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Conserved domains on  [gi|79481163|ref|NP_193898|]
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C-terminal domain phosphatase-like 1 [Arabidopsis thaliana]

Protein Classification

double-stranded RNA binding motif domain-containing protein( domain architecture ID 11576372)

double-stranded RNA binding motif (DSRM) domain-containing protein is mainly involved in posttranscriptional gene regulation, for example by preventing the expression of proteins or by mediating RNAs localization; similar to Human rotavirus non-structural protein 1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 212-377 2.80e-23

human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid dehalogenase-like superfamily; Human CTDP1/FCP1 is a protein phosphatase which dephosphorylates the phosphorylated C terminus (CTD) of RNA polymerase II. CTD phosphorylation is a key mechanism of regulation of gene expression in eukaryotes. CTDP1/FCP1 may have other roles in in transcription regulation independent of its phosphatase activity. This family also includes human translocase of inner mitochondrial membrane 50 (TIMM50), CTD small phosphatase like (CTDSPL) and CTD small phosphatase like 2 (CTDSPL2), Saccharomyces cerevisiae (nuclear envelope morphology protein 1) Nem1p, and Xenopus Dullard. Yeast Nem1p in complex with Spo7p dephosphorylates the nuclear membrane-associated phosphatidic acid phosphatase, Smp2p, which may be part of a signaling cascade playing a role in nuclear membrane biogenesis. Xenopus Dullard is a potential regulator of neural tube development. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


:

Pssm-ID: 319823  Cd Length: 134  Bit Score: 96.13  E-value: 2.80e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 212 LKQYIESDQVVENGEVIKVQSEIVPAlsdnhqplvrplirlqekniiltRINPMIRDTSVLVRMRPSWEELRSYLtakgR 291
Cdd:cd07521   2 LTLVLDLDETLVHSTWKPVLSEDFKI-----------------------PVLPDGREHGYYVKKRPGVDEFLERL----S 54

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 292 KRFEVYVCTMAERDYALEMWRLLDPEGNLIntNDLLARIVCV--KSGFKKSLFNVFLDgtchPKMALVIDDRlkVWDEKD 369
Cdd:cd07521  55 KLYEIVIFTAGTRAYADPVADKLDPNGLFI--DRRLFRDSCVyvDGNYVKDLSKLFRD----LSKVVIIDDS--PGSYWL 126


                ....*...
gi 79481163 370 QPRvHVVP 377
Cdd:cd07521 127 QPE-NAIP 133
DSRM smart00358
Double-stranded RNA binding motif;
857-922 1.07e-11

Double-stranded RNA binding motif;


:

Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 61.12  E-value: 1.07e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79481163    857 ITALRELCASEGLEMAFQSQRQlpSDMVHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERALSS 922
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKE--EGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRS 65
DSRM smart00358
Double-stranded RNA binding motif;
730-790 3.22e-09

Double-stranded RNA binding motif;


:

Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 53.81  E-value: 3.22e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79481163    730 VLHGIAIKCGAKVEYKPSLVSSTDL--RFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:smart00358   4 LLQELAQKRKLPPEYELVKEEGPDHapRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
 
Name Accession Description Interval E-value
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 212-377 2.80e-23

human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid dehalogenase-like superfamily; Human CTDP1/FCP1 is a protein phosphatase which dephosphorylates the phosphorylated C terminus (CTD) of RNA polymerase II. CTD phosphorylation is a key mechanism of regulation of gene expression in eukaryotes. CTDP1/FCP1 may have other roles in in transcription regulation independent of its phosphatase activity. This family also includes human translocase of inner mitochondrial membrane 50 (TIMM50), CTD small phosphatase like (CTDSPL) and CTD small phosphatase like 2 (CTDSPL2), Saccharomyces cerevisiae (nuclear envelope morphology protein 1) Nem1p, and Xenopus Dullard. Yeast Nem1p in complex with Spo7p dephosphorylates the nuclear membrane-associated phosphatidic acid phosphatase, Smp2p, which may be part of a signaling cascade playing a role in nuclear membrane biogenesis. Xenopus Dullard is a potential regulator of neural tube development. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319823  Cd Length: 134  Bit Score: 96.13  E-value: 2.80e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 212 LKQYIESDQVVENGEVIKVQSEIVPAlsdnhqplvrplirlqekniiltRINPMIRDTSVLVRMRPSWEELRSYLtakgR 291
Cdd:cd07521   2 LTLVLDLDETLVHSTWKPVLSEDFKI-----------------------PVLPDGREHGYYVKKRPGVDEFLERL----S 54

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 292 KRFEVYVCTMAERDYALEMWRLLDPEGNLIntNDLLARIVCV--KSGFKKSLFNVFLDgtchPKMALVIDDRlkVWDEKD 369
Cdd:cd07521  55 KLYEIVIFTAGTRAYADPVADKLDPNGLFI--DRRLFRDSCVyvDGNYVKDLSKLFRD----LSKVVIIDDS--PGSYWL 126


                ....*...
gi 79481163 370 QPRvHVVP 377
Cdd:cd07521 127 QPE-NAIP 133
DSRM smart00358
Double-stranded RNA binding motif;
857-922 1.07e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 61.12  E-value: 1.07e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79481163    857 ITALRELCASEGLEMAFQSQRQlpSDMVHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERALSS 922
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKE--EGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRS 65
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 272-366 1.65e-11

FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the pfam03031.


Pssm-ID: 131304  Cd Length: 156  Bit Score: 63.45  E-value: 1.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163   272 LVRMRPSweeLRSYLTaKGRKRFEVYVCTMAERDYALEMWRLLDPEGNLINtNDLLARIVCVKSGFkKSLFNVFLDGTCh 351
Cdd:TIGR02250  56 LTKLRPF---LHEFLK-EASKLYEMHVYTMGTRAYAQAIAKLIDPDGKYFG-DRIISRDESGSPHT-KSLLRLFPADES- 128

                          90
                  ....*....|....*
gi 79481163   352 pkMALVIDDRLKVWD 366
Cdd:TIGR02250 129 --MVVIIDDREDVWP 141
DSRM smart00358
Double-stranded RNA binding motif;
730-790 3.22e-09

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 53.81  E-value: 3.22e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79481163    730 VLHGIAIKCGAKVEYKPSLVSSTDL--RFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:smart00358   4 LLQELAQKRKLPPEYELVKEEGPDHapRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
CPDc smart00577
catalytic domain of ctd-like phosphatases;
271-372 7.61e-07

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 49.53  E-value: 7.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163    271 VLVRMRPSWEELRSYLTakgrKRFEVYVCTMAERDYALEMWRLLDPEGNLINtndllARIVCVKSGFKKSLFNVFLDGT- 349
Cdd:smart00577  42 VYVKKRPGVDEFLKRAS----ELFELVVFTAGLRMYADPVLDLLDPKKYFGY-----RRLFRDECVFVKGKYVKDLSLLn 112

                           90       100
                   ....*....|....*....|...
gi 79481163    350 CHPKMALVIDDRLKVWdeKDQPR 372
Cdd:smart00577 113 RDLSKVIIIDDSPDSW--PFHPE 133
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 856-920 1.32e-06

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 46.49  E-value: 1.32e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79481163 856 SITALRELCASEGLEMAFqsqRQLPSDMVHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERAL 920
Cdd:cd19875   3 PVSALNEYCQKRGLSLEF---VDVSVGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLAL 64
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 730-790 8.78e-06

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 44.14  E-value: 8.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79481163   730 VLHGIAIKCGAKVEYK--PSLVSSTDLRFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:pfam00035   4 LLQEYAQKNGKPPPYEyvSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 267-365 1.06e-05

NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.


Pssm-ID: 397254  Cd Length: 160  Bit Score: 46.46  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163   267 RDTSVLVRMRPSWEELRSYLtakgRKRFEVYVCTMAERDYALEMWRLLDPEGNLIntNDLLARIVCV--KSGFKKSLFNV 344
Cdd:pfam03031  31 ETHGGYVKKRPGLDEFLKEL----SKYYEIVIFTASSKEYADPVLDILDPNGKLF--SHRLYRESCKfeDGVYVKDLSLL 104

                          90       100
                  ....*....|....*....|.
gi 79481163   345 FLDgtchPKMALVIDDRLKVW 365
Cdd:pfam03031 105 GRD----LSRVVIVDNSPDSF 121
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 740-790 2.40e-05

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 42.86  E-value: 2.40e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 79481163 740 AKVEYKpsLVSST----DLRFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:cd10845  17 PLPEYE--LVEEEgpdhNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 856-920 8.48e-05

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 41.45  E-value: 8.48e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79481163   856 SITALRELCASEGLEMAFQ-SQRQLPSdmvHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERAL 920
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEyVSEEGPP---HSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKAL 63
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
755-790 8.77e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 45.09  E-value: 8.77e-05
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 79481163 755 RFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:COG0571 190 TFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKL 225
 
Name Accession Description Interval E-value
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 212-377 2.80e-23

human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid dehalogenase-like superfamily; Human CTDP1/FCP1 is a protein phosphatase which dephosphorylates the phosphorylated C terminus (CTD) of RNA polymerase II. CTD phosphorylation is a key mechanism of regulation of gene expression in eukaryotes. CTDP1/FCP1 may have other roles in in transcription regulation independent of its phosphatase activity. This family also includes human translocase of inner mitochondrial membrane 50 (TIMM50), CTD small phosphatase like (CTDSPL) and CTD small phosphatase like 2 (CTDSPL2), Saccharomyces cerevisiae (nuclear envelope morphology protein 1) Nem1p, and Xenopus Dullard. Yeast Nem1p in complex with Spo7p dephosphorylates the nuclear membrane-associated phosphatidic acid phosphatase, Smp2p, which may be part of a signaling cascade playing a role in nuclear membrane biogenesis. Xenopus Dullard is a potential regulator of neural tube development. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319823  Cd Length: 134  Bit Score: 96.13  E-value: 2.80e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 212 LKQYIESDQVVENGEVIKVQSEIVPAlsdnhqplvrplirlqekniiltRINPMIRDTSVLVRMRPSWEELRSYLtakgR 291
Cdd:cd07521   2 LTLVLDLDETLVHSTWKPVLSEDFKI-----------------------PVLPDGREHGYYVKKRPGVDEFLERL----S 54

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 292 KRFEVYVCTMAERDYALEMWRLLDPEGNLIntNDLLARIVCV--KSGFKKSLFNVFLDgtchPKMALVIDDRlkVWDEKD 369
Cdd:cd07521  55 KLYEIVIFTAGTRAYADPVADKLDPNGLFI--DRRLFRDSCVyvDGNYVKDLSKLFRD----LSKVVIIDDS--PGSYWL 126


                ....*...
gi 79481163 370 QPRvHVVP 377
Cdd:cd07521 127 QPE-NAIP 133
DSRM smart00358
Double-stranded RNA binding motif;
857-922 1.07e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 61.12  E-value: 1.07e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79481163    857 ITALRELCASEGLEMAFQSQRQlpSDMVHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERALSS 922
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKE--EGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRS 65
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 272-366 1.65e-11

FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the pfam03031.


Pssm-ID: 131304  Cd Length: 156  Bit Score: 63.45  E-value: 1.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163   272 LVRMRPSweeLRSYLTaKGRKRFEVYVCTMAERDYALEMWRLLDPEGNLINtNDLLARIVCVKSGFkKSLFNVFLDGTCh 351
Cdd:TIGR02250  56 LTKLRPF---LHEFLK-EASKLYEMHVYTMGTRAYAQAIAKLIDPDGKYFG-DRIISRDESGSPHT-KSLLRLFPADES- 128

                          90
                  ....*....|....*
gi 79481163   352 pkMALVIDDRLKVWD 366
Cdd:TIGR02250 129 --MVVIIDDREDVWP 141
DSRM smart00358
Double-stranded RNA binding motif;
730-790 3.22e-09

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 53.81  E-value: 3.22e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79481163    730 VLHGIAIKCGAKVEYKPSLVSSTDL--RFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:smart00358   4 LLQELAQKRKLPPEYELVKEEGPDHapRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
CPDc smart00577
catalytic domain of ctd-like phosphatases;
271-372 7.61e-07

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 49.53  E-value: 7.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163    271 VLVRMRPSWEELRSYLTakgrKRFEVYVCTMAERDYALEMWRLLDPEGNLINtndllARIVCVKSGFKKSLFNVFLDGT- 349
Cdd:smart00577  42 VYVKKRPGVDEFLKRAS----ELFELVVFTAGLRMYADPVLDLLDPKKYFGY-----RRLFRDECVFVKGKYVKDLSLLn 112

                           90       100
                   ....*....|....*....|...
gi 79481163    350 CHPKMALVIDDRLKVWdeKDQPR 372
Cdd:smart00577 113 RDLSKVIIIDDSPDSW--PFHPE 133
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 856-920 1.32e-06

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 46.49  E-value: 1.32e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79481163 856 SITALRELCASEGLEMAFqsqRQLPSDMVHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERAL 920
Cdd:cd19875   3 PVSALNEYCQKRGLSLEF---VDVSVGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLAL 64
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 730-790 8.78e-06

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 44.14  E-value: 8.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79481163   730 VLHGIAIKCGAKVEYK--PSLVSSTDLRFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:pfam00035   4 LLQEYAQKNGKPPPYEyvSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 267-365 1.06e-05

NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.


Pssm-ID: 397254  Cd Length: 160  Bit Score: 46.46  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163   267 RDTSVLVRMRPSWEELRSYLtakgRKRFEVYVCTMAERDYALEMWRLLDPEGNLIntNDLLARIVCV--KSGFKKSLFNV 344
Cdd:pfam03031  31 ETHGGYVKKRPGLDEFLKEL----SKYYEIVIFTASSKEYADPVLDILDPNGKLF--SHRLYRESCKfeDGVYVKDLSLL 104

                          90       100
                  ....*....|....*....|.
gi 79481163   345 FLDgtchPKMALVIDDRLKVW 365
Cdd:pfam03031 105 GRD----LSRVVIVDNSPDSF 121
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 740-790 2.40e-05

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 42.86  E-value: 2.40e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 79481163 740 AKVEYKpsLVSST----DLRFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:cd10845  17 PLPEYE--LVEEEgpdhNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 856-920 8.48e-05

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 41.45  E-value: 8.48e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79481163   856 SITALRELCASEGLEMAFQ-SQRQLPSdmvHRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERAL 920
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEyVSEEGPP---HSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKAL 63
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
755-790 8.77e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 45.09  E-value: 8.77e-05
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 79481163 755 RFSVEAWLSNQKIGEGIGKSRREALHKAAEASIQNL 790
Cdd:COG0571 190 TFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKL 225
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 857-922 1.99e-03

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 37.33  E-value: 1.99e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79481163 857 ITALRELcaSEGLEMAFQSQrqlpSDMVHRDELHAQVEIDGRVVgEGVGSTWDEARMQAAERALSS 922
Cdd:cd19865   4 LMQLNEL--RPGLQYKLTSQ----TGPVHAPVFTMSVEVNGQTF-EGTGRSKKKAKLEAAEKALRS 62
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 858-920 2.16e-03

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 37.47  E-value: 2.16e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79481163 858 TALRELCASEGLemafqsqrQLPSDMV-------HRDELHAQVEIDGRVVGEGVGSTWDEARMQAAERAL 920
Cdd:cd10845   5 TALQEYLQKRGL--------PLPEYELveeegpdHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAAL 66
 
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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