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Conserved domains on  [gi|752717955|ref|WP_041365079|]
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HD domain-containing protein [Neorhizobium galegae]

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 ...
 19-128 7.52e-14

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: 66.85  E-value: 7.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955  19 QFIRDTESELLFLHSSRVFLWGALMGERTGLkfDPELLYVAAMFHDIGLtSHYHESQRRFEVDGAFAASDFLRAYDIPER 98
Cdd:COG1418    9 KYLRTSYGQHDLQHSLRVAKLAGLIAAEEGA--DVEVAKRAALLHDIGK-AKDHEVEGSHAEIGAELARKYLESLGFPEE 85

                         90       100       110
                 ....*....|....*....|....*....|
gi 752717955  99 DVEKVWNAVALHTTPGIPEHMHPEIFLVQA 128
Cdd:COG1418   86 EIEAVVHAIEAHSFSGGIEPESLEAKIVQD 115
 
Name Accession Description Interval E-value
RnaY COG1418
HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal ...
 19-128 7.52e-14

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: 66.85  E-value: 7.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955  19 QFIRDTESELLFLHSSRVFLWGALMGERTGLkfDPELLYVAAMFHDIGLtSHYHESQRRFEVDGAFAASDFLRAYDIPER 98
Cdd:COG1418    9 KYLRTSYGQHDLQHSLRVAKLAGLIAAEEGA--DVEVAKRAALLHDIGK-AKDHEVEGSHAEIGAELARKYLESLGFPEE 85

                         90       100       110
                 ....*....|....*....|....*....|
gi 752717955  99 DVEKVWNAVALHTTPGIPEHMHPEIFLVQA 128
Cdd:COG1418   86 EIEAVVHAIEAHSFSGGIEPESLEAKIVQD 115
cyanamide_fam TIGR03401
HD domain protein, cyanamide hydratase family; Members of this protein family are known, so ...
 8-156 3.17e-11

HD domain protein, cyanamide hydratase family; Members of this protein family are known, so far, in the Ascomycota, a branch of the Fungi, and contain an HD domain (pfam01966), found typically in various metal-dependent phosphohydrolases. The only characterized member of this family, from the soil fungus Myrothecium verrucaria, is cyanamide hydratase (EC 4.2.1.69), a zinc-containing homohexamer that adds water to the fertilizer cyanamide (NCNH2), a nitrile compound, to produce urea (NH2-CO-NH2). Homologs are likely to be nitrile hydratases.


Pssm-ID: 188314  Cd Length: 228  Bit Score: 60.51  E-value: 3.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955    8 IPDSKLARDVTQFIRDTESELLFLHSSRVFLWGALMGERT--GLKFDPELLYVAAMFHDIGLTSHY-HESQRRFEVDGAF 84
Cdd:TIGR03401  35 LPDTPLVKFAQEYAKARLPPETYNHSLRVYYYGLAIARDQfpEWDLSDETWFLTCLLHDIGTTDENmTATKMSFEFYGGI 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 752717955   85 AASDFLR-AYDIPERDVEKVWNAVALHTTPGIPEHMHPEIFLVQAGAGMDVAGRGYEGFSDEQRHEVVAAYPR 156
Cdd:TIGR03401 115 LALDVLKeQTGANQDQAEAVAEAIIRHQDLGVDGTITTLGQLLQLATIFDNVGANTDLVHPDTVDAVNEAYPR 187
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 29-134 1.89e-08

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: 51.14  E-value: 1.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955    29 LFLHSSRVFLWGALMGERTGLkFDPELLYVAAMFHDIGLTSHYHESQRRFEV--DGAFAASDFLRAYDIPERDVEKVWNA 106
Cdd:smart00471   5 VFEHSLRVAQLAAALAEELGL-LDIELLLLAALLHDIGKPGTPDSFLVKTSVleDHHFIGAEILLEEEEPRILEEILRTA 83

                           90       100
                   ....*....|....*....|....*...
gi 752717955   107 VALHTTPGIPEHMHPEIFLVQAGAGMDV 134
Cdd:smart00471  84 ILSHHERPDGLRGEPITLEARIVKVADR 111
HD pfam01966
HD domain; HD domains are metal dependent phosphohydrolases.
 32-123 5.79e-08

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 460398 [Multi-domain]  Cd Length: 110  Bit Score: 49.16  E-value: 5.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955   32 HSSRVFLWGALMGERTGlKFDPELLYVAAMFHDIGLTSHYHESQRRFEVDG-AFAASDFLRAYDIPERdVEKVWNAVALH 110
Cdd:pfam01966   4 HSLRVALLARELAEELG-ELDRELLLLAALLHDIGKGPFGDEKPEFEIFLGhAVVGAEILRELEKRLG-LEDVLKLILEH 81

                          90
                  ....*....|...
gi 752717955  111 TTPGIPEHMHPEI 123
Cdd:pfam01966  82 HESWEGAGYPEEI 94
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
 29-97 8.23e-04

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 38.47  E-value: 8.23e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 752717955  29 LFLHSSRVFLWGALMGERTGL-KFDPELLYVAAMFHDIG---LTSHYHESQRRFEVDGAFAASDFLRAYDIPE 97
Cdd:cd00077    3 RFEHSLRVAQLARRLAEELGLsEEDIELLRLAALLHDIGkpgTPDAITEEESELEKDHAIVGAEILRELLLEE 75
glnD PRK00227
[protein-PII] uridylyltransferase;
53-112 9.06e-03

[protein-PII] uridylyltransferase;


Pssm-ID: 178937 [Multi-domain]  Cd Length: 693  Bit Score: 36.67  E-value: 9.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955  53 PELLYVAAMFHDIGltshyHESQRRFEVDGAFAASDFLRAYDIPERDVEKVWNAVALHTT 112
Cdd:PRK00227 402 PDLLLLGALYHDIG-----KGYPRPHEQVGAEMVARAARRMGLNLRDRAVVQTLVAEHTT 456
 
Name Accession Description Interval E-value
RnaY COG1418
HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal ...
 19-128 7.52e-14

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: 66.85  E-value: 7.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955  19 QFIRDTESELLFLHSSRVFLWGALMGERTGLkfDPELLYVAAMFHDIGLtSHYHESQRRFEVDGAFAASDFLRAYDIPER 98
Cdd:COG1418    9 KYLRTSYGQHDLQHSLRVAKLAGLIAAEEGA--DVEVAKRAALLHDIGK-AKDHEVEGSHAEIGAELARKYLESLGFPEE 85

                         90       100       110
                 ....*....|....*....|....*....|
gi 752717955  99 DVEKVWNAVALHTTPGIPEHMHPEIFLVQA 128
Cdd:COG1418   86 EIEAVVHAIEAHSFSGGIEPESLEAKIVQD 115
cyanamide_fam TIGR03401
HD domain protein, cyanamide hydratase family; Members of this protein family are known, so ...
 8-156 3.17e-11

HD domain protein, cyanamide hydratase family; Members of this protein family are known, so far, in the Ascomycota, a branch of the Fungi, and contain an HD domain (pfam01966), found typically in various metal-dependent phosphohydrolases. The only characterized member of this family, from the soil fungus Myrothecium verrucaria, is cyanamide hydratase (EC 4.2.1.69), a zinc-containing homohexamer that adds water to the fertilizer cyanamide (NCNH2), a nitrile compound, to produce urea (NH2-CO-NH2). Homologs are likely to be nitrile hydratases.


Pssm-ID: 188314  Cd Length: 228  Bit Score: 60.51  E-value: 3.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955    8 IPDSKLARDVTQFIRDTESELLFLHSSRVFLWGALMGERT--GLKFDPELLYVAAMFHDIGLTSHY-HESQRRFEVDGAF 84
Cdd:TIGR03401  35 LPDTPLVKFAQEYAKARLPPETYNHSLRVYYYGLAIARDQfpEWDLSDETWFLTCLLHDIGTTDENmTATKMSFEFYGGI 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 752717955   85 AASDFLR-AYDIPERDVEKVWNAVALHTTPGIPEHMHPEIFLVQAGAGMDVAGRGYEGFSDEQRHEVVAAYPR 156
Cdd:TIGR03401 115 LALDVLKeQTGANQDQAEAVAEAIIRHQDLGVDGTITTLGQLLQLATIFDNVGANTDLVHPDTVDAVNEAYPR 187
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 29-134 1.89e-08

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: 51.14  E-value: 1.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955    29 LFLHSSRVFLWGALMGERTGLkFDPELLYVAAMFHDIGLTSHYHESQRRFEV--DGAFAASDFLRAYDIPERDVEKVWNA 106
Cdd:smart00471   5 VFEHSLRVAQLAAALAEELGL-LDIELLLLAALLHDIGKPGTPDSFLVKTSVleDHHFIGAEILLEEEEPRILEEILRTA 83

                           90       100
                   ....*....|....*....|....*...
gi 752717955   107 VALHTTPGIPEHMHPEIFLVQAGAGMDV 134
Cdd:smart00471  84 ILSHHERPDGLRGEPITLEARIVKVADR 111
HD pfam01966
HD domain; HD domains are metal dependent phosphohydrolases.
 32-123 5.79e-08

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 460398 [Multi-domain]  Cd Length: 110  Bit Score: 49.16  E-value: 5.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955   32 HSSRVFLWGALMGERTGlKFDPELLYVAAMFHDIGLTSHYHESQRRFEVDG-AFAASDFLRAYDIPERdVEKVWNAVALH 110
Cdd:pfam01966   4 HSLRVALLARELAEELG-ELDRELLLLAALLHDIGKGPFGDEKPEFEIFLGhAVVGAEILRELEKRLG-LEDVLKLILEH 81

                          90
                  ....*....|...
gi 752717955  111 TTPGIPEHMHPEI 123
Cdd:pfam01966  82 HESWEGAGYPEEI 94
HDGYP COG2206
HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal ...
 23-66 7.48e-04

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: 39.57  E-value: 7.48e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 752717955  23 DTESELLFLHSSRVFLWGALMGERTGL-KFDPELLYVAAMFHDIG 66
Cdd:COG2206  138 DAKDPYTYGHSVRVAVLALALARELGLsEEELEDLGLAALLHDIG 182
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
 29-97 8.23e-04

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 38.47  E-value: 8.23e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 752717955  29 LFLHSSRVFLWGALMGERTGL-KFDPELLYVAAMFHDIG---LTSHYHESQRRFEVDGAFAASDFLRAYDIPE 97
Cdd:cd00077    3 RFEHSLRVAQLARRLAEELGLsEEDIELLRLAALLHDIGkpgTPDAITEEESELEKDHAIVGAEILRELLLEE 75
GlnD COG2844
UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, ...
 52-66 7.75e-03

UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms];


Pssm-ID: 442092 [Multi-domain]  Cd Length: 864  Bit Score: 36.66  E-value: 7.75e-03
                         10
                 ....*....|....*
gi 752717955  52 DPELLYVAAMFHDIG 66
Cdd:COG2844  475 KPELLYLAALFHDIA 489
HDOD pfam08668
HDOD domain;
17-66 8.25e-03

HDOD domain;


Pssm-ID: 430141 [Multi-domain]  Cd Length: 196  Bit Score: 36.05  E-value: 8.25e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 752717955   17 VTQFIRDTESEL-----LFLHSSRVFLWGALMGERTGLKfDPELLYVAAMFHDIG 66
Cdd:pfam08668  78 VKRIFRGTPPLGfdlkgFWEHSLACALAARLLARRLGLD-DPEEAFLAGLLHDIG 131
glnD PRK00227
[protein-PII] uridylyltransferase;
53-112 9.06e-03

[protein-PII] uridylyltransferase;


Pssm-ID: 178937 [Multi-domain]  Cd Length: 693  Bit Score: 36.67  E-value: 9.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 752717955  53 PELLYVAAMFHDIGltshyHESQRRFEVDGAFAASDFLRAYDIPERDVEKVWNAVALHTT 112
Cdd:PRK00227 402 PDLLLLGALYHDIG-----KGYPRPHEQVGAEMVARAARRMGLNLRDRAVVQTLVAEHTT 456
 
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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