NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2495702874|ref|WP_279946470|]
View 

hypothetical protein [Stenotrophomonas sp. GD03777]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YorC super family cl42549
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
26-148 1.62e-15

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


The actual alignment was detected with superfamily member COG4502:

Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 70.67  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  26 SRRTIYVDLDGVMADFDAAFPALF------GLDHRVLADDEMWGHIN-----------SHPSFFRDLPPMQGAVEFFHSI 88
Cdd:COG4502     1 MKPRIAVDMDGVLADFYAAFLDIYnkeygtNLTLEDLDGWDLWELVPpehrerireflNEPGFFRDLPPIPGAQEVLKEL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2495702874  89 HHLNPV-ILTACPksNYPLAAMQKRQWVREHlsatclvLP-------VLGGrHKPLFmhqPGDVLIDD 148
Cdd:COG4502    81 SDKYEVyIVTAAM--EFPNSLEEKYEWLDEH-------FPfipwqniIFCG-DKSLV---GGDYLIDD 135
 
Name Accession Description Interval E-value
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
26-148 1.62e-15

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 70.67  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  26 SRRTIYVDLDGVMADFDAAFPALF------GLDHRVLADDEMWGHIN-----------SHPSFFRDLPPMQGAVEFFHSI 88
Cdd:COG4502     1 MKPRIAVDMDGVLADFYAAFLDIYnkeygtNLTLEDLDGWDLWELVPpehrerireflNEPGFFRDLPPIPGAQEVLKEL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2495702874  89 HHLNPV-ILTACPksNYPLAAMQKRQWVREHlsatclvLP-------VLGGrHKPLFmhqPGDVLIDD 148
Cdd:COG4502    81 SDKYEVyIVTAAM--EFPNSLEEKYEWLDEH-------FPfipwqniIFCG-DKSLV---GGDYLIDD 135
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 29-148 3.02e-09

5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. 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: 319786  Cd Length: 161  Bit Score: 53.55  E-value: 3.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  29 TIYVDLDGVMADFDAAF-----------PALFGLDHRVLADDEMWGHIN---------SHPSFFRDLPPMQGAVEFFH-- 86
Cdd:cd02587     2 VILVDMDGVLADFEGALvrairerfpdePHVLLESRRGFWVIEQYKAPElsrkaadilEEPGFFRNLEPIPGAVEALRel 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2495702874  87 SIHHLNPVILTAcPKSNYPLAAMQKRQWVREHLSATCLVLPVLGGRhKPLFMhqpGDVLIDD 148
Cdd:cd02587    82 SDEGTDVYICTS-PLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRD-KTVVL---ADILIDD 138
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 27-152 6.61e-09

5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known.


Pssm-ID: 284381 [Multi-domain]  Cd Length: 180  Bit Score: 52.99  E-value: 6.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  27 RRTIYVDLDGVMADFDAAFPALFGLD-HRVLADDE-----------------MWGHINsHPSFFRDLPPMQGAVEFFH-- 86
Cdd:pfam06941   1 RSIIGVDLDGVCADFYGRMRQIANEWfERPLLPEEvsswgwsewtnpeqydsLHRFVT-QPGFFSDLEPIPGAREYLRql 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2495702874  87 -SIHHLnpVILTACPKSnYPLAAMQKRQWVREHLSATCLVLPVLGGRHKPLfmhqPGDVLIDDFEAN 152
Cdd:pfam06941  80 sDEGRI--VIITHRLFQ-HYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQV----RGDIYIDDSPEN 139
 
Name Accession Description Interval E-value
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
26-148 1.62e-15

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 70.67  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  26 SRRTIYVDLDGVMADFDAAFPALF------GLDHRVLADDEMWGHIN-----------SHPSFFRDLPPMQGAVEFFHSI 88
Cdd:COG4502     1 MKPRIAVDMDGVLADFYAAFLDIYnkeygtNLTLEDLDGWDLWELVPpehrerireflNEPGFFRDLPPIPGAQEVLKEL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2495702874  89 HHLNPV-ILTACPksNYPLAAMQKRQWVREHlsatclvLP-------VLGGrHKPLFmhqPGDVLIDD 148
Cdd:COG4502    81 SDKYEVyIVTAAM--EFPNSLEEKYEWLDEH-------FPfipwqniIFCG-DKSLV---GGDYLIDD 135
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 29-148 3.02e-09

5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. 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: 319786  Cd Length: 161  Bit Score: 53.55  E-value: 3.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  29 TIYVDLDGVMADFDAAF-----------PALFGLDHRVLADDEMWGHIN---------SHPSFFRDLPPMQGAVEFFH-- 86
Cdd:cd02587     2 VILVDMDGVLADFEGALvrairerfpdePHVLLESRRGFWVIEQYKAPElsrkaadilEEPGFFRNLEPIPGAVEALRel 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2495702874  87 SIHHLNPVILTAcPKSNYPLAAMQKRQWVREHLSATCLVLPVLGGRhKPLFMhqpGDVLIDD 148
Cdd:cd02587    82 SDEGTDVYICTS-PLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRD-KTVVL---ADILIDD 138
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 27-152 6.61e-09

5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known.


Pssm-ID: 284381 [Multi-domain]  Cd Length: 180  Bit Score: 52.99  E-value: 6.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2495702874  27 RRTIYVDLDGVMADFDAAFPALFGLD-HRVLADDE-----------------MWGHINsHPSFFRDLPPMQGAVEFFH-- 86
Cdd:pfam06941   1 RSIIGVDLDGVCADFYGRMRQIANEWfERPLLPEEvsswgwsewtnpeqydsLHRFVT-QPGFFSDLEPIPGAREYLRql 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2495702874  87 -SIHHLnpVILTACPKSnYPLAAMQKRQWVREHLSATCLVLPVLGGRHKPLfmhqPGDVLIDDFEAN 152
Cdd:pfam06941  80 sDEGRI--VIITHRLFQ-HYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQV----RGDIYIDDSPEN 139
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH