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Conserved domains on  [gi|6325203|ref|NP_015271|]
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Lee1p [Saccharomyces cerevisiae S288C]

Protein Classification

CPSF4/YTH1 family protein( domain architecture ID 11473782)

CPSF4/YTH1 family protein similar to Homo sapiens cleavage and polyadenylation specificity factor subunit 4, as well as Saccharomyces cerevisiae mRNA 3'-end-processing protein YTH1 and zinc finger protein LEE1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 1-301 2.16e-61

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: 196.25  E-value: 2.16e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203    1 MDAFENMSVSNHPGGNARRNSQSANEMLASQIQDFQNIPRSFNDSNANVNLSKNCTVGNQLPFSSRQQKIIMEHLLITKN 80
Cdd:COG5084  15 LGSGCTYNHSNYTSLNDGLQSVSSKYMGAKQISPSLSSPTFKNKANLMQNTNDNFVPGNTVACISRNFNSIRGSRLSTPN 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203   81 NSQQQKDYSHVPCKFFKMGNCQAGSSCPFSHSPDIISSaNNLPCKYF-AKGNCKFGNKCVNAHVLPNGFKMNSKEPIDit 159
Cdd:COG5084  95 NHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLRSS-QGPPCRSFsLKGSCSSGPSCGYSHIDPDSFAGNCDQYSG-- 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203  160 ppsqnnylsharsasfSTYTSPPLSAQTEFSHSASNANYFSsqylmyspqkSPEALYTEFFspPSSSSSYINYSYNNSNI 239
Cdd:COG5084 172 ----------------ATYGFCPLGASCKFSHTLKRVSYGS----------SPCGNYTPPF--SPPGTPSESVSSWGYGK 223

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6325203  240 NAYSPVSSSSSNIWQEQGQTTLSNPSVNQNLRYRTGPAIQEESDNEIEDLLIHNFNSRYCHE 301
Cdd:COG5084 224 GTSCSLSHPSLNIDIQQPQTAPSRKDSGGTNPIGASSEIGSEADGNMQNSISGSGDSEEIEE 285
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 1-301 2.16e-61

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: 196.25  E-value: 2.16e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203    1 MDAFENMSVSNHPGGNARRNSQSANEMLASQIQDFQNIPRSFNDSNANVNLSKNCTVGNQLPFSSRQQKIIMEHLLITKN 80
Cdd:COG5084  15 LGSGCTYNHSNYTSLNDGLQSVSSKYMGAKQISPSLSSPTFKNKANLMQNTNDNFVPGNTVACISRNFNSIRGSRLSTPN 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203   81 NSQQQKDYSHVPCKFFKMGNCQAGSSCPFSHSPDIISSaNNLPCKYF-AKGNCKFGNKCVNAHVLPNGFKMNSKEPIDit 159
Cdd:COG5084  95 NHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLRSS-QGPPCRSFsLKGSCSSGPSCGYSHIDPDSFAGNCDQYSG-- 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203  160 ppsqnnylsharsasfSTYTSPPLSAQTEFSHSASNANYFSsqylmyspqkSPEALYTEFFspPSSSSSYINYSYNNSNI 239
Cdd:COG5084 172 ----------------ATYGFCPLGASCKFSHTLKRVSYGS----------SPCGNYTPPF--SPPGTPSESVSSWGYGK 223

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6325203  240 NAYSPVSSSSSNIWQEQGQTTLSNPSVNQNLRYRTGPAIQEESDNEIEDLLIHNFNSRYCHE 301
Cdd:COG5084 224 GTSCSLSHPSLNIDIQQPQTAPSRKDSGGTNPIGASSEIGSEADGNMQNSISGSGDSEEIEE 285
ZnF_C3H1 smart00356
zinc finger;
87-113 3.75e-06

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.62  E-value: 3.75e-06
                           10        20
                   ....*....|....*....|....*..
gi 6325203      87 DYSHVPCKFFKMGNCQAGSSCPFSHSP 113
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAHPL 27
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
88-113 1.28e-04

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 38.33  E-value: 1.28e-04
                          10        20
                  ....*....|....*....|....*..
gi 6325203     88 YSHVPCKFF-KMGNCQAGSSCPFSHSP 113
Cdd:pfam00642   1 YKTELCRFFlRTGYCKYGDRCKFAHGQ 27
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 1-301 2.16e-61

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: 196.25  E-value: 2.16e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203    1 MDAFENMSVSNHPGGNARRNSQSANEMLASQIQDFQNIPRSFNDSNANVNLSKNCTVGNQLPFSSRQQKIIMEHLLITKN 80
Cdd:COG5084  15 LGSGCTYNHSNYTSLNDGLQSVSSKYMGAKQISPSLSSPTFKNKANLMQNTNDNFVPGNTVACISRNFNSIRGSRLSTPN 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203   81 NSQQQKDYSHVPCKFFKMGNCQAGSSCPFSHSPDIISSaNNLPCKYF-AKGNCKFGNKCVNAHVLPNGFKMNSKEPIDit 159
Cdd:COG5084  95 NHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLRSS-QGPPCRSFsLKGSCSSGPSCGYSHIDPDSFAGNCDQYSG-- 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325203  160 ppsqnnylsharsasfSTYTSPPLSAQTEFSHSASNANYFSsqylmyspqkSPEALYTEFFspPSSSSSYINYSYNNSNI 239
Cdd:COG5084 172 ----------------ATYGFCPLGASCKFSHTLKRVSYGS----------SPCGNYTPPF--SPPGTPSESVSSWGYGK 223

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6325203  240 NAYSPVSSSSSNIWQEQGQTTLSNPSVNQNLRYRTGPAIQEESDNEIEDLLIHNFNSRYCHE 301
Cdd:COG5084 224 GTSCSLSHPSLNIDIQQPQTAPSRKDSGGTNPIGASSEIGSEADGNMQNSISGSGDSEEIEE 285
ZnF_C3H1 smart00356
zinc finger;
87-113 3.75e-06

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.62  E-value: 3.75e-06
                           10        20
                   ....*....|....*....|....*..
gi 6325203      87 DYSHVPCKFFKMGNCQAGSSCPFSHSP 113
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAHPL 27
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
88-113 1.28e-04

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 38.33  E-value: 1.28e-04
                          10        20
                  ....*....|....*....|....*..
gi 6325203     88 YSHVPCKFF-KMGNCQAGSSCPFSHSP 113
Cdd:pfam00642   1 YKTELCRFFlRTGYCKYGDRCKFAHGQ 27
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 124-142 1.60e-04

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: 38.17  E-value: 1.60e-04
                          10
                  ....*....|....*....
gi 6325203    124 CKYFAKGNCKFGNKCVNAH 142
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
123-144 1.94e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.99  E-value: 1.94e-04
                           10        20
                   ....*....|....*....|..
gi 6325203     123 PCKYFAKGNCKFGNKCVNAHVL 144
Cdd:smart00356   6 LCKFFKRGYCPRGDRCKFAHPL 27
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 93-111 2.15e-04

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: 37.78  E-value: 2.15e-04
                          10
                  ....*....|....*....
gi 6325203     93 CKFFKMGNCQAGSSCPFSH 111
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 123-142 2.18e-03

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 34.87  E-value: 2.18e-03
                          10        20
                  ....*....|....*....|
gi 6325203    123 PCKYFAKGNCKFGNKCVNAH 142
Cdd:pfam18044   2 LCRYFQKGGCRYGDNCRFSH 21
zf-CCCH_2 pfam14608
RNA-binding, Nab2-type zinc finger; This is an unusual zinc-finger family, and is represented ...
 92-111 8.38e-03

RNA-binding, Nab2-type zinc finger; This is an unusual zinc-finger family, and is represented by fingers 5-7 of Nab2. Nab2 ZnF5-7 are zinc-fingers of the type C-x8-C-x5-C-x3-H. Nab2 ZnFs function in the generation of export-competent mRNPs. Mab2 is a conserved polyadenosine-RNA-binding Zn finger protein required for both mRNA export and polyadenylation regulation and becomes attached to the mRNP after splicing and during or immediately after polyadenylation. The three ZnFs, 5-7, have almost identical folds and, most unusually, associate with one another to form a single coherent structural unit. ZnF5-7 bind to eight consecutive adenines, and chemical shift perturbations identify residues on each finger that interact with RNA.


Pssm-ID: 464217  Cd Length: 19  Bit Score: 33.25  E-value: 8.38e-03
                          10        20
                  ....*....|....*....|
gi 6325203     92 PCKFFkmGNCQAGSSCPFSH 111
Cdd:pfam14608   1 PCRFG--GNCTFGPKCPFSH 18
 
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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