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Conserved domains on  [gi|17137188|ref|NP_477156|]
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clipper [Drosophila melanogaster]

Protein Classification

zinc finger CCCH domain-containing protein( domain architecture ID 708395)

zinc finger CCCH domain-containing protein similar to cleavage and polyadenylation specificity factor (CPSF) subunit 4, which is part of the complex that plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YTH1 super family cl25862
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 12-175 2.39e-31

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


The actual alignment was detected with superfamily member COG5084:

Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 118.05  E-value: 2.39e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137188  12 QFKAERDLIEQVGAIPLPfygmdKSIAAVCNFITRNGqeCDKGSACPFRHI--RGDRTIVCKHWLRGLCKKGDQCEFLHE 89
Cdd:COG5084  54 TFKNKANLMQNTNDNFVP-----GNTVACISRNFNSI--RGSRLSTPNNHVnpVLSSSVVCKFFLRGLCKSGFSCEFLHE 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137188  90 YDMTK--MPECYFYSRFNACHN-KECPFLHIDPQSKVKDCPWYKR---GFCRHGPHCRHQHLRRVL------CMDYLAGF 157
Cdd:COG5084 127 YDLRSsqGPPCRSFSLKGSCSSgPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsygsspCGNYTPPF 206

                       170       180       190
                ....*....|....*....|....*....|..
gi 17137188 158 CPEGP--------------SCKHMHPHFELPP 175
Cdd:COG5084 207 SPPGTpsesvsswgygkgtSCSLSHPSLNIDI 238
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 12-175 2.39e-31

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 118.05  E-value: 2.39e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137188  12 QFKAERDLIEQVGAIPLPfygmdKSIAAVCNFITRNGqeCDKGSACPFRHI--RGDRTIVCKHWLRGLCKKGDQCEFLHE 89
Cdd:COG5084  54 TFKNKANLMQNTNDNFVP-----GNTVACISRNFNSI--RGSRLSTPNNHVnpVLSSSVVCKFFLRGLCKSGFSCEFLHE 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137188  90 YDMTK--MPECYFYSRFNACHN-KECPFLHIDPQSKVKDCPWYKR---GFCRHGPHCRHQHLRRVL------CMDYLAGF 157
Cdd:COG5084 127 YDLRSsqGPPCRSFSLKGSCSSgPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsygsspCGNYTPPF 206

                       170       180       190
                ....*....|....*....|....*....|..
gi 17137188 158 CPEGP--------------SCKHMHPHFELPP 175
Cdd:COG5084 207 SPPGTpsesvsswgygkgtSCSLSHPSLNIDI 238
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 51-121 7.76e-04

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 38.21  E-value: 7.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17137188    51 CDKGSACPFRHIR---GDRTiVCKHWLRGLCKKgDQCEFLHEYDMTKMPE--CYFYSRFNACHNKECPFLHIDPQS 121
Cdd:pfam15663  16 CTKGDSCPFRHCEaalGNET-VCTLWQEGRCFR-PVCRFRHMEIDKNRKEipCYWENQPGGCQKPHCAFHHTKPRY 89
ZnF_C3H1 smart00356
zinc finger;
66-90 1.44e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 35.30  E-value: 1.44e-03
                           10        20
                   ....*....|....*....|....*
gi 17137188     66 RTIVCKHWLRGLCKKGDQCEFLHEY 90
Cdd:smart00356   3 KTELCKFFKRGYCPRGDRCKFAHPL 27
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 12-175 2.39e-31

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 118.05  E-value: 2.39e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137188  12 QFKAERDLIEQVGAIPLPfygmdKSIAAVCNFITRNGqeCDKGSACPFRHI--RGDRTIVCKHWLRGLCKKGDQCEFLHE 89
Cdd:COG5084  54 TFKNKANLMQNTNDNFVP-----GNTVACISRNFNSI--RGSRLSTPNNHVnpVLSSSVVCKFFLRGLCKSGFSCEFLHE 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137188  90 YDMTK--MPECYFYSRFNACHN-KECPFLHIDPQSKVKDCPWYKR---GFCRHGPHCRHQHLRRVL------CMDYLAGF 157
Cdd:COG5084 127 YDLRSsqGPPCRSFSLKGSCSSgPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsygsspCGNYTPPF 206

                       170       180       190
                ....*....|....*....|....*....|..
gi 17137188 158 CPEGP--------------SCKHMHPHFELPP 175
Cdd:COG5084 207 SPPGTpsesvsswgygkgtSCSLSHPSLNIDI 238
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 51-121 7.76e-04

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 38.21  E-value: 7.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17137188    51 CDKGSACPFRHIR---GDRTiVCKHWLRGLCKKgDQCEFLHEYDMTKMPE--CYFYSRFNACHNKECPFLHIDPQS 121
Cdd:pfam15663  16 CTKGDSCPFRHCEaalGNET-VCTLWQEGRCFR-PVCRFRHMEIDKNRKEipCYWENQPGGCQKPHCAFHHTKPRY 89
ZnF_C3H1 smart00356
zinc finger;
66-90 1.44e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 35.30  E-value: 1.44e-03
                           10        20
                   ....*....|....*....|....*
gi 17137188     66 RTIVCKHWLRGLCKKGDQCEFLHEY 90
Cdd:smart00356   3 KTELCKFFKRGYCPRGDRCKFAHPL 27
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 70-88 5.72e-03

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 33.54  E-value: 5.72e-03
                          10
                  ....*....|....*....
gi 17137188    70 CKHWLRGLCKKGDQCEFLH 88
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
 
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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