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Conserved domains on  [gi|492535814|ref|WP_005877301|]
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YjjG family noncanonical pyrimidine nucleotidase [Oxalobacter paraformigenes]

Protein Classification

YjjG family noncanonical pyrimidine nucleotidase( domain architecture ID 1007827)

YjjG family noncanonical pyrimidine nucleotidase similar to Streptococcus pneumoniae pyrimidine 5'-nucleotidase PynA that shows high phosphatase activity toward non-canonical pyrimidine nucleotides and three canonical nucleoside 5'-monophosphates (UMP, dUMP and dTMP)

CATH:  1.10.150.240|3.40.50.1000
EC:  3.1.3.5
Gene Ontology:  GO:0008253|GO:0046872

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YjjG/YfnB super family cl31454
noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including ...
 19-228 8.24e-69

noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including YjjG from E. coli and YfnB from B. subtilis. YjjG has been shown to act as a house-cleaning enzyme, cleaving nucleotides with non-canonical nucleotide bases. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).


The actual alignment was detected with superfamily member TIGR02254:

Pssm-ID: 162788 [Multi-domain]  Cd Length: 224  Bit Score: 210.81  E-value: 8.24e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   19 FAKTEKNALDATFRRYGLKLTEEIRDIYHTVNRTLWAAFERGEISKETVTSTRFSRLFAETGFAVNGASFSRDYQKALGE 98
Cdd:TIGR02254  15 FQAAEALALRLLFEDQGIPLTEDMFAQYKEINQGLWRAYEEGKITKDEVVNTRFSALLKEYNTEADEALLNQKYLRFLEE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   99 GYYLIDGAKELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPRFAPDKAL 178
Cdd:TIGR02254  95 GHQLLPGAFELMENLQQKFRLYIVTNGVRETQYKRLRKSGLFPFFDDIFVSEDAGIQKPDKEIFNYALERMPKFSKEEVL 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 492535814  179 IVGDSLTSDIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPIL 228
Cdd:TIGR02254 175 MIGDSLTADIKGGQNAGLDTCWMNPDMHPNPDDIIPTYEIRSLEELYEIL 224
 
Name Accession Description Interval E-value
YjjG/YfnB TIGR02254
noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including ...
 19-228 8.24e-69

noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including YjjG from E. coli and YfnB from B. subtilis. YjjG has been shown to act as a house-cleaning enzyme, cleaving nucleotides with non-canonical nucleotide bases. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).


Pssm-ID: 162788 [Multi-domain]  Cd Length: 224  Bit Score: 210.81  E-value: 8.24e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   19 FAKTEKNALDATFRRYGLKLTEEIRDIYHTVNRTLWAAFERGEISKETVTSTRFSRLFAETGFAVNGASFSRDYQKALGE 98
Cdd:TIGR02254  15 FQAAEALALRLLFEDQGIPLTEDMFAQYKEINQGLWRAYEEGKITKDEVVNTRFSALLKEYNTEADEALLNQKYLRFLEE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   99 GYYLIDGAKELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPRFAPDKAL 178
Cdd:TIGR02254  95 GHQLLPGAFELMENLQQKFRLYIVTNGVRETQYKRLRKSGLFPFFDDIFVSEDAGIQKPDKEIFNYALERMPKFSKEEVL 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 492535814  179 IVGDSLTSDIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPIL 228
Cdd:TIGR02254 175 MIGDSLTADIKGGQNAGLDTCWMNPDMHPNPDDIIPTYEIRSLEELYEIL 224
YigB COG1011
FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ...
 26-228 3.44e-45

FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism];


Pssm-ID: 440635 [Multi-domain]  Cd Length: 220  Bit Score: 150.18  E-value: 3.44e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  26 ALDATFRRYGLKLT-EEIRDIYHTVNRTLWAAFERGEISKETVtstrFSRLFAETGFAVnGASFSRDYQKALGEGYYLID 104
Cdd:COG1011   22 ALRALAERLGLLDEaEELAEAYRAIEYALWRRYERGEITFAEL----LRRLLEELGLDL-AEELAEAFLAALPELVEPYP 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 105 GAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKALIVGDS 183
Cdd:COG1011   97 DALELLEALKARgYRLALLTNGSAELQEAKLRRLGLDDLFDAVVSSEEVGVRKPDPEIFELALERL-GVPPEEALFVGDS 175

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 492535814 184 LTSDIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPIL 228
Cdd:COG1011  176 PETDVAGARAAGMRTVWVNRSGEPAPAEPRPDYVISDLAELLELL 220
PRK09449 PRK09449
dUMP phosphatase; Provisional
 27-230 7.37e-45

dUMP phosphatase; Provisional


Pssm-ID: 181865 [Multi-domain]  Cd Length: 224  Bit Score: 149.67  E-value: 7.37e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  27 LDATFRRYGLKLTEEIRDIYHTVNRTLWAAFERGEISKETVTSTRFSRLFAETGfaVNGASFSRDYQKALGEGYYLIDGA 106
Cdd:PRK09449  23 LQRMFSRYGVDFTAEDFQDYQAVNKPLWVDYQNGAITALQLQHTRFESWAEKLN--VTPGELNSAFLNAMAEICTPLPGA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 107 KELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPRFAPDKALIVGDSLTS 186
Cdd:PRK09449 101 VELLNALRGKVKMGIITNGFTELQQVRLERTGLRDYFDLLVISEQVGVAKPDVAIFDYALEQMGNPDRSRVLMVGDNLHS 180

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 492535814 187 DIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPILEG 230
Cdd:PRK09449 181 DILGGINAGIDTCWLNAHGREQPEGIAPTYQVSSLSELEQLLCK 224
HAD_Neu5Ac-Pase_like cd04305
human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase ...
 102-202 2.12e-41

human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. This family belongs 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: 319800 [Multi-domain]  Cd Length: 109  Bit Score: 136.90  E-value: 2.12e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 102 LIDGAKELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPrFAPDKALIVG 181
Cdd:cd04305   10 LLPGAKELLEELKKGYKLGIITNGPTEVQWEKLEQLGIHKYFDHIVISEEVGVQKPNPEIFDYALNQLG-VKPEETLMVG 88

                         90       100
                 ....*....|....*....|.
gi 492535814 182 DSLTSDIQGGKNTGIDTCWYN 202
Cdd:cd04305   89 DSLESDILGAKNAGIKTVWFN 109
HAD_2 pfam13419
Haloacid dehalogenase-like hydrolase;
39-200 3.72e-19

Haloacid dehalogenase-like hydrolase;


Pssm-ID: 404323 [Multi-domain]  Cd Length: 178  Bit Score: 81.48  E-value: 3.72e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   39 TEEIrdIYHTVNRTLwAAFERGEISKETVTSTR-------FSRLFAETGFAVNGASFSRDYQKALGEGY-YLIDGAKELC 110
Cdd:pfam13419  12 TEEL--IIKSFNYLL-EEFGYGELSEEEILKFIglplreiFRYLGVSEDEEEKIEFYLRKYNEELHDKLvKPYPGIKELL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  111 EKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDyfrAVFRAIPRF--APDKALIVGDSlTSD 187
Cdd:pfam13419  89 EELKEQgYKLGIVTSKSRENVEEFLKQLGLEDYFDVIVGGDDVEGKKPDPD---PILKALEQLglKPEEVIYVGDS-PRD 164

                         170
                  ....*....|...
gi 492535814  188 IQGGKNTGIDTCW 200
Cdd:pfam13419 165 IEAAKNAGIKVIA 177
 
Name Accession Description Interval E-value
YjjG/YfnB TIGR02254
noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including ...
 19-228 8.24e-69

noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including YjjG from E. coli and YfnB from B. subtilis. YjjG has been shown to act as a house-cleaning enzyme, cleaving nucleotides with non-canonical nucleotide bases. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).


Pssm-ID: 162788 [Multi-domain]  Cd Length: 224  Bit Score: 210.81  E-value: 8.24e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   19 FAKTEKNALDATFRRYGLKLTEEIRDIYHTVNRTLWAAFERGEISKETVTSTRFSRLFAETGFAVNGASFSRDYQKALGE 98
Cdd:TIGR02254  15 FQAAEALALRLLFEDQGIPLTEDMFAQYKEINQGLWRAYEEGKITKDEVVNTRFSALLKEYNTEADEALLNQKYLRFLEE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   99 GYYLIDGAKELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPRFAPDKAL 178
Cdd:TIGR02254  95 GHQLLPGAFELMENLQQKFRLYIVTNGVRETQYKRLRKSGLFPFFDDIFVSEDAGIQKPDKEIFNYALERMPKFSKEEVL 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 492535814  179 IVGDSLTSDIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPIL 228
Cdd:TIGR02254 175 MIGDSLTADIKGGQNAGLDTCWMNPDMHPNPDDIIPTYEIRSLEELYEIL 224
YigB COG1011
FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ...
 26-228 3.44e-45

FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism];


Pssm-ID: 440635 [Multi-domain]  Cd Length: 220  Bit Score: 150.18  E-value: 3.44e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  26 ALDATFRRYGLKLT-EEIRDIYHTVNRTLWAAFERGEISKETVtstrFSRLFAETGFAVnGASFSRDYQKALGEGYYLID 104
Cdd:COG1011   22 ALRALAERLGLLDEaEELAEAYRAIEYALWRRYERGEITFAEL----LRRLLEELGLDL-AEELAEAFLAALPELVEPYP 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 105 GAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKALIVGDS 183
Cdd:COG1011   97 DALELLEALKARgYRLALLTNGSAELQEAKLRRLGLDDLFDAVVSSEEVGVRKPDPEIFELALERL-GVPPEEALFVGDS 175

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 492535814 184 LTSDIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPIL 228
Cdd:COG1011  176 PETDVAGARAAGMRTVWVNRSGEPAPAEPRPDYVISDLAELLELL 220
PRK09449 PRK09449
dUMP phosphatase; Provisional
 27-230 7.37e-45

dUMP phosphatase; Provisional


Pssm-ID: 181865 [Multi-domain]  Cd Length: 224  Bit Score: 149.67  E-value: 7.37e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  27 LDATFRRYGLKLTEEIRDIYHTVNRTLWAAFERGEISKETVTSTRFSRLFAETGfaVNGASFSRDYQKALGEGYYLIDGA 106
Cdd:PRK09449  23 LQRMFSRYGVDFTAEDFQDYQAVNKPLWVDYQNGAITALQLQHTRFESWAEKLN--VTPGELNSAFLNAMAEICTPLPGA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 107 KELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPRFAPDKALIVGDSLTS 186
Cdd:PRK09449 101 VELLNALRGKVKMGIITNGFTELQQVRLERTGLRDYFDLLVISEQVGVAKPDVAIFDYALEQMGNPDRSRVLMVGDNLHS 180

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 492535814 187 DIQGGKNTGIDTCWYNPAGKTAQPALAANYEIRKLDELLPILEG 230
Cdd:PRK09449 181 DILGGINAGIDTCWLNAHGREQPEGIAPTYQVSSLSELEQLLCK 224
HAD_Neu5Ac-Pase_like cd04305
human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase ...
 102-202 2.12e-41

human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. This family belongs 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: 319800 [Multi-domain]  Cd Length: 109  Bit Score: 136.90  E-value: 2.12e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 102 LIDGAKELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPrFAPDKALIVG 181
Cdd:cd04305   10 LLPGAKELLEELKKGYKLGIITNGPTEVQWEKLEQLGIHKYFDHIVISEEVGVQKPNPEIFDYALNQLG-VKPEETLMVG 88

                         90       100
                 ....*....|....*....|.
gi 492535814 182 DSLTSDIQGGKNTGIDTCWYN 202
Cdd:cd04305   89 DSLESDILGAKNAGIKTVWFN 109
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
14-229 2.25e-20

Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 85.75  E-value: 2.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  14 DTLLDFAktekNALDATFRRYGL-KLTEEirDIYHTVNRTLWAAFER--GEISKEtvtstRFSRLFAEtgfavngasFSR 90
Cdd:COG0546   14 DSAPDIA----AALNEALAELGLpPLDLE--ELRALIGLGLRELLRRllGEDPDE-----ELEELLAR---------FRE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  91 DYQKALGEGYYLIDGAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAI 169
Cdd:COG0546   74 LYEEELLDETRLFPGVRELLEALKARgIKLAVVTNKPREFAERLLEALGLDDYFDAIVGGDDVPPAKPKPEPLLEALERL 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492535814 170 pRFAPDKALIVGDSlTSDIQGGKNTGIDTCWYNPAGKTAQP--ALAANYEIRKLDELLPILE 229
Cdd:COG0546  154 -GLDPEEVLMVGDS-PHDIEAARAAGVPFIGVTWGYGSAEEleAAGADYVIDSLAELLALLA 213
HAD_2 pfam13419
Haloacid dehalogenase-like hydrolase;
39-200 3.72e-19

Haloacid dehalogenase-like hydrolase;


Pssm-ID: 404323 [Multi-domain]  Cd Length: 178  Bit Score: 81.48  E-value: 3.72e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   39 TEEIrdIYHTVNRTLwAAFERGEISKETVTSTR-------FSRLFAETGFAVNGASFSRDYQKALGEGY-YLIDGAKELC 110
Cdd:pfam13419  12 TEEL--IIKSFNYLL-EEFGYGELSEEEILKFIglplreiFRYLGVSEDEEEKIEFYLRKYNEELHDKLvKPYPGIKELL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  111 EKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDyfrAVFRAIPRF--APDKALIVGDSlTSD 187
Cdd:pfam13419  89 EELKEQgYKLGIVTSKSRENVEEFLKQLGLEDYFDVIVGGDDVEGKKPDPD---PILKALEQLglKPEEVIYVGDS-PRD 164

                         170
                  ....*....|...
gi 492535814  188 IQGGKNTGIDTCW 200
Cdd:pfam13419 165 IEAAKNAGIKVIA 177
HAD_like cd01427
Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily ...
 103-201 1.75e-13

Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others. This superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All of which use a nucleophilic aspartate in their phosphoryl transfer reaction. They catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All 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. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319763 [Multi-domain]  Cd Length: 106  Bit Score: 64.34  E-value: 1.75e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 103 IDG---AKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKAL 178
Cdd:cd01427    6 LDGtllAVELLKRLRAAgIKLAIVTNRSREALRALLEKLGLGDLFDGIIGSDGGGTPKPKPKPLLLLLLKL-GVDPEEVL 84

                         90       100
                 ....*....|....*....|...
gi 492535814 179 IVGDSLTsDIQGGKNTGIDTCWY 201
Cdd:cd01427   85 FVGDSEN-DIEAARAAGGRTVAV 106
HAD-SF-IA-v1 TIGR01549
haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or ...
 92-195 3.27e-13

haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions.The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)(D/E), (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 1 (this model) is found in the enzymes phosphoglycolate phosphatase (TIGR01449) and enolase-phosphatase. These three variant models (see also TIGR01493 and TIGR01509) were created withthe knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly relatedHAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273686 [Multi-domain]  Cd Length: 164  Bit Score: 65.11  E-value: 3.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   92 YQKALGEGYYLIDGAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHqKPSRDYFRAVFRAIP 170
Cdd:TIGR01549  64 FWSEYDAEEAYIRGAADLLARLKSAgIKLGIISNGSLRAQKLLLRLFGLGDYFELILVSDEPGS-KPEPEIFLAALESLG 142

                          90       100
                  ....*....|....*....|....*
gi 492535814  171 rfAPDKALIVGDSLtSDIQGGKNTG 195
Cdd:TIGR01549 143 --VPPEVLHVGDNL-NDIEGARNAG 164
YcjU COG0637
Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];
26-224 3.74e-12

Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440402 [Multi-domain]  Cd Length: 208  Bit Score: 63.30  E-value: 3.74e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  26 ALDATFRRYGLKLTEEIRDIYHTVNRTLWAAfergeisketvtstrfsRLFAETGFAVNGASFSRDYQKALGEGYY---- 101
Cdd:COG0637   23 AWREAFAELGIDLTEEEYRRLMGRSREDILR-----------------YLLEEYGLDLPEEELAARKEELYRELLAeegl 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 102 -LIDGAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFsDVFVS-ETIGHQKPSRDYFRAVFRAIpRFAPDKAL 178
Cdd:COG0637   86 pLIPGVVELLEALKEAgIKIAVATSSPRENAEAVLEAAGLLDYF-DVIVTgDDVARGKPDPDIYLLAAERL-GVDPEECV 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 492535814 179 IVGDSLTsDIQGGKNTGIDTCWYnPAGKTAQPALA-ANYEIRKLDEL 224
Cdd:COG0637  164 VFEDSPA-GIRAAKAAGMRVVGV-PDGGTAEEELAgADLVVDDLAEL 208
PRK13222 PRK13222
N-acetylmuramic acid 6-phosphate phosphatase MupP;
86-229 9.12e-12

N-acetylmuramic acid 6-phosphate phosphatase MupP;


Pssm-ID: 237310 [Multi-domain]  Cd Length: 226  Bit Score: 62.52  E-value: 9.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  86 ASFSRDYQKALGEGYYLIDGAKELCEKLSEK-YRLYCVTNgvAATQYSR--LSGSGLDHYFSDVFVSETIGHQKPSRDYF 162
Cdd:PRK13222  78 ELFDRHYAENVAGGSRLYPGVKETLAALKAAgYPLAVVTN--KPTPFVAplLEALGIADYFSVVIGGDSLPNKKPDPAPL 155

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492535814 163 RAVFRAIPrFAPDKALIVGDSLtSDIQGGKNTGIDTCW----YNpaGKTAQPALAANYEIRKLDELLPILE 229
Cdd:PRK13222 156 LLACEKLG-LDPEEMLFVGDSR-NDIQAARAAGCPSVGvtygYN--YGEPIALSEPDVVIDHFAELLPLLG 222
HAD_PPase cd02616
pyrophosphatase similar to Bacillus subtilis PpaX; This family includes Bacillus subtilis PpaX ...
 26-227 1.09e-11

pyrophosphatase similar to Bacillus subtilis PpaX; This family includes Bacillus subtilis PpaX which hydrolyzes pyrophosphate formed during serine-46-phosphorylated HPr (P-Ser-HPr) dephosphorylation by the bifunctional enzyme HPr kinase/phosphorylase. This family belongs 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: 319797 [Multi-domain]  Cd Length: 207  Bit Score: 61.91  E-value: 1.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  26 ALDATFRRYGL-KLTEEirDIYHTVNRTLWAAFERgeISKETVTstRFSRLFAEtgfavngasFSRDYQKALGEGYyliD 104
Cdd:cd02616   22 SFNHTLKEYGLeGYTRE--EVLPFIGPPLRETFEK--IDPDKLE--DMVEEFRK---------YYREHNDDLTKEY---P 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 105 GAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDyfrAVFRAIPRF--APDKALIVG 181
Cdd:cd02616   84 GVYETLARLKSQgIKLGVVTTKLRETALKGLKLLGLDKYFDVIVGGDDVTHHKPDPE---PVLKALELLgaEPEEALMVG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 492535814 182 DSlTSDIQGGKNTGIDTCWYNPAGKTAQPALAANYE--IRKLDELLPI 227
Cdd:cd02616  161 DS-PHDILAGKNAGVKTVGVTWGYKGREYLKAFNPDfiIDKMSDLLTI 207
HAD_dREG-2_like cd16415
uncharacterized family of the haloacid dehalogenase-like superfamily, similar to ...
 114-206 2.28e-11

uncharacterized family of the haloacid dehalogenase-like superfamily, similar to uncharacterized Drosophila melanogaster rhythmically expressed gene 2 protein and human haloacid dehalogenase-like hydrolase domain-containing protein 3; The haloacid dehalogenase-like (HAD) hydrolases are 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 include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members 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: 319852 [Multi-domain]  Cd Length: 128  Bit Score: 59.23  E-value: 2.28e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 114 SEKYRLYCVTNgVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRavfRAIPRF--APDKALIVGDSLTSDIQGG 191
Cdd:cd16415   21 EKGLKLAVVSN-FDRRLRELLEALGLDDYFDFVVFSYEVGYEKPDPRIFQ---KALERLgvSPEEALHVGDDLKNDYLGA 96

                         90
                 ....*....|....*
gi 492535814 192 KNTGIDTCWYNPAGK 206
Cdd:cd16415   97 RAVGWHALLVDREGA 111
HAD-like cd07515
uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; The ...
 102-189 1.60e-10

uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; The haloacid dehalogenase-like (HAD) hydrolases are 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 include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members 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: 319817 [Multi-domain]  Cd Length: 131  Bit Score: 57.04  E-value: 1.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 102 LIDGAKELCEKLSEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDV-FVSEtighqKPSRDYfRAVFRaIPRFAPDKALIV 180
Cdd:cd07515   18 LLPGVREALAALKADYRLVLITKGDLLDQEQKLARSGLSDYFDAVeVVSE-----KDPDTY-RRVLS-RYGIGPERFVMV 90


                 ....*....
gi 492535814 181 GDSLTSDIQ 189
Cdd:cd07515   91 GNSLRSDIL 99
Hydrolase pfam00702
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ...
 31-193 3.44e-10

haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha/beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain. Those members with the characteriztic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria.


Pssm-ID: 459910 [Multi-domain]  Cd Length: 191  Bit Score: 57.60  E-value: 3.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814   31 FRRYGLKLTEEIRDIYHTV---NRTLWAAFERGEISKETVTSTRFSRLFAEtgfavngasfsRDYQKALGEGYYLIDGAK 107
Cdd:pfam00702  36 IVAAAEDLPIPVEDFTARLllgKRDWLEELDILRGLVETLEAEGLTVVLVE-----------LLGVIALADELKLYPGAA 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  108 ELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKALIVGDSLTs 186
Cdd:pfam00702 105 EALKALKERgIKVAILTGDNPEAAEALLRLLGLDDYFDVVISGDDVGVGKPKPEIYLAALERL-GVKPEEVLMVGDGVN- 182


                  ....*..
gi 492535814  187 DIQGGKN 193
Cdd:pfam00702 183 DIPAAKA 189
PRK10748 PRK10748
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB;
112-228 5.39e-10

5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB;


Pssm-ID: 182696 [Multi-domain]  Cd Length: 238  Bit Score: 57.44  E-value: 5.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 112 KLSEKYRLYCVTNGVAatqysRLSGSGLDHYFSDVFVSETIGHQKPSRD-YFRAVFR-AIPrfaPDKALIVGDSLTSDIQ 189
Cdd:PRK10748 124 QLAKKWPLVAITNGNA-----QPELFGLGDYFEFVLRAGPHGRSKPFSDmYHLAAEKlNVP---IGEILHVGDDLTTDVA 195

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 492535814 190 GGKNTGIDTCWYNPAG----KTAQPALAANYEIRKLDELLPIL 228
Cdd:PRK10748 196 GAIRCGMQACWINPENgdlmQTWDSRLLPHIEISRLASLTSLI 238
HAD_PGPase cd16417
Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the ...
 44-199 1.21e-09

Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the haloacid dehalogenase-like superfamily; Phosphoglycolate phosphatase (PGP; EC 3.1.3.18) catalyzes the conversion of 2-phosphoglycolate into glycolate and phosphate. 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 (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) 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: 319854 [Multi-domain]  Cd Length: 212  Bit Score: 56.09  E-value: 1.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  44 DIYHTVNRTLwAAFERGEISKETVTS---------------TRFSRLFAETGFAVNGASFSRDYQKALGEGYYLIDGAKE 108
Cdd:cd16417   16 DLAEAANAML-AALGLPPLPEETVRTwigngadvlveraltGAREAEPDEELFKEARALFDRHYAETLSVHSHLYPGVKE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 109 LCEKL-SEKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDyfrAVFRAIPRF--APDKALIVGDSLt 185
Cdd:cd16417   95 GLAALkAQGYPLACVTNKPERFVAPLLEALGISDYFSLVLGGDSLPEKKPDPA---PLLHACEKLgiAPAQMLMVGDSR- 170

                        170
                 ....*....|....
gi 492535814 186 SDIQGGKNTGIDTC 199
Cdd:cd16417  171 NDILAARAAGCPSV 184
NagD COG0647
Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism];
156-225 1.54e-09

Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism];


Pssm-ID: 440412 [Multi-domain]  Cd Length: 259  Bit Score: 56.66  E-value: 1.54e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492535814 156 KPSRDYFRAVFRAIPrFAPDKALIVGDSLTSDIQGGKNTGIDTCWYNpAGKTAQPALAA-----NYEIRKLDELL 225
Cdd:COG0647  186 KPSPPIYELALERLG-VDPERVLMVGDRLDTDILGANAAGLDTLLVL-TGVTTAEDLEAapirpDYVLDSLAELL 258
HAD_L2-DEX cd02588
L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation ...
 111-224 2.66e-08

L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloacids to produce the corresponding D-2-hydroxyacids with an inversion of the C2-configuration. 2-haloacid dehalogenases are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. This family belongs 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: 319787 [Multi-domain]  Cd Length: 216  Bit Score: 52.66  E-value: 2.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 111 EKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPrFAPDKALIVGDSlTSDIQ 189
Cdd:cd02588  101 RRLREAgYRLAILSNGSPDLIEDVVANAGLRDLFDAVLSAEDVRAYKPAPAVYELAAERLG-VPPDEILHVASH-AWDLA 178

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 492535814 190 GGKNTGIDTCWYN-PAGKTAQPALAANYEIRKLDEL 224
Cdd:cd02588  179 GARALGLRTAWINrPGEVPDPLGPAPDFVVPDLGEL 214
HAD_PGPase cd07512
haloacid dehalogenase-like superfamily phosphoglycolate phosphatase, similar to Rhodobacter ...
 44-196 9.74e-08

haloacid dehalogenase-like superfamily phosphoglycolate phosphatase, similar to Rhodobacter sphaeroides CbbZ; Phosphoglycolate phosphatase catalyzes the dephosphorylation of phosphoglycolate; its activity requires divalent cations, especially Mg++. This family belongs 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: 319815 [Multi-domain]  Cd Length: 214  Bit Score: 50.78  E-value: 9.74e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  44 DIYHTVNRTLwAAFERGEISKETVTSTRF-------SRLFAETGFAVNGASFSRDYQKALgEGYY--------LIDGAKE 108
Cdd:cd07512   16 DLHAALNAVL-AAEGLAPLSLAEVRSFVGhgapaliRRAFAAAGEDLDGPLHDALLARFL-DHYEadppgltrPYPGVIE 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 109 LCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIPRfAPDKALIVGDSLTsD 187
Cdd:cd07512   94 ALERLRAAgWRLAICTNKPEAPARALLSALGLADLFAAVVGGDTLPQRKPDPAPLRAAIRRLGG-DVSRALMVGDSET-D 171


                 ....*....
gi 492535814 188 IQGGKNTGI 196
Cdd:cd07512  172 AATARAAGV 180
Hydrolase_like pfam13242
HAD-hyrolase-like;
156-214 4.22e-07

HAD-hyrolase-like;


Pssm-ID: 433056 [Multi-domain]  Cd Length: 75  Bit Score: 46.07  E-value: 4.22e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 492535814  156 KPSRDYFRAVFRAIpRFAPDKALIVGDSLTSDIQGGKNTGIDTCWYnPAGKTAQPALAA 214
Cdd:pfam13242   4 KPNPGMLERALARL-GLDPERTVMIGDRLDTDILGAREAGARTILV-LTGVTRPADLEK 60
PRK13288 PRK13288
pyrophosphatase PpaX; Provisional
 104-229 8.43e-07

pyrophosphatase PpaX; Provisional


Pssm-ID: 237336 [Multi-domain]  Cd Length: 214  Bit Score: 48.10  E-value: 8.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 104 DGAKELCEKLSEK-YRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDyfrAVFRAIPRFA--PDKALIV 180
Cdd:PRK13288  85 ETVYETLKTLKKQgYKLGIVTTKMRDTVEMGLKLTGLDEFFDVVITLDDVEHAKPDPE---PVLKALELLGakPEEALMV 161

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 492535814 181 GDSlTSDIQGGKNTGIDTCW--YNPAGKTAQPALAANYEIRKLDELLPILE 229
Cdd:PRK13288 162 GDN-HHDILAGKNAGTKTAGvaWTIKGREYLEQYKPDFMLDKMSDLLAIVG 211
HAD_sEH-N_like cd02603
N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX ...
 53-198 1.10e-06

N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive; This family includes the N-terminal phosphatase domain of human soluble epoxide hydrolase (sEH). sEH is a bifunctional enzyme with two distinct enzyme activities, the C-terminal domain has epoxide hydrolysis activity and the N-terminal domain (Ntermphos), which belongs to this family, has lipid phosphatase activity. The latter prefers mono-phosphate esters, and lysophosphatidic acids (LPAs) are the best natural substrates found to date. In addition this family includes Gallus gallus sEH and Xenopus sEH which appears to lack phosphatase activity, and Escherichia coli YihX/HAD4 which selectively hydrolyzes alpha-Glucose-1-P, phosphatase, has significant phosphatase activity against pyridoxal phosphate, and has low beta phosphoglucomutase activity. This family belongs 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: 319790 [Multi-domain]  Cd Length: 195  Bit Score: 47.72  E-value: 1.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  53 LWAAFERGEISKEtvtstRFSRLFAE-TGFAVNGASFSRDYQKALGegyyLIDGAKELCEKLSEK-YRLYCVTNGVAATQ 130
Cdd:cd02603   44 AFLELERGRITEE-----EFWEELREeLGRPLSAELFEELVLAAVD----PNPEMLDLLEALRAKgYKVYLLSNTWPDHF 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492535814 131 YSRLSGS-GLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKALIVGDSLtSDIQGGKNTGIDT 198
Cdd:cd02603  115 KFQLELLpRRGDLFDGVVESCRLGVRKPDPEIYQLALERL-GVKPEEVLFIDDRE-ENVEAARALGIHA 181
HAD_type_II TIGR01428
2-haloalkanoic acid dehalogenase, type II; Catalyzes the hydrolytic dehalogenation of small ...
 103-205 6.37e-06

2-haloalkanoic acid dehalogenase, type II; Catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Belongs to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related.


Pssm-ID: 130495 [Multi-domain]  Cd Length: 198  Bit Score: 45.41  E-value: 6.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814  103 IDGAKELCEKlseKYRLYCVTNGVAATQYSRLSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKALIVGD 182
Cdd:TIGR01428  98 PAGLRALKER---GYRLAILSNGSPAMLKSLVKHAGLDDPFDAVLSADAVRAYKPAPQVYQLALEAL-GVPPDEVLFVAS 173

                          90       100
                  ....*....|....*....|...
gi 492535814  183 SLTsDIQGGKNTGIDTCWYNPAG 205
Cdd:TIGR01428 174 NPW-DLGGAKKFGFKTAWINRPG 195
COG5610 COG5610
Predicted sugar hydrolase, contains GT1 and HAD domains [General function prediction only];
134-204 2.28e-04

Predicted sugar hydrolase, contains GT1 and HAD domains [General function prediction only];


Pssm-ID: 444341 [Multi-domain]  Cd Length: 501  Bit Score: 41.72  E-value: 2.28e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492535814 134 LSGSGLDHYFSDVFVSETIGHQKPSRDYFRAVFRAIpRFAPDKALIVGDSLTSDIQGGKNTGIDTCWYNPA 204
Cdd:COG5610  151 LDRNGLGLLFDPLYVSSDYGLSKASGELFDYVLEEE-GVDPKQILHIGDNPRSDVQRPRKLGIQALHYPRA 220
HAD-SF-IIA TIGR01460
Haloacid Dehalogenase Superfamily Class (subfamily) IIA; This model represents one structural ...
 156-200 3.82e-04

Haloacid Dehalogenase Superfamily Class (subfamily) IIA; This model represents one structural subclass of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The classes are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Class I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Class II consists of sequences in which the capping domain is found between the second and third motifs. Class III sequences have no capping domain in iether of these positions. The Class IIA capping domain is predicted by PSI-PRED to consist of a mixed alpha-beta fold with the basic pattern: Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently, this subfamily encompasses a single equivalog model (TIGR01452) for the eukaryotic phosphoglycolate phosphatase, as well as four hypothetical equivalogs covering closely related sequences (TIGR01456 and TIGR01458 in eukaryotes, TIGR01457 in gram positive bacteria and TIGR01459 in gram negative bacteria). The Escherishia coli NagD gene and the Bacillus subtilus AraL gene are members of this subfamily but are not members of the any of the presently defined equivalogs within it. NagD is part of the NAG operon responsible for N-acetylglucosamine metabolism. The function of this gene is unknown. Genes from several organisms have been annotated as NagD, or NagD-like. However, without data on the presence of other members of this pathway, (such as in the case of Yersinia pestis) these assignments should not be given great weight. The AraL gene is similar: it is part of the L-arabinose operon, but the function is unknown. A gene from Halobacterium has been annotated as AraL, but no other Ara operon genes have been annotated. Many of the genes in this subfamily have been annotated as "pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273637 [Multi-domain]  Cd Length: 236  Bit Score: 40.39  E-value: 3.82e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 492535814  156 KPSRDYFRAVFRAIPRFAPDKALIVGDSLTSDIQGGKNTGIDTCW 200
Cdd:TIGR01460 188 KPSPAIYRAALNLLQARPERRDVMVGDNLRTDILGAKNAGFDTLL 232
HAD_YsbA-like cd07523
uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the ...
 102-199 2.91e-03

uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the uncharacterized Lactococcus lactis YsbA; The specific function of Lactococcus lactis YsbA is unknown. 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: 319825 [Multi-domain]  Cd Length: 173  Bit Score: 37.36  E-value: 2.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535814 102 LIDGAKELCEKLSEKY-RLYCVT---NGVaatqYSRLSGSGLDHYFSDVFVSETIGHQKP---SRDYFRAVFRaiprFAP 174
Cdd:cd07523   76 LFPGAKAVLRWIKEQGgKNFLMThrdHSA----LTILKKDGIASYFTEIVTSDNGFPRKPnpeAINYLLNKYQ----LNP 147

                         90       100
                 ....*....|....*....|....*
gi 492535814 175 DKALIVGDSlTSDIQGGKNTGIDTC 199
Cdd:cd07523  148 EETVMIGDR-ELDIEAGHNAGISTI 171
HAD-SF-IIA-hyp4 TIGR01459
HAD-superfamily class IIA hydrolase, TIGR01459; This hypothetical equivalog is a member of the ...
 136-200 6.76e-03

HAD-superfamily class IIA hydrolase, TIGR01459; This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram negative and primarily alpha proteobacteria. Only one sequence hase been annotated as other than "hypothetical." That one, from Brucella, is annotated as related to NagD, but only by sequence similarity and should be treated with some skepticism. (See comments for Class IIA subfamily model)


Pssm-ID: 130526 [Multi-domain]  Cd Length: 242  Bit Score: 36.79  E-value: 6.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492535814  136 GSGldhYFSDVFVSE---TIGHQKPSRDYFRAVFRAIPRFAPDKALIVGDSLTSDIQGGKNTGIDTCW 200
Cdd:TIGR01459 175 GAG---YYAELIKQLggkVIYSGKPYPAIFHKALKECSNIPKNRMLMVGDSFYTDILGANRLGIDTAL 239
 
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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