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Conserved domains on  [gi|564332810|ref|XP_006231076|]
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pre-mRNA-processing factor 19 isoform X1 [Rattus norvegicus]

Protein Classification

RING-Ubox_PRP19 and Prp19 domain-containing protein( domain architecture ID 11616145)

protein containing domains RING-Ubox_PRP19, Prp19, and WD40

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
252-523 2.09e-60

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 204.37  E-value: 2.09e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 252 DTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTGL 331
Cdd:COG2319  131 DGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSV 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 332 SLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSgcSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHS 411
Cdd:COG2319  211 AFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSG--SVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHS 288

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 412 GPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQlDNNFEVKSLIFDQSGTYLALGGTD--VQIYICKQWTEILH 489
Cdd:COG2319  289 GGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLT-GHTGAVRSVAFSPDGKTLASGSDDgtVRLWDLATGELLRT 367

                        250       260       270
                 ....*....|....*....|....*....|....
gi 564332810 490 FTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  368 LTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
Prp19 pfam08606
Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region ...
 69-152 1.05e-33

Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly.


:

Pssm-ID: 400774  Cd Length: 65  Bit Score: 121.85  E-value: 1.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810   69 TSIPAILKALQDEWgwpnspalpqssqwptlsqDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARLTKEVTAARE 148
Cdd:pfam08606   1 TSIPSLLSTLQNEW-------------------DALMLETFTLRKQLDQTRQELSHALYQHDAACRVIARLIKERDEARE 61


                  ....
gi 564332810  149 ALAT 152
Cdd:pfam08606  62 ALAN 65
RING-Ubox_PRP19 cd16656
U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and ...
 3-56 2.40e-33

U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and similar proteins; Prp19, also known as nuclear matrix protein 200 (NMP200), senescence evasion factor (SNEV), or DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signaling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerization and is essential for its auto-ubiquitination activity in vitro or when overexpressed, a coiled-coil Prp19 homology region that mediates its tetramerization and interaction with CDC5L and SPF27, and a C-terminal seven-bladed WD40 beta-propeller type of leucine-rich architectural repeats that form an asymmetrical barrel-shaped structure important for substrate recognition and recruitment.


:

Pssm-ID: 438318  Cd Length: 54  Bit Score: 120.36  E-value: 2.40e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564332810   3 LICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIK 56
Cdd:cd16656    1 MVCAISGEVPEEPVVSPKSGHVFEKRLIEKYIAENGTDPVTGEPLTEEDLIEIK 54
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
252-523 2.09e-60

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 204.37  E-value: 2.09e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 252 DTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTGL 331
Cdd:COG2319  131 DGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSV 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 332 SLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSgcSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHS 411
Cdd:COG2319  211 AFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSG--SVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHS 288

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 412 GPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQlDNNFEVKSLIFDQSGTYLALGGTD--VQIYICKQWTEILH 489
Cdd:COG2319  289 GGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLT-GHTGAVRSVAFSPDGKTLASGSDDgtVRLWDLATGELLRT 367

                        250       260       270
                 ....*....|....*....|....*....|....
gi 564332810 490 FTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  368 LTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 242-522 1.54e-59

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 198.33  E-value: 1.54e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 242 GILALDLCPsDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVV 321
Cdd:cd00200   11 GVTCVAFSP-DGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 322 RAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETsgCSLTCAQFHPDGLIFGTGTMDSQIKIWDLKER 401
Cdd:cd00200   90 TGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHT--DWVNSVAFSPDGTFVASSSQDGTIKLWDLRTG 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 402 TNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQLDNNFeVKSLIFDQSGTYLALGGTD--VQIY 479
Cdd:cd00200  168 KCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENG-VNSVAFSPDGYLLASGSEDgtIRVW 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 564332810 480 ICKQWTEILHFTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYS 522
Cdd:cd00200  247 DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Prp19 pfam08606
Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region ...
 69-152 1.05e-33

Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly.


Pssm-ID: 400774  Cd Length: 65  Bit Score: 121.85  E-value: 1.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810   69 TSIPAILKALQDEWgwpnspalpqssqwptlsqDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARLTKEVTAARE 148
Cdd:pfam08606   1 TSIPSLLSTLQNEW-------------------DALMLETFTLRKQLDQTRQELSHALYQHDAACRVIARLIKERDEARE 61


                  ....
gi 564332810  149 ALAT 152
Cdd:pfam08606  62 ALAN 65
RING-Ubox_PRP19 cd16656
U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and ...
 3-56 2.40e-33

U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and similar proteins; Prp19, also known as nuclear matrix protein 200 (NMP200), senescence evasion factor (SNEV), or DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signaling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerization and is essential for its auto-ubiquitination activity in vitro or when overexpressed, a coiled-coil Prp19 homology region that mediates its tetramerization and interaction with CDC5L and SPF27, and a C-terminal seven-bladed WD40 beta-propeller type of leucine-rich architectural repeats that form an asymmetrical barrel-shaped structure important for substrate recognition and recruitment.


Pssm-ID: 438318  Cd Length: 54  Bit Score: 120.36  E-value: 2.40e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564332810   3 LICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIK 56
Cdd:cd16656    1 MVCAISGEVPEEPVVSPKSGHVFEKRLIEKYIAENGTDPVTGEPLTEEDLIEIK 54
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
 2-68 1.12e-20

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 85.36  E-value: 1.12e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564332810     2 SLICSISNEVPEHPCVSPVSnHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIkvaHPIRPKPPSA 68
Cdd:smart00504   1 EFLCPISLEVMKDPVILPSG-QTYERSAIEKWLLSHGTDPVTGQPLTHEDLIPN---LALKSAIQEW 63
PTZ00421 PTZ00421
coronin; Provisional
 250-400 5.85e-12

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 68.00  E-value: 5.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 250 PSDTNKILTGGADKNVVVFDKSTEQI-------LATLKGHTKKVTSVVFHPSQELVF-SASPDATIRIWSVPNTSCVQVV 321
Cdd:PTZ00421  85 PFDPQKLFTASEDGTIMGWGIPEEGLtqnisdpIVHLQGHTKKVGIVSFHPSAMNVLaSAGADMVVNVWDVERGKAVEVI 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 322 RAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHPDGLI--FGTGTMDS-QIKIWDL 398
Cdd:PTZ00421 165 KCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSSVEAHASAKSQRCLWAKRKDLIitLGCSKSQQrQIMLWDT 244


                 ..
gi 564332810 399 KE 400
Cdd:PTZ00421 245 RK 246
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 404-439 1.42e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 53.47  E-value: 1.42e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 564332810   404 VANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 439
Cdd:smart00320   5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
401-439 7.04e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 51.58  E-value: 7.04e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 564332810  401 RTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 439
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
U-box pfam04564
U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast ...
 3-53 1.10e-06

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.


Pssm-ID: 398320 [Multi-domain]  Cd Length: 73  Bit Score: 46.15  E-value: 1.10e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 564332810    3 LICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENG-TDPINNQPLSEEQLI 53
Cdd:pfam04564   5 FLDPITFELMTDPVILP-SGITYDRSTIERHLLSVDpTDPFTREPLTHDQLI 55
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
252-523 2.09e-60

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 204.37  E-value: 2.09e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 252 DTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTGL 331
Cdd:COG2319  131 DGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSV 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 332 SLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSgcSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHS 411
Cdd:COG2319  211 AFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSG--SVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHS 288

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 412 GPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQlDNNFEVKSLIFDQSGTYLALGGTD--VQIYICKQWTEILH 489
Cdd:COG2319  289 GGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLT-GHTGAVRSVAFSPDGKTLASGSDDgtVRLWDLATGELLRT 367

                        250       260       270
                 ....*....|....*....|....*....|....
gi 564332810 490 FTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  368 LTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 242-522 1.54e-59

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 198.33  E-value: 1.54e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 242 GILALDLCPsDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVV 321
Cdd:cd00200   11 GVTCVAFSP-DGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 322 RAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETsgCSLTCAQFHPDGLIFGTGTMDSQIKIWDLKER 401
Cdd:cd00200   90 TGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHT--DWVNSVAFSPDGTFVASSSQDGTIKLWDLRTG 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 402 TNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQLDNNFeVKSLIFDQSGTYLALGGTD--VQIY 479
Cdd:cd00200  168 KCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENG-VNSVAFSPDGYLLASGSEDgtIRVW 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 564332810 480 ICKQWTEILHFTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYS 522
Cdd:cd00200  247 DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 236-480 3.39e-58

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 194.86  E-value: 3.39e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 236 HSASIPGILALdlcpSDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNT 315
Cdd:cd00200   50 HTGPVRDVAAS----ADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETG 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 316 SCVQVVRAHESAVTGLSLHATGDYLLSSSDDQY---WafsDIQTGRVLTKVTDETSgcSLTCAQFHPDGLIFGTGTMDSQ 392
Cdd:cd00200  126 KCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTiklW---DLRTGKCVATLTGHTG--EVNSVAFSPDGEKLLSSSSDGT 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 393 IKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQLDNNFeVKSLIFDQSGTYLALG 472
Cdd:cd00200  201 IKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNS-VTSLAWSPDGKRLASG 279


                 ....*...
gi 564332810 473 GTDVQIYI 480
Cdd:cd00200  280 SADGTIRI 287
WD40 COG2319
WD40 repeat [General function prediction only];
251-523 7.27e-56

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 192.43  E-value: 7.27e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 251 SDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTG 330
Cdd:COG2319   88 PDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTS 167

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 331 LSLHATGDYLLSSSDD---QYWafsDIQTGRVLTKVTDETSgcSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANF 407
Cdd:COG2319  168 VAFSPDGKLLASGSDDgtvRLW---DLATGKLLRTLTGHTG--AVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTL 242

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 408 PGHSGPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQlDNNFEVKSLIFDQSGTYLALGGTD--VQIYICKQWT 485
Cdd:COG2319  243 TGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLT-GHSGGVNSVAFSPDGKLLASGSDDgtVRLWDLATGK 321

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 564332810 486 EILHFTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  322 LLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDL 359
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 276-523 1.17e-49

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 172.52  E-value: 1.17e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 276 LATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTGLSLHATGDYLLSSSDDQY---Wafs 352
Cdd:cd00200    2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTirlW--- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 353 DIQTGRVLTKVTDETSGCSltCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADD 432
Cdd:cd00200   79 DLETGECVRTLTGHTSYVS--SVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 433 SSVKLWDLRKLKNFKTLqLDNNFEVKSLIFDQSGTYLALGGTDVQIYI--CKQWTEILHFTEHSGLTTGVAFGHHAKFIA 510
Cdd:cd00200  157 GTIKLWDLRTGKCVATL-TGHTGEVNSVAFSPDGEKLLSSSSDGTIKLwdLSTGKCLGTLRGHENGVNSVAFSPDGYLLA 235

                        250
                 ....*....|...
gi 564332810 511 STGMDRSLKFYSL 523
Cdd:cd00200  236 SGSEDGTIRVWDL 248
WD40 COG2319
WD40 repeat [General function prediction only];
233-523 1.24e-47

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 170.09  E-value: 1.24e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 233 VGLHSASIPGILALDLCPSDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSV 312
Cdd:COG2319   28 LLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDL 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 313 PNTSCVQVVRAHESAVTGLSLHATGDYLLSSSDDQY---WafsDIQTGRVLTKVTDETSGcsLTCAQFHPDGLIFGTGTM 389
Cdd:COG2319  108 ATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTvrlW---DLATGKLLRTLTGHSGA--VTSVAFSPDGKLLASGSD 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 390 DSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQLDNNfEVKSLIFDQSGTYL 469
Cdd:COG2319  183 DGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSG-SVRSVAFSPDGRLL 261

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564332810 470 ALGGTDVQIYICK-QWTEILH-FTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  262 ASGSADGTVRLWDlATGELLRtLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL 317
WD40 COG2319
WD40 repeat [General function prediction only];
242-441 3.77e-46

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 166.24  E-value: 3.77e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 242 GILALDLCPsDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVV 321
Cdd:COG2319  206 AVRSVAFSP-DGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTL 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 322 RAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGcsLTCAQFHPDGLIFGTGTMDSQIKIWDLKER 401
Cdd:COG2319  285 TGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGA--VRSVAFSPDGKTLASGSDDGTVRLWDLATG 362

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 564332810 402 TNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWDLR 441
Cdd:COG2319  363 ELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLA 402
WD40 COG2319
WD40 repeat [General function prediction only];
256-523 1.03e-39

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 148.52  E-value: 1.03e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 256 ILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTGLSLHA 335
Cdd:COG2319    9 LAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 336 TGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSgcSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPIT 415
Cdd:COG2319   89 DGRLLASASADGTVRLWDLATGLLLRTLTGHTG--AVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 416 SIAFSENGYYLATAADDSSVKLWDLRKLKNFKTLQLDNNfEVKSLIFDQSGTYLALGGTD--VQIYICKQWTEILHFTEH 493
Cdd:COG2319  167 SVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTG-AVRSVAFSPDGKLLASGSADgtVRLWDLATGKLLRTLTGH 245

                        250       260       270
                 ....*....|....*....|....*....|
gi 564332810 494 SGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  246 SGSVRSVAFSPDGRLLASGSADGTVRLWDL 275
Prp19 pfam08606
Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region ...
 69-152 1.05e-33

Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly.


Pssm-ID: 400774  Cd Length: 65  Bit Score: 121.85  E-value: 1.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810   69 TSIPAILKALQDEWgwpnspalpqssqwptlsqDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARLTKEVTAARE 148
Cdd:pfam08606   1 TSIPSLLSTLQNEW-------------------DALMLETFTLRKQLDQTRQELSHALYQHDAACRVIARLIKERDEARE 61


                  ....
gi 564332810  149 ALAT 152
Cdd:pfam08606  62 ALAN 65
RING-Ubox_PRP19 cd16656
U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and ...
 3-56 2.40e-33

U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and similar proteins; Prp19, also known as nuclear matrix protein 200 (NMP200), senescence evasion factor (SNEV), or DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signaling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerization and is essential for its auto-ubiquitination activity in vitro or when overexpressed, a coiled-coil Prp19 homology region that mediates its tetramerization and interaction with CDC5L and SPF27, and a C-terminal seven-bladed WD40 beta-propeller type of leucine-rich architectural repeats that form an asymmetrical barrel-shaped structure important for substrate recognition and recruitment.


Pssm-ID: 438318  Cd Length: 54  Bit Score: 120.36  E-value: 2.40e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564332810   3 LICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIK 56
Cdd:cd16656    1 MVCAISGEVPEEPVVSPKSGHVFEKRLIEKYIAENGTDPVTGEPLTEEDLIEIK 54
WD40 COG2319
WD40 repeat [General function prediction only];
290-523 5.05e-31

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 124.25  E-value: 5.05e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 290 VFHPSQELVFSASPDATIRIWSVPNTSCVQVVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSg 369
Cdd:COG2319    1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 370 cSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWDLRKLKNFKTL 449
Cdd:COG2319   80 -AVLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTL 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564332810 450 QLDNNfEVKSLIFDQSGTYLALGGTD--VQIYICKQWTEILHFTEHSGLTTGVAFGHHAKFIASTGMDRSLKFYSL 523
Cdd:COG2319  159 TGHSG-AVTSVAFSPDGKLLASGSDDgtVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL 233
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
 2-68 1.12e-20

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 85.36  E-value: 1.12e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564332810     2 SLICSISNEVPEHPCVSPVSnHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIkvaHPIRPKPPSA 68
Cdd:smart00504   1 EFLCPISLEVMKDPVILPSG-QTYERSAIEKWLLSHGTDPVTGQPLTHEDLIPN---LALKSAIQEW 63
WD40 COG2319
WD40 repeat [General function prediction only];
236-314 5.27e-13

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 70.71  E-value: 5.27e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564332810 236 HSASIPGILALDLCPsDTNKILTGGADKNVVVFDKSTEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWSVPN 314
Cdd:COG2319  326 LTGHTGAVRSVAFSP-DGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
PTZ00421 PTZ00421
coronin; Provisional
 250-400 5.85e-12

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 68.00  E-value: 5.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 250 PSDTNKILTGGADKNVVVFDKSTEQI-------LATLKGHTKKVTSVVFHPSQELVF-SASPDATIRIWSVPNTSCVQVV 321
Cdd:PTZ00421  85 PFDPQKLFTASEDGTIMGWGIPEEGLtqnisdpIVHLQGHTKKVGIVSFHPSAMNVLaSAGADMVVNVWDVERGKAVEVI 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 322 RAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHPDGLI--FGTGTMDS-QIKIWDL 398
Cdd:PTZ00421 165 KCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSSVEAHASAKSQRCLWAKRKDLIitLGCSKSQQrQIMLWDT 244


                 ..
gi 564332810 399 KE 400
Cdd:PTZ00421 245 RK 246
RING-Ubox cd16453
U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that ...
 3-47 4.96e-11

U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that also includes the HECT family and the RING finger family. The E3 enzyme is ubiquitin-protein ligase that cooperates with a ubiquitin-activating enzyme (E1) and a ubiquitin-conjugating enzyme (E2), and plays a central role in determining the specificity of the ubiquitination system. It removes the ubiquitin molecule from the E2 enzyme and attaches it to the target substrate, forming a covalent bond between ubiquitin and the target. U-box proteins are characterized by the presence of a U-box domain of approximately 70 amino acids. The U-box is a modified form of the RING finger domain that lacks metal chelating cysteines and histidines. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms.


Pssm-ID: 438117 [Multi-domain]  Cd Length: 44  Bit Score: 57.56  E-value: 4.96e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564332810   3 LICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENGTDPINNQPL 47
Cdd:cd16453    1 FLCPISGELMKDPVITP-SGITYDRSAIERWLLSDNTDPFTREPL 44
RING-Ubox_WDSUB1-like cd16655
U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing ...
 2-53 1.44e-10

U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing protein 1 (WDSUB1) and similar proteins; WDSUB1 is an uncharacterized protein containing seven WD40 repeats and a SAM domain in addition to the U-box. Its biological role remains unclear. This subfamily also includes many uncharacterized kinase domain-containing U-box (AtPUB) proteins and several MIF4G motif-containing AtPUB proteins from Arabidopsis.


Pssm-ID: 438317 [Multi-domain]  Cd Length: 55  Bit Score: 56.74  E-value: 1.44e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564332810   2 SLICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENGTDPINNQPLSEEQLI 53
Cdd:cd16655    3 EFLCPITQELMRDPVVAA-DGHTYERSAIEEWLETHNTSPMTRLPLSSTDLV 53
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 404-439 1.42e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 53.47  E-value: 1.42e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 564332810   404 VANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 439
Cdd:smart00320   5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
401-439 7.04e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 51.58  E-value: 7.04e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 564332810  401 RTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 439
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
RING-Ubox_CHIP cd16654
U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein ...
 3-53 1.29e-08

U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins; CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase.


Pssm-ID: 438316 [Multi-domain]  Cd Length: 71  Bit Score: 51.42  E-value: 1.29e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564332810   3 LICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENG-TDPINNQPLSEEQLI 53
Cdd:cd16654    5 LCCKISFELMRDPVITP-SGITYERKDIEEHLQRVGhFDPITREPLTQDQLI 55
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 272-311 1.52e-08

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 50.39  E-value: 1.52e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 564332810   272 TEQILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWS 311
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
274-311 2.11e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.04  E-value: 2.11e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 564332810  274 QILATLKGHTKKVTSVVFHPSQELVFSASPDATIRIWS 311
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 235-440 2.18e-08

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 57.02  E-value: 2.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 235 LHSASIPGILALDlcpSDTNKILTGGADKNVVVFD-----KSTEQI---LATLKGHTKkVTSVVFHPS-QELVFSASPDA 305
Cdd:PLN00181 480 LNSSNLVCAIGFD---RDGEFFATAGVNKKIKIFEcesiiKDGRDIhypVVELASRSK-LSGICWNSYiKSQVASSNFEG 555

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 306 TIRIWSVPNTSCVQVVRAHESAVTGLSLHATGDYLLSS-SDDQYWAFSDIQTGRVLTKVTDETSGCsltCAQFHPD-GLI 383
Cdd:PLN00181 556 VVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASgSDDGSVKLWSINQGVSIGTIKTKANIC---CVQFPSEsGRS 632

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564332810 384 FGTGTMDSQIKIWDLKE-RTNVANFPGHSGPITSIAFSENGyYLATAADDSSVKLWDL 440
Cdd:PLN00181 633 LAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVRFVDSS-TLVSSSTDNTLKLWDL 689
RING-Ubox_PUB cd16664
U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and ...
 3-52 1.92e-07

U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins; The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain.


Pssm-ID: 438326 [Multi-domain]  Cd Length: 53  Bit Score: 47.56  E-value: 1.92e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564332810   3 LICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENG-TDPINNQPLSEEQL 52
Cdd:cd16664    4 FICPISLELMKDPVILA-TGQTYERAAIEKWLDSGNnTCPITGQPLTHTDL 53
PTZ00420 PTZ00420
coronin; Provisional
 279-453 1.06e-06

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 51.49  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 279 LKGHTKKVTSVVFHPS-QELVFSASPDATIRIWSVP-NTSCVQ-------VVRAHESAVTGLSLHATGDYLLSSSD-DQY 348
Cdd:PTZ00420  70 LKGHTSSILDLQFNPCfSEILASGSEDLTIRVWEIPhNDESVKeikdpqcILKGHKKKISIIDWNPMNYYIMCSSGfDSF 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 349 WAFSDIQTGRVLTKVTDETSGCSLtcaQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGP--------------- 413
Cdd:PTZ00420 150 VNIWDIENEKRAFQINMPKKLSSL---KWNIKGNLLSGTCVGKHMHIIDPRKQEIASSFHIHDGGkntkniwidglggdd 226

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 564332810 414 --ITSIAFSENGYylataaddSSVKLWDLRKLKN-FKTLQLDN 453
Cdd:PTZ00420 227 nyILSTGFSKNNM--------REMKLWDLKNTTSaLVTMSIDN 261
U-box pfam04564
U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast ...
 3-53 1.10e-06

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.


Pssm-ID: 398320 [Multi-domain]  Cd Length: 73  Bit Score: 46.15  E-value: 1.10e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 564332810    3 LICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENG-TDPINNQPLSEEQLI 53
Cdd:pfam04564   5 FLDPITFELMTDPVILP-SGITYDRSTIERHLLSVDpTDPFTREPLTHDQLI 55
RING-Ubox_LubX-like_rpt1 cd23149
first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX ...
 3-53 5.35e-06

first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins; LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the first one.


Pssm-ID: 438511 [Multi-domain]  Cd Length: 55  Bit Score: 43.63  E-value: 5.35e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564332810   3 LICSISNEVPEHPCVSPvSNHVYERRLIEKYIAENGTDPINNQPLSEEQLI 53
Cdd:cd23149    1 FTCPITSGFMEDPVITP-SGFSYERSAIERWLETKPEDPQTREPLTAKDLQ 50
CDC55 COG5170
Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms];
315-451 1.47e-05

Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms];


Pssm-ID: 227498 [Multi-domain]  Cd Length: 460  Bit Score: 47.33  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 315 TSCVQVVRAHESAVTGLSLHATGDYLLSSSD-----------DQYWAFSDIQTgrvlTKVTDETSgcSLTCAQFHP-DGL 382
Cdd:COG5170  162 KPCRVYANAHPYHINSISFNSDKETLLSADDlrinlwnleiiDGSFNIVDIKP----HNMEELTE--VITSAEFHPeMCN 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810 383 IFGTGTMDSQIKIWDLKERT----------------NVANFPGHSGPITSIAFSENGYYLAtAADDSSVKLWDLRKLKN- 445
Cdd:COG5170  236 VFMYSSSKGEIKLNDLRQSAlcdnskklfeltidgvDVDFFEEIVSSISDFKFSDNGRYIL-SRDYLTVKIWDVNMAKNp 314


                 ....*.
gi 564332810 446 FKTLQL 451
Cdd:COG5170  315 IKTIPM 320
SPL-RING_NSE2 cd16651
SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as ...
 3-62 2.70e-04

SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. Moreover, NSE2 together with its partner proteins SMC6 and SMC5 form a tight subcomplex of the structural maintenance of chromosomes SMC5-6 complex, which includes another two subcomplexes, NSE1-NSE3-NSE4 and NSE5-NSE6. SMC6 and NSE3 are sumoylated in an NSE2-dependent manner, but SMC5 and NSE1 are not. NSE2-dependent E3 SUMO ligase activity is required for efficient DNA repair, but not for SMC5-6 complex stability. NSE2 contains a RING variant known as a Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription)-like RING (SPL-RING) finger that is likely shared by the SP-RING type SUMO E3 ligases, such as PIAS family proteins. The SPL-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It harbors only one Zn binding site and is required for the sumoylating activity.


Pssm-ID: 438313 [Multi-domain]  Cd Length: 67  Bit Score: 39.17  E-value: 2.70e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564332810   3 LICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTD---PIN--NQPLSEEQLI-DIKVAHPIR 62
Cdd:cd16651    1 LKCPITQQLMVDPVRNKKCGHTYEKAAILQYLQSRKKKakcPVAgcRNTVSKSDLVpDPELKRRIE 66
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 356-397 5.24e-04

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 37.68  E-value: 5.24e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 564332810   356 TGRVLTKVTDETSGCslTCAQFHPDGLIFGTGTMDSQIKIWD 397
Cdd:smart00320   1 SGELLKTLKGHTGPV--TSVAFSPDGKYLASGSDDGTIKLWD 40
RING-Ubox_PPIL2 cd16663
U-box domain, a modified RING finger, found in peptidyl-prolyl cis-trans isomerase-like 2 ...
 5-56 6.09e-04

U-box domain, a modified RING finger, found in peptidyl-prolyl cis-trans isomerase-like 2 (PPIL2) and similar proteins; PPIL2 (EC 5.2.1.8), also known as PPIase, CYC4, cyclophilin-60 (Cyp60), cyclophilin-like protein Cyp-60, or Rotamase PPIL2, is a nuclear-specific cyclophilin which interacts with the proteinase inhibitor eglin c and regulates gene expression. PPIL2 belongs to the cyclophilin family of peptidylprolyl isomerases and catalyzes cis-trans isomerization of proline-peptide bonds, which is often a rate-limiting step in protein folding. It positively regulates beta-site amyloid precursor protein cleaving enzyme (BACE1) expression and beta-secretase activity. Moreover, PPIL2 plays an important role in the translocation of CD147 to the cell surface, and thus may present a novel target for therapeutic interventions in diseases where CD147 functions as a pathogenic factor in cancer, human immunodeficiency virus infection, or rheumatoid arthritis. PPIL2 contains an N-terminal RING-like U-box domain and a C-terminal cyclophilin (Cyp)-like chaperone domain.


Pssm-ID: 438325  Cd Length: 73  Bit Score: 38.31  E-value: 6.09e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564332810   5 CSISNEVPEHPCVSPvSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIK 56
Cdd:cd16663    5 CALSLQPFENPVCTP-DGIVFDLLNIVPYLKKYGKNPVTGEPLEAKDLIKLN 55
WD40 pfam00400
WD domain, G-beta repeat;
316-346 1.51e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 36.17  E-value: 1.51e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 564332810  316 SCVQVVRAHESAVTGLSLHATGDYLLSSSDD 346
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDD 32
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 316-346 1.64e-03

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 36.14  E-value: 1.64e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 564332810   316 SCVQVVRAHESAVTGLSLHATGDYLLSSSDD 346
Cdd:smart00320   3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDD 33
RING-Ubox_UBE4A cd16657
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and ...
 15-54 2.41e-03

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and similar proteins; This subfamily includes yeast ubiquitin fusion degradation protein 2 (UFD2p) and its mammalian homolog, UBE4A. Yeast UFD2p, also known as ubiquitin conjugation factor E4 or UB fusion protein 2, is a polyubiquitin chain conjugation factor (E4) in the ubiquitin fusion degradation (UFD) pathway which catalyzes elongation of the ubiquitin chain through Lys48 linkage. It binds to substrates conjugated with one to three ubiquitin molecules and catalyzes the addition of further ubiquitin moieties in the presence of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3), yielding multiubiquitylated substrates that are targets for the 26S proteasome. UFD2p is implicated in cell survival under stress conditions and is essential for homoeostasis of unsaturated fatty acids. It interacts with UBL-UBA proteins Rad23 and Dsk2, which are involved in the endoplasmic reticulum-associated degradation, ubiquitin fusion degradation, and OLE-1 gene induction pathways. UBE4A is a U-box-type ubiquitin-protein ligase that is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. It may have a specific role in different biochemical processes other than ubiquitination, including growth or differentiation. Members of this family contain an N-terminal ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438319  Cd Length: 70  Bit Score: 36.48  E-value: 2.41e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 564332810  15 PCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLID 54
Cdd:cd16657   15 PVILPSSKVTVDRSTIKRHLLSDQTDPFNRSPLTLDMVIP 54
RING-Ubox_UBE4B cd16658
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and ...
 19-53 4.20e-03

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and similar proteins; UBE4B, also known as UFD2a, is a U-box-type ubiquitin-protein ligase that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor, which catalyzes formation of Lys27- and Lys33-linked polyubiquitin chains rather than the Lys48-linked chain. It is a mammalian homolog of yeast UFD2 ubiquitination factor and it participates in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. It is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. UBE4B has contradictory functions upon tumorigenesis as an oncogene or tumor suppressor in different types of cancers. It is essential for Hdm2 (also known as Mdm2)-mediated p53 degradation. It mediates p53 polyubiquitination and degradation, as well as inhibits p53-dependent transactivation and apoptosis, and thus plays an important role in regulating phosphorylated p53 following DNA damage. UBE4B is also associated with other pathways independent of the p53 family, such as polyglutamine aggregation and Wallerian degeneration, both of which are critical in neurodegenerative diseases. Moreover, UBE4B acts as a regulator of epidermal growth factor receptor (EGFR) degradation. It is recruited to endosomes in response to EGFR activation by binding to Hrs, a key component of endosomal sorting complex required for transport (ESCRT) 0, and then regulates endosomal sorting, affecting cellular levels of the EGFR and its downstream signaling. UBE4B contains a ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438320  Cd Length: 74  Bit Score: 36.10  E-value: 4.20e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564332810  19 PV---SNHVYERRLIEKYIAENGTDPINNQPLSEEQLI 53
Cdd:cd16658   20 PVilpSGTIMDRSIILRHLLNSQTDPFNRQPLTEDMLE 57
WD40 pfam00400
WD domain, G-beta repeat;
371-397 4.55e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 35.01  E-value: 4.55e-03
                          10        20
                  ....*....|....*....|....*..
gi 564332810  371 SLTCAQFHPDGLIFGTGTMDSQIKIWD 397
Cdd:pfam00400  13 SVTSLAFSPDGKLLASGSDDGTVKVWD 39
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 341-422 4.71e-03

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 36.49  E-value: 4.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564332810  341 LSSSDDQYWAF-SDIQtgRVLTKVTDETsGCSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAF 419
Cdd:pfam12894  12 LATEDGELLLHrLNWQ--RVWTLSPDKE-DLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCLGW 88


                  ...
gi 564332810  420 SEN 422
Cdd:pfam12894  89 GEN 91
zf-Nse pfam11789
Zinc-finger of the MIZ type in Nse subunit; Nse1 and Nse2 are novel non-SMC subunits of the ...
 2-39 7.32e-03

Zinc-finger of the MIZ type in Nse subunit; Nse1 and Nse2 are novel non-SMC subunits of the fission yeast Smc5-6 DNA repair complex. This family is the zinc-finger domain similar to the MIZ type of zinc-finger.


Pssm-ID: 403098 [Multi-domain]  Cd Length: 57  Bit Score: 34.96  E-value: 7.32e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 564332810    2 SLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGT 39
Cdd:pfam11789  11 SLTCPLTLQPFVEPVTSKKCNHVFEKDAILEMLKRNPT 48
 
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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