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Conserved domains on  [gi|1063714581|ref|NP_001325861|]
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Haloacid dehalogenase-like hydrolase (HAD) superfamily protein [Arabidopsis thaliana]

Protein Classification

HAD family hydrolase( domain architecture ID 10503442)

HAD (haloacid dehalogenase) family hydrolase belongs to a phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates; HAD (haloacid dehalogenase) family hydrolase catalyzes a nucleophilic substitution reaction at a phosphorus or carbon center, using a conserved Asp carboxylate in covalent catalysis; similar to Dictyostelium discoideum CTD small phosphatase-like protein 2 and mitochondrial import inner membrane translocase subunit TIM50

CATH:  3.30.1240.10
EC:  3.1.3.-
Gene Ontology:  GO:0016787
PubMed:  16889794
SCOP:  3001890

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 338-489 2.24e-14

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: 70.73  E-value: 2.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 338 IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFCWDMSYcattsvgslenrYKYVVFKDLNRL 415
Cdd:pfam03031  37 VKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILdpNGKLFSHRLYRESCKF------------EDGVYVKDLSLL 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063714581 416 WekhdprlpwkmgdYNETNTVLLDDSPYKALLNpPYTAIFPHSYNHqNKTDTSLgngGDLRLHLEKLVEAENVQ 489
Cdd:pfam03031 105 G-------------RDLSRVVIVDNSPDSFLLQ-PDNGIPIPPFFG-DPDDNEL---LKLLPFLEGLAGVDDVR 160
PTZ00341 super family cl31759
Ring-infected erythrocyte surface antigen; Provisional
 85-288 2.52e-04

Ring-infected erythrocyte surface antigen; Provisional


The actual alignment was detected with superfamily member PTZ00341:

Pssm-ID: 173534 [Multi-domain]  Cd Length: 1136  Bit Score: 44.01  E-value: 2.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581   85 DENVEKKEEGSVISAVTSSDEVPVVKNNDSCVvsgDETVEKNEEGCVilavtssdEVPVVKNNdscvvsgEETIEKNKEG 164
Cdd:PTZ00341   952 EENVEEDAEENVEENVEENVEENVEENVEENV---EENVEENVEENV--------EENVEENI-------EENVEENVEE 1013

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581  165 SVISAVTSNDEVPVVKNNDSCVVSGDETVEKNEEGcvilaVTSSDEVPVVKNNDSCVVSGEETIEKNKEGSVISAVTSND 244
Cdd:PTZ00341  1014 NIEENVEEYDEENVEEVEENVEEYDEENVEEIEEN-----AEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENV 1088

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1063714581  245 EVPVVKNNDSCVVSGDETIEKNEEGSVISAVMSSDEVSVVENND 288
Cdd:PTZ00341  1089 EENVEEIEENVEENVEENAEENAEENAEENAEEYDDENPEEHNE 1132
 
Name Accession Description Interval E-value
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 338-489 2.24e-14

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: 70.73  E-value: 2.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 338 IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFCWDMSYcattsvgslenrYKYVVFKDLNRL 415
Cdd:pfam03031  37 VKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILdpNGKLFSHRLYRESCKF------------EDGVYVKDLSLL 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063714581 416 WekhdprlpwkmgdYNETNTVLLDDSPYKALLNpPYTAIFPHSYNHqNKTDTSLgngGDLRLHLEKLVEAENVQ 489
Cdd:pfam03031 105 G-------------RDLSRVVIVDNSPDSFLLQ-PDNGIPIPPFFG-DPDDNEL---LKLLPFLEGLAGVDDVR 160
CPDc smart00577
catalytic domain of ctd-like phosphatases;
325-449 1.29e-07

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 51.07  E-value: 1.29e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581  325 KDVPADINIGRRA----IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFCWDMSYcattsvg 398
Cdd:smart00577  27 RDFIVPVLIDGHPhgvyVKKRPGVDEFLKRASELFELVVFTAGLRMYADPVLDLLdpKKYFGYRRLFRDECVF------- 99

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1063714581  399 slenrYKYVVFKDLNRLWEkhdprlpwkmgdyNETNTVLLDDSPYKALLNP 449
Cdd:smart00577 100 -----VKGKYVKDLSLLNR-------------DLSKVIIIDDSPDSWPFHP 132
HAD_IIID1 TIGR02245
HAD-superfamily subfamily IIID hydrolase, TIGR02245; This family of sequences appears to ...
 340-495 1.86e-04

HAD-superfamily subfamily IIID hydrolase, TIGR02245; This family of sequences appears to belong to the Haloacid Dehalogenase (HAD) superfamily of enzymes by virtue of the presence of three catalytic domains, in this case: LLVLD(ILV)D(YH)T, I(VMG)IWS, and (DN)(VC)K(PA)Lx{15-17}T(IL)(MH)(FV)DD(IL)(GRS)(RK)N. Since this family has no large "cap" domain between motifs 1 and 2 or between 2 and 3, it is formally a "class III" HAD.


Pssm-ID: 131299  Cd Length: 195  Bit Score: 42.50  E-value: 1.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 340 KRPFCDEFLRFCFDKFEVGIWSSRKQNNV-VRITEF-LLGDLKSKLLFCwdMSYCATTSVGSlENRYKYVVfKDLNRLWe 417
Cdd:TIGR02245  46 MRPYLHEFLTSAYEDYDIVIWSATSMKWIeIKMTELgVLTNPNYKITFL--LDSTAMITVHT-PRRGKFDV-KPLGVIW- 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 418 KHDPRLpwkmgdYNETNTVLLDDSPYKALLNPPY-TAIFPHSYNHQNK-TDTSLgnggdlrLHLEK-LVEAENVQDFIKK 494
Cdd:TIGR02245 121 ALLPEF------YSMKNTIMFDDLRRNFLMNPKNgLKIRPFKKAHANRgTDQEL-------LKLTQyLKTIAELEDFSSL 187


                  .
gi 1063714581 495 N 495
Cdd:TIGR02245 188 D 188
PTZ00341 PTZ00341
Ring-infected erythrocyte surface antigen; Provisional
 85-288 2.52e-04

Ring-infected erythrocyte surface antigen; Provisional


Pssm-ID: 173534 [Multi-domain]  Cd Length: 1136  Bit Score: 44.01  E-value: 2.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581   85 DENVEKKEEGSVISAVTSSDEVPVVKNNDSCVvsgDETVEKNEEGCVilavtssdEVPVVKNNdscvvsgEETIEKNKEG 164
Cdd:PTZ00341   952 EENVEEDAEENVEENVEENVEENVEENVEENV---EENVEENVEENV--------EENVEENI-------EENVEENVEE 1013

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581  165 SVISAVTSNDEVPVVKNNDSCVVSGDETVEKNEEGcvilaVTSSDEVPVVKNNDSCVVSGEETIEKNKEGSVISAVTSND 244
Cdd:PTZ00341  1014 NIEENVEEYDEENVEEVEENVEEYDEENVEEIEEN-----AEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENV 1088

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1063714581  245 EVPVVKNNDSCVVSGDETIEKNEEGSVISAVMSSDEVSVVENND 288
Cdd:PTZ00341  1089 EENVEEIEENVEENVEENAEENAEENAEENAEEYDDENPEEHNE 1132
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 322-450 2.77e-04

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: 41.04  E-value: 2.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 322 TPLKDVPADINIGRRA----IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFcwdmsycaTT 395
Cdd:cd07521    20 VLSEDFKIPVLPDGREhgyyVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLdpNGLFIDRRLF--------RD 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063714581 396 SVGSLENRYkyvvFKDLNRLwekhdprlpwkmgDYNETNTVLLDDSPYKALLNPP 450
Cdd:cd07521    92 SCVYVDGNY----VKDLSKL-------------FRDLSKVVIIDDSPGSYWLQPE 129
 
Name Accession Description Interval E-value
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 338-489 2.24e-14

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: 70.73  E-value: 2.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 338 IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFCWDMSYcattsvgslenrYKYVVFKDLNRL 415
Cdd:pfam03031  37 VKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILdpNGKLFSHRLYRESCKF------------EDGVYVKDLSLL 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063714581 416 WekhdprlpwkmgdYNETNTVLLDDSPYKALLNpPYTAIFPHSYNHqNKTDTSLgngGDLRLHLEKLVEAENVQ 489
Cdd:pfam03031 105 G-------------RDLSRVVIVDNSPDSFLLQ-PDNGIPIPPFFG-DPDDNEL---LKLLPFLEGLAGVDDVR 160
CPDc smart00577
catalytic domain of ctd-like phosphatases;
325-449 1.29e-07

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 51.07  E-value: 1.29e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581  325 KDVPADINIGRRA----IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFCWDMSYcattsvg 398
Cdd:smart00577  27 RDFIVPVLIDGHPhgvyVKKRPGVDEFLKRASELFELVVFTAGLRMYADPVLDLLdpKKYFGYRRLFRDECVF------- 99

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1063714581  399 slenrYKYVVFKDLNRLWEkhdprlpwkmgdyNETNTVLLDDSPYKALLNP 449
Cdd:smart00577 100 -----VKGKYVKDLSLLNR-------------DLSKVIIIDDSPDSWPFHP 132
HAD_IIID1 TIGR02245
HAD-superfamily subfamily IIID hydrolase, TIGR02245; This family of sequences appears to ...
 340-495 1.86e-04

HAD-superfamily subfamily IIID hydrolase, TIGR02245; This family of sequences appears to belong to the Haloacid Dehalogenase (HAD) superfamily of enzymes by virtue of the presence of three catalytic domains, in this case: LLVLD(ILV)D(YH)T, I(VMG)IWS, and (DN)(VC)K(PA)Lx{15-17}T(IL)(MH)(FV)DD(IL)(GRS)(RK)N. Since this family has no large "cap" domain between motifs 1 and 2 or between 2 and 3, it is formally a "class III" HAD.


Pssm-ID: 131299  Cd Length: 195  Bit Score: 42.50  E-value: 1.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 340 KRPFCDEFLRFCFDKFEVGIWSSRKQNNV-VRITEF-LLGDLKSKLLFCwdMSYCATTSVGSlENRYKYVVfKDLNRLWe 417
Cdd:TIGR02245  46 MRPYLHEFLTSAYEDYDIVIWSATSMKWIeIKMTELgVLTNPNYKITFL--LDSTAMITVHT-PRRGKFDV-KPLGVIW- 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 418 KHDPRLpwkmgdYNETNTVLLDDSPYKALLNPPY-TAIFPHSYNHQNK-TDTSLgnggdlrLHLEK-LVEAENVQDFIKK 494
Cdd:TIGR02245 121 ALLPEF------YSMKNTIMFDDLRRNFLMNPKNgLKIRPFKKAHANRgTDQEL-------LKLTQyLKTIAELEDFSSL 187


                  .
gi 1063714581 495 N 495
Cdd:TIGR02245 188 D 188
PTZ00341 PTZ00341
Ring-infected erythrocyte surface antigen; Provisional
 85-288 2.52e-04

Ring-infected erythrocyte surface antigen; Provisional


Pssm-ID: 173534 [Multi-domain]  Cd Length: 1136  Bit Score: 44.01  E-value: 2.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581   85 DENVEKKEEGSVISAVTSSDEVPVVKNNDSCVvsgDETVEKNEEGCVilavtssdEVPVVKNNdscvvsgEETIEKNKEG 164
Cdd:PTZ00341   952 EENVEEDAEENVEENVEENVEENVEENVEENV---EENVEENVEENV--------EENVEENI-------EENVEENVEE 1013

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581  165 SVISAVTSNDEVPVVKNNDSCVVSGDETVEKNEEGcvilaVTSSDEVPVVKNNDSCVVSGEETIEKNKEGSVISAVTSND 244
Cdd:PTZ00341  1014 NIEENVEEYDEENVEEVEENVEEYDEENVEEIEEN-----AEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENV 1088

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1063714581  245 EVPVVKNNDSCVVSGDETIEKNEEGSVISAVMSSDEVSVVENND 288
Cdd:PTZ00341  1089 EENVEEIEENVEENVEENAEENAEENAEENAEEYDDENPEEHNE 1132
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 322-450 2.77e-04

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: 41.04  E-value: 2.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063714581 322 TPLKDVPADINIGRRA----IFKRPFCDEFLRFCFDKFEVGIWSSRKQNNVVRITEFL--LGDLKSKLLFcwdmsycaTT 395
Cdd:cd07521    20 VLSEDFKIPVLPDGREhgyyVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLdpNGLFIDRRLF--------RD 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063714581 396 SVGSLENRYkyvvFKDLNRLwekhdprlpwkmgDYNETNTVLLDDSPYKALLNPP 450
Cdd:cd07521    92 SCVYVDGNY----VKDLSKL-------------FRDLSKVVIIDDSPGSYWLQPE 129
 
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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