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Conserved domains on  [gi|29789008|ref|NP_036404|]
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pre-mRNA-processing factor 40 homolog B isoform 2 [Homo sapiens]

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];
83-568 4.68e-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: 174.50  E-value: 4.68e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008  83 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSKESRWTRPKDLD 162
Cdd:COG5104   8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 163 DLEVLVKQEAAgkqqqqlpqtlqpqppqpqpdpppvppgptpvptglLEPEPGGSEDCDVLEATQPLEQGFL--QQLEEG 240
Cdd:COG5104  88 KVEPIAEQKHD------------------------------------ERSMIGGNGNDMAITDHETSEPKYLlgRLMSQY 131

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 241 PSSSGQHQPQQEeeeskpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNA 320
Cdd:COG5104 132 GITSTKDAVYRL----------------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKK 195

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 321 YKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGELEVW-AVVPERDRKEVYDDVLFFLAKKEKEQ 399
Cdd:COG5104 196 YFENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYV 275

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 400 AKQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDHQLQNMDKEDALICFEEHIRALEREEEEERERARLR 479
Cdd:COG5104 276 GKHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAA 354

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 480 ERRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDI 559
Cdd:COG5104 355 AAQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYERE 434


                ....*....
gi 29789008 560 LKVNTAFED 568
Cdd:COG5104 435 TRTGQISPT 443
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 620-668 2.29e-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: 42.56  E-value: 2.29e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 29789008    620 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 668
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
83-568 4.68e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.50  E-value: 4.68e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008  83 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSKESRWTRPKDLD 162
Cdd:COG5104   8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 163 DLEVLVKQEAAgkqqqqlpqtlqpqppqpqpdpppvppgptpvptglLEPEPGGSEDCDVLEATQPLEQGFL--QQLEEG 240
Cdd:COG5104  88 KVEPIAEQKHD------------------------------------ERSMIGGNGNDMAITDHETSEPKYLlgRLMSQY 131

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 241 PSSSGQHQPQQEeeeskpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNA 320
Cdd:COG5104 132 GITSTKDAVYRL----------------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKK 195

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 321 YKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGELEVW-AVVPERDRKEVYDDVLFFLAKKEKEQ 399
Cdd:COG5104 196 YFENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYV 275

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 400 AKQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDHQLQNMDKEDALICFEEHIRALEREEEEERERARLR 479
Cdd:COG5104 276 GKHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAA 354

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 480 ERRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDI 559
Cdd:COG5104 355 AAQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYERE 434


                ....*....
gi 29789008 560 LKVNTAFED 568
Cdd:COG5104 435 TRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 272-321 5.01e-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: 66.71  E-value: 5.01e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 29789008   272 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 321
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 131-160 1.05e-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: 51.37  E-value: 1.05e-08
                        10        20        30
                ....*....|....*....|....*....|
gi 29789008 131 CPWKEYKSDTGKPYYYNNQSKESRWTRPKD 160
Cdd:cd00201   2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 271-324 3.72e-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: 50.26  E-value: 3.72e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 29789008    271 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 324
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 620-668 2.29e-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: 42.56  E-value: 2.29e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 29789008    620 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 668
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
83-568 4.68e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.50  E-value: 4.68e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008  83 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSKESRWTRPKDLD 162
Cdd:COG5104   8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 163 DLEVLVKQEAAgkqqqqlpqtlqpqppqpqpdpppvppgptpvptglLEPEPGGSEDCDVLEATQPLEQGFL--QQLEEG 240
Cdd:COG5104  88 KVEPIAEQKHD------------------------------------ERSMIGGNGNDMAITDHETSEPKYLlgRLMSQY 131

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 241 PSSSGQHQPQQEeeeskpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNA 320
Cdd:COG5104 132 GITSTKDAVYRL----------------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKK 195

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 321 YKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGELEVW-AVVPERDRKEVYDDVLFFLAKKEKEQ 399
Cdd:COG5104 196 YFENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYV 275

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 400 AKQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDHQLQNMDKEDALICFEEHIRALEREEEEERERARLR 479
Cdd:COG5104 276 GKHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAA 354

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789008 480 ERRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDI 559
Cdd:COG5104 355 AAQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYERE 434


                ....*....
gi 29789008 560 LKVNTAFED 568
Cdd:COG5104 435 TRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 272-321 5.01e-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: 66.71  E-value: 5.01e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 29789008   272 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 321
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 131-160 1.05e-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: 51.37  E-value: 1.05e-08
                        10        20        30
                ....*....|....*....|....*....|
gi 29789008 131 CPWKEYKSDTGKPYYYNNQSKESRWTRPKD 160
Cdd:cd00201   2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 92-117 1.95e-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: 1.95e-08
                          10        20
                  ....*....|....*....|....*.
gi 29789008    92 WSEHVAPDGRIYYYNADDKQSVWEKP 117
Cdd:pfam00397   5 WEERWDPDGRVYYYNHETGETQWEKP 30
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 271-324 3.72e-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: 50.26  E-value: 3.72e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 29789008    271 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 324
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 132-160 5.97e-08

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: 49.14  E-value: 5.97e-08
                           10        20
                   ....*....|....*....|....*....
gi 29789008    132 PWKEYKSDTGKPYYYNNQSKESRWTRPKD 160
Cdd:smart00456   5 GWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 132-158 7.45e-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: 49.04  E-value: 7.45e-08
                          10        20
                  ....*....|....*....|....*..
gi 29789008   132 PWKEYKSDTGKPYYYNNQSKESRWTRP 158
Cdd:pfam00397   4 GWEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 92-117 1.70e-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: 1.70e-07
                        10        20
                ....*....|....*....|....*.
gi 29789008  92 WSEHVAPDGRIYYYNADDKQSVWEKP 117
Cdd:cd00201   4 WEERWDPDGRVYYYNHNTKETQWEDP 29
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 92-117 3.84e-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: 3.84e-07
                           10        20
                   ....*....|....*....|....*.
gi 29789008     92 WSEHVAPDGRIYYYNADDKQSVWEKP 117
Cdd:smart00456   6 WEERKDPDGRPYYYNHETKETQWEKP 31
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 486-541 1.71e-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: 1.71e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 29789008   486 KNREAFQTFLDELHetgqLHSMSTWMELYPAVSTDVRFANMlgQPGSTPLDLFKFY 541
Cdd:pfam01846   1 KAREAFKELLKEHK----ITPYSTWSEIKKKIENDPRYKAL--LDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 620-668 2.29e-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: 42.56  E-value: 2.29e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 29789008    620 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 668
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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