099  114 PFRKRLLVPQAQPPMPAQ 131
Cdd:pfam09606 236 GAPNQVAMQQQQPQQQGQ 253
 
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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