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Conserved domains on  [gi|17559826|ref|NP_505799|]
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Minichromosome loss protein Mcl1 middle region domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 442-764 2.64e-78

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


:

Pssm-ID: 463539  Cd Length: 288  Bit Score: 258.66  E-value: 2.64e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    442 FVSNSSPMDLdATQRFLKYNRFGIIRSYVNEANKvSTIDIEFHNKSIHGDIHIDNFeINYELADISLKVVALASvesrkk 521
Cdd:pfam12341    3 FQPGSTPWHL-GDRRYLCWNLIGYVWTVKQDTDS-NSITVEFHDTSRHREYHFTDY-FGYDLASLNEEGALLAS------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    522 ekeldkanddiedletdePAKTEKkgTSLLHVIPIQAFDSQR-WSMVLPRGDGCIDVLCSNTQVVVLTKKRNIRVFTIGG 600
Cdd:pfam12341   74 ------------------PAKQSK--PSTLYYRPHESWGSNSeWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGG 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    601 IQRQIFTHFAPILTAACFEDRLAIASVCGSEFyeqkkTPQWRFEVVEYTLNPKSWyrenrhhgstgaVSRIDVPIETGEQ 680
Cdd:pfam12341  134 VQRRVFSLPGPVVTMAASEDYLFVVYHNGGPL-----DGDQNLSYSLLDVSRDEL------------QREGPLPLSPGST 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    681 LDWIAYSNQGKLAVMDSAYTVHVLS-----APGLWIPIFQGSSALR--APSDAIFPIGLTVKEFRYIYCRGS-RSPLVNG 752
Cdd:pfam12341  197 LKWLGFSEEGDPCIYDSDGVLRVLSkwrspGQARWVPVLDTKLLLRkgGKSDTYWPVGVSEDKLRCIICKGGeKYPGFLP 276

                          330
                   ....*....|..
gi 17559826    753 INAPTTVEFKVP 764
Cdd:pfam12341  277 RPLLSELPLKLP 288
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 112-282 6.56e-12

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.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 67.75  E-value: 6.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  112 DVTTVDANREN--VIGGSSDYAVKCTNMKDLDAELKTRSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLT 189
Cdd:cd00200   95 YVSSVAFSPDGriLSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLT 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  190 kvfprFETIDVSRpriqLSWSKDGQWLFVPS-KGCVKSYRRNGWEESGVYRLKDHA--SVDFsvtalSPCGKYLASSTMD 266
Cdd:cd00200  175 -----GHTGEVNS----VAFSPDGEKLLSSSsDGTIKLWDLSTGKCLGTLRGHENGvnSVAF-----SPDGYLLASGSED 240

                        170
                 ....*....|....*.
gi 17559826  267 NQIAVWNSDELDIVCC 282
Cdd:cd00200  241 GTIRVWDLRTGECVQT 256
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1043-1094 1.32e-08

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


The actual alignment was detected with superfamily member cd21993:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 62  Bit Score: 52.26  E-value: 1.32e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17559826 1043 KKSVSPYEMWLTESKSSLEFDF-DGDNADFSKFCIQTFRALSKNEKEEWKAKA 1094
Cdd:cd21993    3 KKKKSGFQLWLEENRSSIEEENpELSEAEIIKLAMQRFRALPKEEKQKWNEKA 55
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 240-330 9.87e-04

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.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 42.32  E-value: 9.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  240 LKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDELDIVCCEKfvrnapGITI-ITSIVFSPFSpKKLIVADSNRGIC 318
Cdd:cd00200    5 LKGHTGGVTCV-AFSPDGKLLATGSGDGTIKVWDLETGELLRTLK------GHTGpVRDVAASADG-TYLASGSSDKTIR 76

                         90
                 ....*....|..
gi 17559826  319 LFNVFKDDSSNE 330
Cdd:cd00200   77 LWDLETGECVRT 88
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 442-764 2.64e-78

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


Pssm-ID: 463539  Cd Length: 288  Bit Score: 258.66  E-value: 2.64e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    442 FVSNSSPMDLdATQRFLKYNRFGIIRSYVNEANKvSTIDIEFHNKSIHGDIHIDNFeINYELADISLKVVALASvesrkk 521
Cdd:pfam12341    3 FQPGSTPWHL-GDRRYLCWNLIGYVWTVKQDTDS-NSITVEFHDTSRHREYHFTDY-FGYDLASLNEEGALLAS------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    522 ekeldkanddiedletdePAKTEKkgTSLLHVIPIQAFDSQR-WSMVLPRGDGCIDVLCSNTQVVVLTKKRNIRVFTIGG 600
Cdd:pfam12341   74 ------------------PAKQSK--PSTLYYRPHESWGSNSeWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGG 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    601 IQRQIFTHFAPILTAACFEDRLAIASVCGSEFyeqkkTPQWRFEVVEYTLNPKSWyrenrhhgstgaVSRIDVPIETGEQ 680
Cdd:pfam12341  134 VQRRVFSLPGPVVTMAASEDYLFVVYHNGGPL-----DGDQNLSYSLLDVSRDEL------------QREGPLPLSPGST 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    681 LDWIAYSNQGKLAVMDSAYTVHVLS-----APGLWIPIFQGSSALR--APSDAIFPIGLTVKEFRYIYCRGS-RSPLVNG 752
Cdd:pfam12341  197 LKWLGFSEEGDPCIYDSDGVLRVLSkwrspGQARWVPVLDTKLLLRkgGKSDTYWPVGVSEDKLRCIICKGGeKYPGFLP 276

                          330
                   ....*....|..
gi 17559826    753 INAPTTVEFKVP 764
Cdd:pfam12341  277 RPLLSELPLKLP 288
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 112-282 6.56e-12

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: 67.75  E-value: 6.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  112 DVTTVDANREN--VIGGSSDYAVKCTNMKDLDAELKTRSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLT 189
Cdd:cd00200   95 YVSSVAFSPDGriLSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLT 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  190 kvfprFETIDVSRpriqLSWSKDGQWLFVPS-KGCVKSYRRNGWEESGVYRLKDHA--SVDFsvtalSPCGKYLASSTMD 266
Cdd:cd00200  175 -----GHTGEVNS----VAFSPDGEKLLSSSsDGTIKLWDLSTGKCLGTLRGHENGvnSVAF-----SPDGYLLASGSED 240

                        170
                 ....*....|....*.
gi 17559826  267 NQIAVWNSDELDIVCC 282
Cdd:cd00200  241 GTIRVWDLRTGECVQT 256
WD40 COG2319
WD40 repeat [General function prediction only];
126-322 1.61e-11

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 67.63  E-value: 1.61e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  126 GSSDYAVKCTNMKDLDAELKTRSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLTkvfprfetiDVSRPRI 205
Cdd:COG2319  222 GSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLT---------GHSGGVN 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  206 QLSWSKDGQWLFVPSKGC-VKSYRRNGWEEsgVYRLKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDELdivcceK 284
Cdd:COG2319  293 SVAFSPDGKLLASGSDDGtVRLWDLATGKL--LRTLTGHTGAVRSV-AFSPDGKTLASGSDDGTVRLWDLATG------E 363

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 17559826  285 FVRNAPGIT-IITSIVFSPfSPKKLIVADSNRGICLFNV 322
Cdd:COG2319  364 LLRTLTGHTgAVTSVAFSP-DGRTLASGSADGTVRLWDL 401
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1043-1094 1.32e-08

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 52.26  E-value: 1.32e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17559826 1043 KKSVSPYEMWLTESKSSLEFDF-DGDNADFSKFCIQTFRALSKNEKEEWKAKA 1094
Cdd:cd21993    3 KKKKSGFQLWLEENRSSIEEENpELSEAEIIKLAMQRFRALPKEEKQKWNEKA 55
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 240-330 9.87e-04

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: 42.32  E-value: 9.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  240 LKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDELDIVCCEKfvrnapGITI-ITSIVFSPFSpKKLIVADSNRGIC 318
Cdd:cd00200    5 LKGHTGGVTCV-AFSPDGKLLATGSGDGTIKVWDLETGELLRTLK------GHTGpVRDVAASADG-TYLASGSSDKTIR 76

                         90
                 ....*....|..
gi 17559826  319 LFNVFKDDSSNE 330
Cdd:cd00200   77 LWDLETGECVRT 88
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 442-764 2.64e-78

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


Pssm-ID: 463539  Cd Length: 288  Bit Score: 258.66  E-value: 2.64e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    442 FVSNSSPMDLdATQRFLKYNRFGIIRSYVNEANKvSTIDIEFHNKSIHGDIHIDNFeINYELADISLKVVALASvesrkk 521
Cdd:pfam12341    3 FQPGSTPWHL-GDRRYLCWNLIGYVWTVKQDTDS-NSITVEFHDTSRHREYHFTDY-FGYDLASLNEEGALLAS------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    522 ekeldkanddiedletdePAKTEKkgTSLLHVIPIQAFDSQR-WSMVLPRGDGCIDVLCSNTQVVVLTKKRNIRVFTIGG 600
Cdd:pfam12341   74 ------------------PAKQSK--PSTLYYRPHESWGSNSeWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGG 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    601 IQRQIFTHFAPILTAACFEDRLAIASVCGSEFyeqkkTPQWRFEVVEYTLNPKSWyrenrhhgstgaVSRIDVPIETGEQ 680
Cdd:pfam12341  134 VQRRVFSLPGPVVTMAASEDYLFVVYHNGGPL-----DGDQNLSYSLLDVSRDEL------------QREGPLPLSPGST 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826    681 LDWIAYSNQGKLAVMDSAYTVHVLS-----APGLWIPIFQGSSALR--APSDAIFPIGLTVKEFRYIYCRGS-RSPLVNG 752
Cdd:pfam12341  197 LKWLGFSEEGDPCIYDSDGVLRVLSkwrspGQARWVPVLDTKLLLRkgGKSDTYWPVGVSEDKLRCIICKGGeKYPGFLP 276

                          330
                   ....*....|..
gi 17559826    753 INAPTTVEFKVP 764
Cdd:pfam12341  277 RPLLSELPLKLP 288
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 112-282 6.56e-12

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: 67.75  E-value: 6.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  112 DVTTVDANREN--VIGGSSDYAVKCTNMKDLDAELKTRSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLT 189
Cdd:cd00200   95 YVSSVAFSPDGriLSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLT 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  190 kvfprFETIDVSRpriqLSWSKDGQWLFVPS-KGCVKSYRRNGWEESGVYRLKDHA--SVDFsvtalSPCGKYLASSTMD 266
Cdd:cd00200  175 -----GHTGEVNS----VAFSPDGEKLLSSSsDGTIKLWDLSTGKCLGTLRGHENGvnSVAF-----SPDGYLLASGSED 240

                        170
                 ....*....|....*.
gi 17559826  267 NQIAVWNSDELDIVCC 282
Cdd:cd00200  241 GTIRVWDLRTGECVQT 256
WD40 COG2319
WD40 repeat [General function prediction only];
126-322 1.61e-11

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 67.63  E-value: 1.61e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  126 GSSDYAVKCTNMKDLDAELKTRSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLTkvfprfetiDVSRPRI 205
Cdd:COG2319  222 GSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLT---------GHSGGVN 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  206 QLSWSKDGQWLFVPSKGC-VKSYRRNGWEEsgVYRLKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDELdivcceK 284
Cdd:COG2319  293 SVAFSPDGKLLASGSDDGtVRLWDLATGKL--LRTLTGHTGAVRSV-AFSPDGKTLASGSDDGTVRLWDLATG------E 363

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 17559826  285 FVRNAPGIT-IITSIVFSPfSPKKLIVADSNRGICLFNV 322
Cdd:COG2319  364 LLRTLTGHTgAVTSVAFSP-DGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
126-322 3.17e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 63.39  E-value: 3.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  126 GSSDYAVKCTNMKDLDAELKTRSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLTKvfprfETIDVSRpri 205
Cdd:COG2319   96 ASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG-----HSGAVTS--- 167

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  206 qLSWSKDGQWLFVPSK-GCVKSYRRNGWEEsgVYRLKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDEldivccEK 284
Cdd:COG2319  168 -VAFSPDGKLLASGSDdGTVRLWDLATGKL--LRTLTGHTGAVRSV-AFSPDGKLLASGSADGTVRLWDLAT------GK 237

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 17559826  285 FVRNAPGIT-IITSIVFSPfSPKKLIVADSNRGICLFNV 322
Cdd:COG2319  238 LLRTLTGHSgSVRSVAFSP-DGRLLASGSADGTVRLWDL 275
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 150-304 8.17e-09

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: 58.12  E-value: 8.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  150 EAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLT--KVFPRfetidvsrpriQLSWSKDGQWLFVPSK-GCVKS 226
Cdd:cd00200    9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKghTGPVR-----------DVAASADGTYLASGSSdKTIRL 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17559826  227 YRRNGWEEsgVYRLKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDEldivccEKFVRNAPGITI-ITSIVFSPFS 304
Cdd:cd00200   78 WDLETGEC--VRTLTGHTSYVSSV-AFSPDGRILSSSSRDKTIKVWDVET------GKCLTTLRGHTDwVNSVAFSPDG 147
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1043-1094 1.32e-08

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 52.26  E-value: 1.32e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17559826 1043 KKSVSPYEMWLTESKSSLEFDF-DGDNADFSKFCIQTFRALSKNEKEEWKAKA 1094
Cdd:cd21993    3 KKKKSGFQLWLEENRSSIEEENpELSEAEIIKLAMQRFRALPKEEKQKWNEKA 55
WD40 COG2319
WD40 repeat [General function prediction only];
123-273 7.39e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.07  E-value: 7.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  123 VIGGSSDYAVKctnMKDLDAELKTRSLEAE---VLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKHTLTkvfprFETID 199
Cdd:COG2319  261 LASGSADGTVR---LWDLATGELLRTLTGHsggVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLT-----GHTGA 332

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17559826  200 VSRpriqLSWSKDGQWLFVPSK-GCVKSYRRNGWEEsgVYRLKDHASVDFSVtALSPCGKYLASSTMDNQIAVWN 273
Cdd:COG2319  333 VRS----VAFSPDGKTLASGSDdGTVRLWDLATGEL--LRTLTGHTGAVTSV-AFSPDGRTLASGSADGTVRLWD 400
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 240-330 9.87e-04

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: 42.32  E-value: 9.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  240 LKDHASVDFSVtALSPCGKYLASSTMDNQIAVWNSDELDIVCCEKfvrnapGITI-ITSIVFSPFSpKKLIVADSNRGIC 318
Cdd:cd00200    5 LKGHTGGVTCV-AFSPDGKLLATGSGDGTIKVWDLETGELLRTLK------GHTGpVRDVAASADG-TYLASGSSDKTIR 76

                         90
                 ....*....|..
gi 17559826  319 LFNVFKDDSSNE 330
Cdd:cd00200   77 LWDLETGECVRT 88
Pgl COG2706
6-phosphogluconolactonase, cycloisomerase 2 family [Carbohydrate transport and metabolism];
158-276 1.49e-03

6-phosphogluconolactonase, cycloisomerase 2 family [Carbohydrate transport and metabolism];


Pssm-ID: 442025 [Multi-domain]  Cd Length: 352  Bit Score: 42.20  E-value: 1.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  158 LDPKNEFVAV-STVDGNVTIIDID--------SFSIKHTLTKvfPRFETIDVSRPRiQLSWSKDGQWLFVPSKG--CVKS 226
Cdd:COG2706  100 VDPDGRFLFVaNYGGGSVSVFPIDadgslgepVQVIQHEGSG--PNPERQEGPHAH-SVVFDPDGRFLYVPDLGtdRIYV 176

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 17559826  227 YRRNgwEESGvyRLKDHASVDFSVT------ALSPCGKYLASST-MDNQIAVWNSDE 276
Cdd:COG2706  177 YRLD--PATG--KLPEPPEVSLPPGsgprhlAFHPNGRFAYVINeLDSTVSVYAYDA 229
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1044-1094 2.31e-03

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 37.66  E-value: 2.31e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 17559826 1044 KSVSPYEMWLTESKSSLEFDFDG-DNADFSKFCIQTFRALSKNEKEEWKAKA 1094
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGiSVTEISKKAGEIWKELDEEDKEKWEQKA 52
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 110-218 2.73e-03

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: 41.17  E-value: 2.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  110 QMDVTTV--DANRENVIGGSSDYAVKCTNMKDlDAELKT-RSLEAEVLCVKLDPKNEFVAVSTVDGNVTIIDIDSFSIKH 186
Cdd:cd00200  177 TGEVNSVafSPDGEKLLSSSSDGTIKLWDLST-GKCLGTlRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQ 255

                         90       100       110
                 ....*....|....*....|....*....|..
gi 17559826  187 TLTKVFPRFetidvsrprIQLSWSKDGQWLFV 218
Cdd:cd00200  256 TLSGHTNSV---------TSLAWSPDGKRLAS 278
8prop_heme-binding_NirN cd20777
eight-bladed heme d1-binding beta-propeller domain in dihydro-heme d1 dehydrogenase NirN; The ...
 159-261 5.04e-03

eight-bladed heme d1-binding beta-propeller domain in dihydro-heme d1 dehydrogenase NirN; The monomeric dihydro-heme d1 dehydrogenase NirN is part of the denitrification process that enables biofilm formation of the opportunistic human pathogen Pseudomonas aeruginosa, making it more resilient to antibiotics and highly adaptable to different habitats. NirN, similar to the homodimeric cytochrome cd1 (nitrite reductase; NirS), consists of an eight-bladed heme d1-binding beta-propeller and a cytochrome c domain, but their relative orientation differs with respect to NirS. His147, His323 and Tyr461, but not His417 are essential for activity. All 8 blades of the propeller are included in this alignment.


Pssm-ID: 467721 [Multi-domain]  Cd Length: 405  Bit Score: 40.42  E-value: 5.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559826  159 DPKNEFVAVSTVDGNVTIIDIDSFsikhtltKVFPRFETidvsRPRIQLS--WSKDGQWLFVPSkgcvksyrRNGW-EES 235
Cdd:cd20777   30 DPLNLFVVVESGDHHVTVLDGDRF-------EPLARFPT----RFALHGGpkFSPDGRFVYFAS--------RDGWvTKY 90

                         90       100       110
                 ....*....|....*....|....*....|
gi 17559826  236 GVYRLKDHASV----DFSVTALSPCGKYLA 261
Cdd:cd20777   91 DLWNLKVVAEVraglNTRNLAVSSDGRYVA 120
 
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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