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Conserved domains on  [gi|119189407|ref|XP_001245310|]
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mRNA 3'-end-processing protein yth1 [Coccidioides immitis RS]

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 ...
 19-181 7.68e-27

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: 104.95  E-value: 7.68e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119189407  19 DPNFTNFAFSPFLRKTFGFGL-ASDVPVCKAYreghcplgpmcPDRHPTPSRISTATSPAIAPSSTHGslVCKHYLKGLC 97
Cdd:COG5084   49 SLSSPTFKNKANLMQNTNDNFvPGNTVACISR-----------NFNSIRGSRLSTPNNHVNPVLSSSV--VCKFFLRGLC 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119189407  98 KKGIKCEYLHEYNLRR--MPECQSFARSGYCANGDDCLYQHVSEEAKLPPCEHYDK---GFCPLGPLCAKKHVRRKI--- 169
Cdd:COG5084  116 KSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSGPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsyg 195

                        170
                 ....*....|....*
gi 119189407 170 ---CPFYLAGFCPEG 181
Cdd:COG5084  196 sspCGNYTPPFSPPG 210
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 19-181 7.68e-27

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: 104.95  E-value: 7.68e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119189407  19 DPNFTNFAFSPFLRKTFGFGL-ASDVPVCKAYreghcplgpmcPDRHPTPSRISTATSPAIAPSSTHGslVCKHYLKGLC 97
Cdd:COG5084   49 SLSSPTFKNKANLMQNTNDNFvPGNTVACISR-----------NFNSIRGSRLSTPNNHVNPVLSSSV--VCKFFLRGLC 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119189407  98 KKGIKCEYLHEYNLRR--MPECQSFARSGYCANGDDCLYQHVSEEAKLPPCEHYDK---GFCPLGPLCAKKHVRRKI--- 169
Cdd:COG5084  116 KSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSGPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsyg 195

                        170
                 ....*....|....*
gi 119189407 170 ---CPFYLAGFCPEG 181
Cdd:COG5084  196 sspCGNYTPPFSPPG 210
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 19-181 7.68e-27

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: 104.95  E-value: 7.68e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119189407  19 DPNFTNFAFSPFLRKTFGFGL-ASDVPVCKAYreghcplgpmcPDRHPTPSRISTATSPAIAPSSTHGslVCKHYLKGLC 97
Cdd:COG5084   49 SLSSPTFKNKANLMQNTNDNFvPGNTVACISR-----------NFNSIRGSRLSTPNNHVNPVLSSSV--VCKFFLRGLC 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119189407  98 KKGIKCEYLHEYNLRR--MPECQSFARSGYCANGDDCLYQHVSEEAKLPPCEHYDK---GFCPLGPLCAKKHVRRKI--- 169
Cdd:COG5084  116 KSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSGPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsyg 195

                        170
                 ....*....|....*
gi 119189407 170 ---CPFYLAGFCPEG 181
Cdd:COG5084  196 sspCGNYTPPFSPPG 210
 
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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