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Conserved domains on  [gi|6325194|ref|NP_015262|]
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protein translocase subunit TIM50 [Saccharomyces cerevisiae S288C]

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 ...
 193-339 5.45e-57

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: 185.90  E-value: 5.45e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    193 TLVITLEDFLVHSEWS-------------QKHGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIHAFV 259
Cdd:pfam03031   2 TLVLDLDETLVHSSFEpplksdfilpvpgETHGGYVKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILDPNGKLF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    260 SYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNGEADDK-LVRLIPFLEYLAtqQTKDV 338
Cdd:pfam03031  82 SHRLYRESCKFEDGVYVKDLSLLGRDLSRVVIVDNSPDSFLLQPDNGIPIPPFFGDPDDNeLLKLLPFLEGLA--GVDDV 159


                  .
gi 6325194    339 R 339
Cdd:pfam03031 160 R 160
 
Name Accession Description Interval E-value
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 193-339 5.45e-57

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: 185.90  E-value: 5.45e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    193 TLVITLEDFLVHSEWS-------------QKHGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIHAFV 259
Cdd:pfam03031   2 TLVLDLDETLVHSSFEpplksdfilpvpgETHGGYVKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILDPNGKLF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    260 SYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNGEADDK-LVRLIPFLEYLAtqQTKDV 338
Cdd:pfam03031  82 SHRLYRESCKFEDGVYVKDLSLLGRDLSRVVIVDNSPDSFLLQPDNGIPIPPFFGDPDDNeLLKLLPFLEGLA--GVDDV 159


                  .
gi 6325194    339 R 339
Cdd:pfam03031 160 R 160
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 193-309 3.05e-55

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: 180.48  E-value: 3.05e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194  193 TLVITLEDFLVHSEWS---------------QKHGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIHA 257
Cdd:cd07521   3 TLVLDLDETLVHSTWKpvlsedfkipvlpdgREHGYYVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLDPNGL 82

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 6325194  258 FVSYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPM 309
Cdd:cd07521  83 FIDRRLFRDSCVYVDGNYVKDLSKLFRDLSKVVIIDDSPGSYWLQPENAIPI 134
CPDc smart00577
catalytic domain of ctd-like phosphatases;
193-319 3.35e-53

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 175.88  E-value: 3.35e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194     193 TLVITLEDFLVHS------EWSQK------------HGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDP 254
Cdd:smart00577   4 TLVLDLDETLVHSthrsfkEWTNRdfivpvlidghpHGVYVKKRPGVDEFLKRASELFELVVFTAGLRMYADPVLDLLDP 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6325194     255 IHAFVSYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNGEADDK 319
Cdd:smart00577  84 KKYFGYRRLFRDECVFVKGKYVKDLSLLNRDLSKVIIIDDSPDSWPFHPENLIPIKPWFGDPDDT 148
HIF-SF_euk TIGR02251
Dullard-like phosphatase domain; This model represents the putative phosphatase domain of a ...
 193-337 1.00e-36

Dullard-like phosphatase domain; This model represents the putative phosphatase domain of a family of eukaryotic proteins including "Dullard", and the NLI interacting factor (NIF)-like phosphatases. 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 (hhhhDNxPxxa) and aparrently lacking the last aspartate. 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 FCP1-like phosphatases (TIGR02250), and together both are detected by the pfam03031.


Pssm-ID: 274055  Cd Length: 162  Bit Score: 132.80  E-value: 1.00e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    193 TLVITLEDFLVHSEWSQK----------------HGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIH 256
Cdd:TIGR02251   3 TLVLDLDETLVHSTFKMPkvdadfkvpvlidgkiIQVYVFKRPHVDEFLERVSKWYELVIFTASLEEYADPVLDILDRGG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    257 AFVSYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNG-EADDKLVRLIPFLEYLatQQT 335
Cdd:TIGR02251  83 KVISRRLYRESCVFTNGKYVKDLSLVGKDLSKVIIIDNSPYSYSLQPDNAIPIKSWFSdPNDTELLNLIPFLEGL--RFE 160


                  ..
gi 6325194    336 KD 337
Cdd:TIGR02251 161 DD 162
 
Name Accession Description Interval E-value
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 193-339 5.45e-57

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: 185.90  E-value: 5.45e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    193 TLVITLEDFLVHSEWS-------------QKHGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIHAFV 259
Cdd:pfam03031   2 TLVLDLDETLVHSSFEpplksdfilpvpgETHGGYVKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILDPNGKLF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    260 SYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNGEADDK-LVRLIPFLEYLAtqQTKDV 338
Cdd:pfam03031  82 SHRLYRESCKFEDGVYVKDLSLLGRDLSRVVIVDNSPDSFLLQPDNGIPIPPFFGDPDDNeLLKLLPFLEGLA--GVDDV 159


                  .
gi 6325194    339 R 339
Cdd:pfam03031 160 R 160
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 193-309 3.05e-55

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: 180.48  E-value: 3.05e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194  193 TLVITLEDFLVHSEWS---------------QKHGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIHA 257
Cdd:cd07521   3 TLVLDLDETLVHSTWKpvlsedfkipvlpdgREHGYYVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLDPNGL 82

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 6325194  258 FVSYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPM 309
Cdd:cd07521  83 FIDRRLFRDSCVYVDGNYVKDLSKLFRDLSKVVIIDDSPGSYWLQPENAIPI 134
CPDc smart00577
catalytic domain of ctd-like phosphatases;
193-319 3.35e-53

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 175.88  E-value: 3.35e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194     193 TLVITLEDFLVHS------EWSQK------------HGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDP 254
Cdd:smart00577   4 TLVLDLDETLVHSthrsfkEWTNRdfivpvlidghpHGVYVKKRPGVDEFLKRASELFELVVFTAGLRMYADPVLDLLDP 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6325194     255 IHAFVSYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNGEADDK 319
Cdd:smart00577  84 KKYFGYRRLFRDECVFVKGKYVKDLSLLNRDLSKVIIIDDSPDSWPFHPENLIPIKPWFGDPDDT 148
HIF-SF_euk TIGR02251
Dullard-like phosphatase domain; This model represents the putative phosphatase domain of a ...
 193-337 1.00e-36

Dullard-like phosphatase domain; This model represents the putative phosphatase domain of a family of eukaryotic proteins including "Dullard", and the NLI interacting factor (NIF)-like phosphatases. 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 (hhhhDNxPxxa) and aparrently lacking the last aspartate. 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 FCP1-like phosphatases (TIGR02250), and together both are detected by the pfam03031.


Pssm-ID: 274055  Cd Length: 162  Bit Score: 132.80  E-value: 1.00e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    193 TLVITLEDFLVHSEWSQK----------------HGWRTAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPIH 256
Cdd:TIGR02251   3 TLVLDLDETLVHSTFKMPkvdadfkvpvlidgkiIQVYVFKRPHVDEFLERVSKWYELVIFTASLEEYADPVLDILDRGG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    257 AFVSYNLFKEHCVYKDGVHIKDLSKLNRDLSKVIIIDTDPNSYKLQPENAIPMEPWNG-EADDKLVRLIPFLEYLatQQT 335
Cdd:TIGR02251  83 KVISRRLYRESCVFTNGKYVKDLSLVGKDLSKVIIIDNSPYSYSLQPDNAIPIKSWFSdPNDTELLNLIPFLEGL--RFE 160


                  ..
gi 6325194    336 KD 337
Cdd:TIGR02251 161 DD 162
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 215-313 9.51e-04

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: 39.57  E-value: 9.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325194    215 TAKRPGADYFLGYLSQYYEIVLFSSNYMMYSDKIAEKLDPihafvSYNLFKEHCVYKD---GVHIKDLSKL-NRDLSKVI 290
Cdd:TIGR02250  57 TKLRPFLHEFLKEASKLYEMHVYTMGTRAYAQAIAKLIDP-----DGKYFGDRIISRDesgSPHTKSLLRLfPADESMVV 131

                          90       100
                  ....*....|....*....|...
gi 6325194    291 IIDTDPNSYKLQPENAIPMEPWN 313
Cdd:TIGR02250 132 IIDDREDVWPWHKRNLIQIEPYN 154
 
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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