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Conserved domains on  [gi|79503115|ref|NP_195747|]
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carboxyl-terminal domain (ctd) phosphatase-like 2 [Arabidopsis thaliana]

Protein Classification

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 ...
 244-355 2.14e-19

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: 84.95  E-value: 2.14e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115 244 RIKPEIRDTSVLVKLRPAWEELRSYLtaktRKRFEVYVCTMAERDYALEMWRLLDPEAHLISLKELRDRIVCVKPDAKKS 323
Cdd:cd07521  28 PVLPDGREHGYYVKKRPGVDEFLERL----SKLYEIVIFTAGTRAYADPVADKLDPNGLFIDRRLFRDSCVYVDGNYVKD 103

                        90       100       110
                ....*....|....*....|....*....|..
gi 79503115 324 LLSVFNggicHPKMAMVIDDRMKVWedKDQPR 355
Cdd:cd07521 104 LSKLFR----DLSKVVIIDDSPGSY--WLQPE 129
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 657-720 6.52e-13

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: 64.05  E-value: 6.52e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79503115 657 FVSALQEIGRRCG-SKVEFRTVISTNKE--LQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd10845   3 YKTALQEYLQKRGlPLPEYELVEEEGPDhnKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 461-654 9.73e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 9.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   461 AAAADHSTLPATSNAEQKPETPKPQIAVIPNNASTATAAALLPSHKPSLLG---AP----RRDGFTFSDGGRPL------ 527
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGgsvAPggdvRRRPPSRSPAAKPAaparpp 2882

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   528 ---MMRPGVDIRNQNFNQPPILAKIPMQPPSSSMHSPGGWLVDDEN---RPSFPGRP-SGLYPSQFPHGTPGSAPVGPFA 600
Cdd:PHA03247 2883 vrrLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQpqpPPPPPPRPqPPLAPTTDPAGAGEPSGAVPQP 2962

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79503115   601 HPSHLRSEEVAMDDDLKRQN-PSRQTTEGGISQNHlvsngreHHTDGGKSNGGQS 654
Cdd:PHA03247 2963 WLGALVPGRVAVPRFRVPQPaPSREAPASSTPPLT-------GHSLSRVSSWASS 3010
 
Name Accession Description Interval E-value
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 244-355 2.14e-19

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: 84.95  E-value: 2.14e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115 244 RIKPEIRDTSVLVKLRPAWEELRSYLtaktRKRFEVYVCTMAERDYALEMWRLLDPEAHLISLKELRDRIVCVKPDAKKS 323
Cdd:cd07521  28 PVLPDGREHGYYVKKRPGVDEFLERL----SKLYEIVIFTAGTRAYADPVADKLDPNGLFIDRRLFRDSCVYVDGNYVKD 103

                        90       100       110
                ....*....|....*....|....*....|..
gi 79503115 324 LLSVFNggicHPKMAMVIDDRMKVWedKDQPR 355
Cdd:cd07521 104 LSKLFR----DLSKVVIIDDSPGSY--WLQPE 129
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 657-720 6.52e-13

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: 64.05  E-value: 6.52e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79503115 657 FVSALQEIGRRCG-SKVEFRTVISTNKE--LQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd10845   3 YKTALQEYLQKRGlPLPEYELVEEEGPDhnKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 255-348 1.77e-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: 63.07  E-value: 1.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   255 LVKLRPAweeLRSYLTaKTRKRFEVYVCTMAERDYALEMWRLLDPEAHLISlkelrDRIV----CVKPDaKKSLLSVFng 330
Cdd:TIGR02250  56 LTKLRPF---LHEFLK-EASKLYEMHVYTMGTRAYAQAIAKLIDPDGKYFG-----DRIIsrdeSGSPH-TKSLLRLF-- 123

                          90
                  ....*....|....*...
gi 79503115   331 gICHPKMAMVIDDRMKVW 348
Cdd:TIGR02250 124 -PADESMVVIIDDREDVW 140
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 658-720 3.94e-11

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: 59.17  E-value: 3.94e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79503115   658 VSALQEIGRRCGSKVEFRTVIST--NKELQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEgpPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM smart00358
Double-stranded RNA binding motif;
658-720 4.50e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 58.81  E-value: 4.50e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79503115    658 VSALQEIGRRCGSKVEFRTV-ISTNKELQ-FSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVkEEGPDHAPrFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
CPDc smart00577
catalytic domain of ctd-like phosphatases;
228-355 1.96e-08

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 53.77  E-value: 1.96e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115    228 VCRPVIRLPEKNTVLTRIKPEIRDTS--VLVKLRPAWEELRSYLTaktrKRFEVYVCTMAERDYALEMWRLLDPEaHLIS 305
Cdd:smart00577  14 VHSTHRSFKEWTNRDFIVPVLIDGHPhgVYVKKRPGVDEFLKRAS----ELFELVVFTAGLRMYADPVLDLLDPK-KYFG 88

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 79503115    306 LKEL-RDRIVCVKPDAKKSlLSVFNggiCHPKMAMVIDDRMKVWedKDQPR 355
Cdd:smart00577  89 YRRLfRDECVFVKGKYVKD-LSLLN---RDLSKVIIIDDSPDSW--PFHPE 133
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
659-723 6.57e-08

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 53.95  E-value: 6.57e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79503115 659 SALQEI--GRRcGSKVEFRtVIST-----NKElqFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSLAEK 723
Cdd:COG0571 161 TALQEWlqARG-LPLPEYE-VVEEegpdhAKT--FTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 244-355 1.85e-06

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: 48.39  E-value: 1.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   244 RIKPEIRDTSVLVKLRPAWEELRSYLtaktRKRFEVYVCTMAERDYALEMWRLLDPEAHLISLKELRDRIVCVKPDAKKS 323
Cdd:pfam03031  25 ILPVPGETHGGYVKKRPGLDEFLKEL----SKYYEIVIFTASSKEYADPVLDILDPNGKLFSHRLYRESCKFEDGVYVKD 100

                          90       100       110
                  ....*....|....*....|....*....|..
gi 79503115   324 lLSVFNGgicHPKMAMVIDDRMKVWEdkDQPR 355
Cdd:pfam03031 101 -LSLLGR---DLSRVVIVDNSPDSFL--LQPD 126
PHA03247 PHA03247
large tegument protein UL36; Provisional
 461-654 9.73e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 9.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   461 AAAADHSTLPATSNAEQKPETPKPQIAVIPNNASTATAAALLPSHKPSLLG---AP----RRDGFTFSDGGRPL------ 527
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGgsvAPggdvRRRPPSRSPAAKPAaparpp 2882

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   528 ---MMRPGVDIRNQNFNQPPILAKIPMQPPSSSMHSPGGWLVDDEN---RPSFPGRP-SGLYPSQFPHGTPGSAPVGPFA 600
Cdd:PHA03247 2883 vrrLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQpqpPPPPPPRPqPPLAPTTDPAGAGEPSGAVPQP 2962

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79503115   601 HPSHLRSEEVAMDDDLKRQN-PSRQTTEGGISQNHlvsngreHHTDGGKSNGGQS 654
Cdd:PHA03247 2963 WLGALVPGRVAVPRFRVPQPaPSREAPASSTPPLT-------GHSLSRVSSWASS 3010
 
Name Accession Description Interval E-value
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 244-355 2.14e-19

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: 84.95  E-value: 2.14e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115 244 RIKPEIRDTSVLVKLRPAWEELRSYLtaktRKRFEVYVCTMAERDYALEMWRLLDPEAHLISLKELRDRIVCVKPDAKKS 323
Cdd:cd07521  28 PVLPDGREHGYYVKKRPGVDEFLERL----SKLYEIVIFTAGTRAYADPVADKLDPNGLFIDRRLFRDSCVYVDGNYVKD 103

                        90       100       110
                ....*....|....*....|....*....|..
gi 79503115 324 LLSVFNggicHPKMAMVIDDRMKVWedKDQPR 355
Cdd:cd07521 104 LSKLFR----DLSKVVIIDDSPGSY--WLQPE 129
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 657-720 6.52e-13

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: 64.05  E-value: 6.52e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79503115 657 FVSALQEIGRRCG-SKVEFRTVISTNKE--LQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd10845   3 YKTALQEYLQKRGlPLPEYELVEEEGPDhnKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 255-348 1.77e-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: 63.07  E-value: 1.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   255 LVKLRPAweeLRSYLTaKTRKRFEVYVCTMAERDYALEMWRLLDPEAHLISlkelrDRIV----CVKPDaKKSLLSVFng 330
Cdd:TIGR02250  56 LTKLRPF---LHEFLK-EASKLYEMHVYTMGTRAYAQAIAKLIDPDGKYFG-----DRIIsrdeSGSPH-TKSLLRLF-- 123

                          90
                  ....*....|....*...
gi 79503115   331 gICHPKMAMVIDDRMKVW 348
Cdd:TIGR02250 124 -PADESMVVIIDDREDVW 140
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 658-720 3.94e-11

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: 59.17  E-value: 3.94e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79503115   658 VSALQEIGRRCGSKVEFRTVIST--NKELQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEgpPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM smart00358
Double-stranded RNA binding motif;
658-720 4.50e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 58.81  E-value: 4.50e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79503115    658 VSALQEIGRRCGSKVEFRTV-ISTNKELQ-FSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVkEEGPDHAPrFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
CPDc smart00577
catalytic domain of ctd-like phosphatases;
228-355 1.96e-08

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 53.77  E-value: 1.96e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115    228 VCRPVIRLPEKNTVLTRIKPEIRDTS--VLVKLRPAWEELRSYLTaktrKRFEVYVCTMAERDYALEMWRLLDPEaHLIS 305
Cdd:smart00577  14 VHSTHRSFKEWTNRDFIVPVLIDGHPhgVYVKKRPGVDEFLKRAS----ELFELVVFTAGLRMYADPVLDLLDPK-KYFG 88

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 79503115    306 LKEL-RDRIVCVKPDAKKSlLSVFNggiCHPKMAMVIDDRMKVWedKDQPR 355
Cdd:smart00577  89 YRRLfRDECVFVKGKYVKD-LSLLN---RDLSKVIIIDDSPDSW--PFHPE 133
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 658-720 6.24e-08

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: 49.96  E-value: 6.24e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 79503115 658 VSALQEIGRRCGSKVEFRTVISTNKELQ-FSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd19875   4 VSALNEYCQKRGLSLEFVDVSVGPDHCPgFTASATIDGIVFASATGTSKKEAKRAAAKLALKKL 67
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
659-723 6.57e-08

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 53.95  E-value: 6.57e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79503115 659 SALQEI--GRRcGSKVEFRtVIST-----NKElqFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSLAEK 723
Cdd:COG0571 161 TALQEWlqARG-LPLPEYE-VVEEegpdhAKT--FTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 244-355 1.85e-06

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: 48.39  E-value: 1.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   244 RIKPEIRDTSVLVKLRPAWEELRSYLtaktRKRFEVYVCTMAERDYALEMWRLLDPEAHLISLKELRDRIVCVKPDAKKS 323
Cdd:pfam03031  25 ILPVPGETHGGYVKKRPGLDEFLKEL----SKYYEIVIFTASSKEYADPVLDILDPNGKLFSHRLYRESCKFEDGVYVKD 100

                          90       100       110
                  ....*....|....*....|....*....|..
gi 79503115   324 lLSVFNGgicHPKMAMVIDDRMKVWEdkDQPR 355
Cdd:pfam03031 101 -LSLLGR---DLSRVVIVDNSPDSFL--LQPD 126
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 657-720 6.88e-06

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains 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: 380696  Cd Length: 74  Bit Score: 44.63  E-value: 6.88e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79503115 657 FVSALQEIGRRCgSKV--EFRTVISTNKELQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd19867   8 PVCILHEYCQRV-LKVqpEYNFTETENAATPFSAEVFINGVEYGSGEASSKKLAKQKAARATLEIL 72
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 658-722 1.51e-05

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 43.43  E-value: 1.51e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79503115 658 VSALQEIGRRCGSKVEFRTVISTN--KELQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSLAE 722
Cdd:cd19902   4 VSALMEYAQSRGVTAEIEVLSQSGppHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALIA 70
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 662-717 1.44e-04

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 40.35  E-value: 1.44e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 79503115 662 QEIGRRCG-SKVEFRTV-ISTNKELQFSVEVLFTGeKIGIGMAKTKKDAHQQAAENAL 717
Cdd:cd00048   1 NELCQKNKwPPPEYETVeEGGPHNPRFTCTVTVNG-QTFEGEGKSKKEAKQAAAEKAL 57
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 685-720 1.65e-03

double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380706  Cd Length: 75  Bit Score: 37.64  E-value: 1.65e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 79503115 685 QFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd19877  40 VYTVAVYFRGERIATGTGSSIQQAEMNAAEKALEKL 75
DSRM_ADAD1 cd19905
double-stranded RNA binding motif of adenosine deaminase domain-containing protein 1 (ADAD1) ...
 658-720 1.95e-03

double-stranded RNA binding motif of adenosine deaminase domain-containing protein 1 (ADAD1) and similar proteins; ADAD1 (also known as testis nuclear RNA-binding protein (TENR)) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It 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. ADAD1 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380734  Cd Length: 69  Bit Score: 37.25  E-value: 1.95e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79503115 658 VSALQEIGRRCGSKVEFR-TVISTNKELQ-FSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSL 720
Cdd:cd19905   4 VSALHEYAQMTRLKLSFKeTVTTGNVAGPyFAFCAVVDGIEYPTGVGKTKKEAKANAAKIALDEL 68
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 671-721 3.11e-03

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380705  Cd Length: 69  Bit Score: 36.93  E-value: 3.11e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 79503115 671 KVEFRTVIS-TNKELQFSVEVLFTGEKIGIGMAKTKKDAHQQAAENALRSLA 721
Cdd:cd19876  18 KPEYVVVKKeGGNDPNYTVACRINGEVLGTGVGRSIKKAGQRAAMSALSNKK 69
PHA03247 PHA03247
large tegument protein UL36; Provisional
 461-654 9.73e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 9.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   461 AAAADHSTLPATSNAEQKPETPKPQIAVIPNNASTATAAALLPSHKPSLLG---AP----RRDGFTFSDGGRPL------ 527
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGgsvAPggdvRRRPPSRSPAAKPAaparpp 2882

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79503115   528 ---MMRPGVDIRNQNFNQPPILAKIPMQPPSSSMHSPGGWLVDDEN---RPSFPGRP-SGLYPSQFPHGTPGSAPVGPFA 600
Cdd:PHA03247 2883 vrrLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQpqpPPPPPPRPqPPLAPTTDPAGAGEPSGAVPQP 2962

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79503115   601 HPSHLRSEEVAMDDDLKRQN-PSRQTTEGGISQNHlvsngreHHTDGGKSNGGQS 654
Cdd:PHA03247 2963 WLGALVPGRVAVPRFRVPQPaPSREAPASSTPPLT-------GHSLSRVSSWASS 3010
 
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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