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Conserved domains on  [gi|197381696|ref|NP_001128055|]
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pre-mRNA-processing factor 40 homolog B [Rattus norvegicus]

Protein Classification

pre-mRNA-processing factor 40 family protein( domain architecture ID 13418230)

pre-mRNA-processing factor 40 (PRPF40) family protein similar to mammalian PRPF40 homologs A and B that may be involved in pre-mRNA splicing; contains WW and FF domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRP40 super family cl34905
Splicing factor [RNA processing and modification];
84-579 9.30e-46

Splicing factor [RNA processing and modification];


The actual alignment was detected with superfamily member COG5104:

Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 173.73  E-value: 9.30e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696  84 ASSAVPgTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSALKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTR 163
Cdd:COG5104    4 ALLGMA-SGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 164 PKDLDDLEALVKQESAgkqqtqqlqtlqpqppqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREE 242
Cdd:COG5104   83 PPERKKVEPIAEQKHD-----------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 243 gpsSSTGQHRLPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAF 322
Cdd:COG5104  128 ---MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLF 193

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 323 NAYKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERDRKEVYDDVLFFLAKKEK 401
Cdd:COG5104  194 KKYFENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEK 273

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 402 EQAKQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERAR 481
Cdd:COG5104  274 YVGKHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERK 352

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 482 LRERRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIK 561
Cdd:COG5104  353 AAAAQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYE 432

                        490
                 ....*....|....*...
gi 197381696 562 DilkdrgfCVEVNTAFED 579
Cdd:COG5104  433 R-------ETRTGQISPT 443
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 631-679 1.85e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


:

Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 42.95  E-value: 1.85e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 197381696   631 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 679
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
84-579 9.30e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 173.73  E-value: 9.30e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696  84 ASSAVPgTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSALKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTR 163
Cdd:COG5104    4 ALLGMA-SGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 164 PKDLDDLEALVKQESAgkqqtqqlqtlqpqppqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREE 242
Cdd:COG5104   83 PPERKKVEPIAEQKHD-----------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 243 gpsSSTGQHRLPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAF 322
Cdd:COG5104  128 ---MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLF 193

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 323 NAYKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERDRKEVYDDVLFFLAKKEK 401
Cdd:COG5104  194 KKYFENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEK 273

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 402 EQAKQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERAR 481
Cdd:COG5104  274 YVGKHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERK 352

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 482 LRERRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIK 561
Cdd:COG5104  353 AAAAQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYE 432

                        490
                 ....*....|....*...
gi 197381696 562 DilkdrgfCVEVNTAFED 579
Cdd:COG5104  433 R-------ETRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 276-325 4.55e-14

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 67.10  E-value: 4.55e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 197381696  276 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 325
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 137-166 2.75e-08

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 50.22  E-value: 2.75e-08
                         10        20        30
                 ....*....|....*....|....*....|
gi 197381696 137 CPWKEYKSDTGKPYYYNNQSQESRWTRPKD 166
Cdd:cd00201    2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 275-328 2.77e-08

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 50.65  E-value: 2.77e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 197381696   275 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 328
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 631-679 1.85e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 42.95  E-value: 1.85e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 197381696   631 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 679
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
84-579 9.30e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 173.73  E-value: 9.30e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696  84 ASSAVPgTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSALKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTR 163
Cdd:COG5104    4 ALLGMA-SGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 164 PKDLDDLEALVKQESAgkqqtqqlqtlqpqppqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREE 242
Cdd:COG5104   83 PPERKKVEPIAEQKHD-----------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 243 gpsSSTGQHRLPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAF 322
Cdd:COG5104  128 ---MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLF 193

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 323 NAYKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERDRKEVYDDVLFFLAKKEK 401
Cdd:COG5104  194 KKYFENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEK 273

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 402 EQAKQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERAR 481
Cdd:COG5104  274 YVGKHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERK 352

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197381696 482 LRERRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIK 561
Cdd:COG5104  353 AAAAQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYE 432

                        490
                 ....*....|....*...
gi 197381696 562 DilkdrgfCVEVNTAFED 579
Cdd:COG5104  433 R-------ETRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 276-325 4.55e-14

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 67.10  E-value: 4.55e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 197381696  276 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 325
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 98-123 2.17e-08

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 50.58  E-value: 2.17e-08
                          10        20
                  ....*....|....*....|....*.
gi 197381696   98 WSEHVAPDGRIYYYNADDKQSVWEKP 123
Cdd:pfam00397   5 WEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 137-166 2.75e-08

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 50.22  E-value: 2.75e-08
                         10        20        30
                 ....*....|....*....|....*....|
gi 197381696 137 CPWKEYKSDTGKPYYYNNQSQESRWTRPKD 166
Cdd:cd00201    2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 275-328 2.77e-08

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 50.65  E-value: 2.77e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 197381696   275 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 328
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 138-164 1.29e-07

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 48.27  E-value: 1.29e-07
                          10        20
                  ....*....|....*....|....*..
gi 197381696  138 PWKEYKSDTGKPYYYNNQSQESRWTRP 164
Cdd:pfam00397   4 GWEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 98-123 1.87e-07

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 47.91  E-value: 1.87e-07
                         10        20
                 ....*....|....*....|....*.
gi 197381696  98 WSEHVAPDGRIYYYNADDKQSVWEKP 123
Cdd:cd00201    4 WEERWDPDGRVYYYNHNTKETQWEDP 29
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 138-166 2.26e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 47.60  E-value: 2.26e-07
                           10        20
                   ....*....|....*....|....*....
gi 197381696   138 PWKEYKSDTGKPYYYNNQSQESRWTRPKD 166
Cdd:smart00456   5 GWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 98-123 4.15e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 46.83  E-value: 4.15e-07
                           10        20
                   ....*....|....*....|....*.
gi 197381696    98 WSEHVAPDGRIYYYNADDKQSVWEKP 123
Cdd:smart00456   6 WEERKDPDGRPYYYNHETKETQWEKP 31
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 490-545 1.61e-06

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 45.53  E-value: 1.61e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 197381696  490 KNREAFQTFLDELHetgqLHSMSTWMELYPAVSTDVRFANMlgQPGSTPLDLFKFY 545
Cdd:pfam01846   1 KAREAFKELLKEHK----ITPYSTWSEIKKKIENDPRYKAL--LDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 631-679 1.85e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 42.95  E-value: 1.85e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 197381696   631 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 679
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
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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