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Conserved domains on  [gi|497172012|ref|WP_009496189|]
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MULTISPECIES: HD domain-containing protein [Weissella]

Protein Classification

HD domain-containing protein( domain architecture ID 707124)

HD domain-containing protein may function as a metal dependent phosphohydrolase; similar to Bacillus subtilis phosphohydrolase YueE

CATH:  3.30.70.1370|1.20.58.1910
EC:  3.1.-.-
Gene Ontology:  GO:0046872|GO:0016787
PubMed:  9868367
SCOP:  4000705

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RnaY super family cl28470
HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal ...
 22-132 3.51e-08

HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal structure and biogenesis, General function prediction only];


The actual alignment was detected with superfamily member COG1418:

Pssm-ID: 441028 [Multi-domain]  Cd Length: 191  Bit Score: 50.28  E-value: 3.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497172012  22 AVQQLSDYVQHHHSDRLTHSISVSYRSYRIAKRLDLNATAVARAGILHDLFyyDWRDTKFESGthayvHPRIALRNAEKL 101
Cdd:COG1418    4 LIKLVKYLRTSYGQHDLQHSLRVAKLAGLIAAEEGADVEVAKRAALLHDIG--KAKDHEVEGS-----HAEIGAELARKY 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497172012 102 -------TTLSPMEKDIIIKHMWGATAAfPKYRESLLV 132
Cdd:COG1418   77 leslgfpEEEIEAVVHAIEAHSFSGGIE-PESLEAKIV 113
 
Name Accession Description Interval E-value
RnaY COG1418
HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal ...
 22-132 3.51e-08

HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal structure and biogenesis, General function prediction only];


Pssm-ID: 441028 [Multi-domain]  Cd Length: 191  Bit Score: 50.28  E-value: 3.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497172012  22 AVQQLSDYVQHHHSDRLTHSISVSYRSYRIAKRLDLNATAVARAGILHDLFyyDWRDTKFESGthayvHPRIALRNAEKL 101
Cdd:COG1418    4 LIKLVKYLRTSYGQHDLQHSLRVAKLAGLIAAEEGADVEVAKRAALLHDIG--KAKDHEVEGS-----HAEIGAELARKY 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497172012 102 -------TTLSPMEKDIIIKHMWGATAAfPKYRESLLV 132
Cdd:COG1418   77 leslgfpEEEIEAVVHAIEAHSFSGGIE-PESLEAKIV 113
HD pfam01966
HD domain; HD domains are metal dependent phosphohydrolases.
 37-141 2.69e-03

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 460398 [Multi-domain]  Cd Length: 110  Bit Score: 35.67  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497172012   37 RLTHSISVSYRSYRIAKRLD-LNATAVARAGILHDLFYYDWRDTKFESGTHaYVHPRIALRNAEKLTTLSPME--KDIII 113
Cdd:pfam01966   1 RLEHSLRVALLARELAEELGeLDRELLLLAALLHDIGKGPFGDEKPEFEIF-LGHAVVGAEILRELEKRLGLEdvLKLIL 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 497172012  114 KH---MWGATAAFPKYRESLLVDIVDDYLAI 141
Cdd:pfam01966  80 EHhesWEGAGYPEEISLEARIVKLADRLDAL 110
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 33-71 5.58e-03

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 34.96  E-value: 5.58e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 497172012    33 HHSDRLTHSISVSYRSYRIAKRLDL-NATAVARAGILHDL 71
Cdd:smart00471   1 SDYHVFEHSLRVAQLAAALAEELGLlDIELLLLAALLHDI 40
 
Name Accession Description Interval E-value
RnaY COG1418
HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal ...
 22-132 3.51e-08

HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal structure and biogenesis, General function prediction only];


Pssm-ID: 441028 [Multi-domain]  Cd Length: 191  Bit Score: 50.28  E-value: 3.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497172012  22 AVQQLSDYVQHHHSDRLTHSISVSYRSYRIAKRLDLNATAVARAGILHDLFyyDWRDTKFESGthayvHPRIALRNAEKL 101
Cdd:COG1418    4 LIKLVKYLRTSYGQHDLQHSLRVAKLAGLIAAEEGADVEVAKRAALLHDIG--KAKDHEVEGS-----HAEIGAELARKY 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497172012 102 -------TTLSPMEKDIIIKHMWGATAAfPKYRESLLV 132
Cdd:COG1418   77 leslgfpEEEIEAVVHAIEAHSFSGGIE-PESLEAKIV 113
HD pfam01966
HD domain; HD domains are metal dependent phosphohydrolases.
 37-141 2.69e-03

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 460398 [Multi-domain]  Cd Length: 110  Bit Score: 35.67  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497172012   37 RLTHSISVSYRSYRIAKRLD-LNATAVARAGILHDLFYYDWRDTKFESGTHaYVHPRIALRNAEKLTTLSPME--KDIII 113
Cdd:pfam01966   1 RLEHSLRVALLARELAEELGeLDRELLLLAALLHDIGKGPFGDEKPEFEIF-LGHAVVGAEILRELEKRLGLEdvLKLIL 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 497172012  114 KH---MWGATAAFPKYRESLLVDIVDDYLAI 141
Cdd:pfam01966  80 EHhesWEGAGYPEEISLEARIVKLADRLDAL 110
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 33-71 5.58e-03

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 34.96  E-value: 5.58e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 497172012    33 HHSDRLTHSISVSYRSYRIAKRLDL-NATAVARAGILHDL 71
Cdd:smart00471   1 SDYHVFEHSLRVAQLAAALAEELGLlDIELLLLAALLHDI 40
HDGYP COG2206
HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal ...
 1-71 8.08e-03

HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal transduction mechanisms];


Pssm-ID: 441808 [Multi-domain]  Cd Length: 316  Bit Score: 35.72  E-value: 8.08e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497172012   1 MQNWQNDQAYREIVDELLEKpAVQQLSDYVQHHHSDRLTHSISVSYRSYRIAKRLDLNAT---AVARAGILHDL 71
Cdd:COG2206  109 LGLLEELKKLVEELDELLPD-ALLALLAALDAKDPYTYGHSVRVAVLALALARELGLSEEeleDLGLAALLHDI 181
 
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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