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Conserved domains on  [gi|1252953592|ref|WP_096863975|]
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MULTISPECIES: ribonuclease T [Providencia]

Protein Classification

ribonuclease T( domain architecture ID 10150094)

ribonuclease T is a 3'-5' exonuclease implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA

CATH:  3.30.420.10
EC:  3.1.13.-
Gene Ontology:  GO:0008033|GO:0016896|GO:0003676
PubMed:  11988770|11222749|8506149
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 13-201 2.35e-125

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


:

Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 351.98  E-value: 2.35e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  13 RFRGYYPVVIDVETGGFNAKTDGLLEIAAITLKMDKDGWLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNPLRGAVSE 92
Cdd:cd06134     1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  93 YEALHAIFKVIRKGMKNTDCNRAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFATFDTAALSGLVFGQTILAKACVSAG 172
Cdd:cd06134    81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160

                         170       180
                  ....*....|....*....|....*....
gi 1252953592 173 IPFDGKQAHGALYDTNRTALLFCEIVNKW 201
Cdd:cd06134   161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189
 
Name Accession Description Interval E-value
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 13-201 2.35e-125

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 351.98  E-value: 2.35e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  13 RFRGYYPVVIDVETGGFNAKTDGLLEIAAITLKMDKDGWLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNPLRGAVSE 92
Cdd:cd06134     1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  93 YEALHAIFKVIRKGMKNTDCNRAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFATFDTAALSGLVFGQTILAKACVSAG 172
Cdd:cd06134    81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160

                         170       180
                  ....*....|....*....|....*....
gi 1252953592 173 IPFDGKQAHGALYDTNRTALLFCEIVNKW 201
Cdd:cd06134   161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189
RNaseT TIGR01298
ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in ...
 10-208 1.54e-121

ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. [Transcription, RNA processing]


Pssm-ID: 188129 [Multi-domain]  Cd Length: 200  Bit Score: 342.58  E-value: 1.54e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  10 LVNRFRGYYPVVIDVETGGFNAKTDGLLEIAAITLKMDKDGWLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNPLRGA 89
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  90 VSEYEALHAIFKVIRKGMKNTDCNRAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFATFDTAALSGLVFGQTILAKACV 169
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1252953592 170 SAGIPFDGKQAHGALYDTNRTALLFCEIVNKWKKLGGWP 208
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNRWKELGGWP 199
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 20-199 5.13e-42

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 139.54  E-value: 5.13e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKmdkDGWLSmdETLHFHVEPFEgaNLEPSALAFTGIDPTNpLRGAVSEYEALHAI 99
Cdd:COG0847     3 VVLDTETTGLDPAKDRIIEIGAVKVD---DGRIV--ETFHTLVNPER--PIPPEATAIHGITDED-VADAPPFAEVLPEL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRKgmkntdcnrAIIVAHNANFDHSFVMNAAERAGLKRNPFHpfaTFDTAALSGLVF---GQTILAKACVSAGIPFD 176
Cdd:COG0847    75 LEFLGG---------AVLVAHNAAFDLGFLNAELRRAGLPLPPFP---VLDTLRLARRLLpglPSYSLDALCERLGIPFD 142

                         170       180
                  ....*....|....*....|...
gi 1252953592 177 GkqAHGALYDTNRTALLFCEIVN 199
Cdd:COG0847   143 E--RHRALADAEATAELFLALLR 163
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 20-194 4.13e-30

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 108.98  E-value: 4.13e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKMDKdgwLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNpLRGAVSEYEALHAI 99
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGE---NEIGETFHTYVKPTRLPKLTDECTKFTGITQAM-LDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRKGMkntdcnraIIVAHNANFDHSFVMNAAERAGL----KRNPFHPFATFDTAALSGlvFGQTILAKACVSAGIPF 175
Cdd:pfam00929  77 LEFLRKGN--------LLVAHNASFDVGFLRYDDKRFLKkpmpKLNPVIDTLILDKATYKE--LPGRSLDALAEKLGLEH 146

                         170
                  ....*....|....*....
gi 1252953592 176 DGKqAHGALYDTNRTALLF 194
Cdd:pfam00929 147 IGR-AHRALDDARATAKLF 164
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 18-202 1.52e-27

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 102.76  E-value: 1.52e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   18 YPVVIDVETGGFNAKTDGLLEIAAITLKMDKdgwlsMDETLHFHVEPFEgaNLEPSALAFTGIDPtNPLRGAVSEYEALH 97
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE-----IIEVFDTYVKPDR--PITDYATEIHGITP-EMLDDAPTFEEVLE 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   98 AIFKVIRKGmkntdcnraIIVAHN-ANFDHSFVMNAAERAGLKRNPFHPfaTFDTAALSGLVFGQTI---LAKACVSAGI 173
Cdd:smart00479  73 ELLEFLRGR---------ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGLPkysLKKLAKRLLL 141

                          170       180
                   ....*....|....*....|....*....
gi 1252953592  174 PFDGKqAHGALYDTNRTALLFCEIVNKWK 202
Cdd:smart00479 142 EVIQR-AHRALDDARATAKLFKKLLERLE 169
polC PRK00448
DNA polymerase III PolC; Validated
 20-205 1.14e-15

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 74.87  E-value: 1.14e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   20 VVIDVETGGFNAKTDGLLEIAAItlKMdKDGwlSMDETLHFHVEPfeGANLEPSALAFTGIDpTNPLRGAVSEYEALhai 99
Cdd:PRK00448   422 VVFDVETTGLSAVYDEIIEIGAV--KI-KNG--EIIDKFEFFIKP--GHPLSAFTTELTGIT-DDMVKDAPSIEEVL--- 490

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  100 fKVIRKGMKNTdcnraIIVAHNANFDHSFVMNAAERAGLKR--NPFhpfatFDTAALSGLVF------GQTILAKacvSA 171
Cdd:PRK00448   491 -PKFKEFCGDS-----ILVAHNASFDVGFINTNYEKLGLEKikNPV-----IDTLELSRFLYpelkshRLNTLAK---KF 556

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1252953592  172 GIPFDgkQAHGALYDTNRTALLFCEIVNKWKKLG 205
Cdd:PRK00448   557 GVELE--HHHRADYDAEATAYLLIKFLKDLKEKG 588
 
Name Accession Description Interval E-value
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 13-201 2.35e-125

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 351.98  E-value: 2.35e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  13 RFRGYYPVVIDVETGGFNAKTDGLLEIAAITLKMDKDGWLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNPLRGAVSE 92
Cdd:cd06134     1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  93 YEALHAIFKVIRKGMKNTDCNRAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFATFDTAALSGLVFGQTILAKACVSAG 172
Cdd:cd06134    81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160

                         170       180
                  ....*....|....*....|....*....
gi 1252953592 173 IPFDGKQAHGALYDTNRTALLFCEIVNKW 201
Cdd:cd06134   161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189
RNaseT TIGR01298
ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in ...
 10-208 1.54e-121

ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. [Transcription, RNA processing]


Pssm-ID: 188129 [Multi-domain]  Cd Length: 200  Bit Score: 342.58  E-value: 1.54e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  10 LVNRFRGYYPVVIDVETGGFNAKTDGLLEIAAITLKMDKDGWLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNPLRGA 89
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  90 VSEYEALHAIFKVIRKGMKNTDCNRAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFATFDTAALSGLVFGQTILAKACV 169
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1252953592 170 SAGIPFDGKQAHGALYDTNRTALLFCEIVNKWKKLGGWP 208
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNRWKELGGWP 199
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 20-199 5.13e-42

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 139.54  E-value: 5.13e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKmdkDGWLSmdETLHFHVEPFEgaNLEPSALAFTGIDPTNpLRGAVSEYEALHAI 99
Cdd:COG0847     3 VVLDTETTGLDPAKDRIIEIGAVKVD---DGRIV--ETFHTLVNPER--PIPPEATAIHGITDED-VADAPPFAEVLPEL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRKgmkntdcnrAIIVAHNANFDHSFVMNAAERAGLKRNPFHpfaTFDTAALSGLVF---GQTILAKACVSAGIPFD 176
Cdd:COG0847    75 LEFLGG---------AVLVAHNAAFDLGFLNAELRRAGLPLPPFP---VLDTLRLARRLLpglPSYSLDALCERLGIPFD 142

                         170       180
                  ....*....|....*....|...
gi 1252953592 177 GkqAHGALYDTNRTALLFCEIVN 199
Cdd:COG0847   143 E--RHRALADAEATAELFLALLR 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 20-205 7.41e-31

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 111.39  E-value: 7.41e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAItlKMdKDGWLSmdETLHFHVEPfeGANLEPSALAFTGIDPtNPLRGAVSEYEALHAI 99
Cdd:COG2176    11 VVFDLETTGLSPKKDEIIEIGAV--KV-ENGEIV--DRFSTLVNP--GRPIPPFITELTGITD-EMVADAPPFEEVLPEF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRkgmkntDCnraIIVAHNANFDHSFVMNAAERAGLK-RNPFhpfatFDTAALSGLVFGQTI---LAKACVSAGIPF 175
Cdd:COG2176    83 LEFLG------DA---VLVAHNASFDLGFLNAALKRLGLPfDNPV-----LDTLELARRLLPELKsykLDTLAERLGIPL 148

                         170       180       190
                  ....*....|....*....|....*....|
gi 1252953592 176 DgkQAHGALYDTNRTALLFCEIVNKWKKLG 205
Cdd:COG2176   149 E--DRHRALGDAEATAELFLKLLEKLEEKG 176
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 20-194 4.13e-30

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 108.98  E-value: 4.13e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKMDKdgwLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNpLRGAVSEYEALHAI 99
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGE---NEIGETFHTYVKPTRLPKLTDECTKFTGITQAM-LDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRKGMkntdcnraIIVAHNANFDHSFVMNAAERAGL----KRNPFHPFATFDTAALSGlvFGQTILAKACVSAGIPF 175
Cdd:pfam00929  77 LEFLRKGN--------LLVAHNASFDVGFLRYDDKRFLKkpmpKLNPVIDTLILDKATYKE--LPGRSLDALAEKLGLEH 146

                         170
                  ....*....|....*....
gi 1252953592 176 DGKqAHGALYDTNRTALLF 194
Cdd:pfam00929 147 IGR-AHRALDDARATAKLF 164
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 18-202 1.52e-27

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 102.76  E-value: 1.52e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   18 YPVVIDVETGGFNAKTDGLLEIAAITLKMDKdgwlsMDETLHFHVEPFEgaNLEPSALAFTGIDPtNPLRGAVSEYEALH 97
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE-----IIEVFDTYVKPDR--PITDYATEIHGITP-EMLDDAPTFEEVLE 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   98 AIFKVIRKGmkntdcnraIIVAHN-ANFDHSFVMNAAERAGLKRNPFHPfaTFDTAALSGLVFGQTI---LAKACVSAGI 173
Cdd:smart00479  73 ELLEFLRGR---------ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGLPkysLKKLAKRLLL 141

                          170       180
                   ....*....|....*....|....*....
gi 1252953592  174 PFDGKqAHGALYDTNRTALLFCEIVNKWK 202
Cdd:smart00479 142 EVIQR-AHRALDDARATAKLFKKLLERLE 169
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 20-194 8.97e-24

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 92.36  E-value: 8.97e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAItlKMDKDGWLSmdETLHFHVEPfeGANLEPSALAFTGIDPTnPLRGAVSEYEALHAI 99
Cdd:cd06127     1 VVFDTETTGLDPKKDRIIEIGAV--KVDGGIEIV--ERFETLVNP--GRPIPPEATAIHGITDE-MLADAPPFEEVLPEF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRkgmkntdcnRAIIVAHNANFDHSFVMNAAERAGLkrnPFHPFATFDTAALSGLVFGQTI----LAKACVSAGIPF 175
Cdd:cd06127    74 LEFLG---------GRVLVAHNASFDLRFLNRELRRLGG---PPLPNPWIDTLRLARRLLPGLRshrlGLLLAERYGIPL 141

                         170
                  ....*....|....*....
gi 1252953592 176 DgkQAHGALYDTNRTALLF 194
Cdd:cd06127   142 E--GAHRALADALATAELL 158
polC PRK00448
DNA polymerase III PolC; Validated
 20-205 1.14e-15

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 74.87  E-value: 1.14e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   20 VVIDVETGGFNAKTDGLLEIAAItlKMdKDGwlSMDETLHFHVEPfeGANLEPSALAFTGIDpTNPLRGAVSEYEALhai 99
Cdd:PRK00448   422 VVFDVETTGLSAVYDEIIEIGAV--KI-KNG--EIIDKFEFFIKP--GHPLSAFTTELTGIT-DDMVKDAPSIEEVL--- 490

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  100 fKVIRKGMKNTdcnraIIVAHNANFDHSFVMNAAERAGLKR--NPFhpfatFDTAALSGLVF------GQTILAKacvSA 171
Cdd:PRK00448   491 -PKFKEFCGDS-----ILVAHNASFDVGFINTNYEKLGLEKikNPV-----IDTLELSRFLYpelkshRLNTLAK---KF 556

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1252953592  172 GIPFDgkQAHGALYDTNRTALLFCEIVNKWKKLG 205
Cdd:PRK00448   557 GVELE--HHHRADYDAEATAYLLIKFLKDLKEKG 588
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 20-186 8.26e-09

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 52.92  E-value: 8.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKT-DGLLEIAAITLKmdkDGWLSmDETLHFHVEPfeGANLEPSALAFTGIDptnplrgavSEYEALHA 98
Cdd:cd06131     2 IVLDTETTGLDPREgHRIIEIGCVELI---NRRLT-GNTFHVYINP--ERDIPEEAFKVHGIT---------DEFLADKP 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  99 IFKVIRKGMKNTdCNRAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFATFDTAALSGLVF-GQTI-LAKACVSAGIPFD 176
Cdd:cd06131    67 KFAEIADEFLDF-IRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFpGKPNsLDALCKRFGIDNS 145

                         170
                  ....*....|
gi 1252953592 177 GKQAHGALYD 186
Cdd:cd06131   146 HRTLHGALLD 155
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 12-204 8.89e-09

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 54.57  E-value: 8.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  12 NRFrgyypVVIDVETGGfNA--KTDGLLEIAAITLKMDKdgwlsMDETLHFHVEPfeganlEPSALAF----TGIDPtnp 85
Cdd:PRK08074    3 KRF-----VVVDLETTG-NSpkKGDKIIQIAAVVVEDGE-----ILERFSSFVNP------ERPIPPFitelTGISE--- 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  86 lrGAVSEYEALHAIFKVIRKGMKNtdcnrAIIVAHNANFDHSFVMNAAERAGLkrNPFHpFATFDTAALSGLVF-GQ--- 161
Cdd:PRK08074   63 --EMVKQAPLFEDVAPEIVELLEG-----AYFVAHNVHFDLNFLNEELERAGY--TEIH-CPKLDTVELARILLpTAesy 132

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1252953592 162 --TILAKacvSAGIPFDgkQAHGALYDTNRTALLFCEIVNKWKKL 204
Cdd:PRK08074  133 klRDLSE---ELGLEHD--QPHRADSDAEVTAELFLQLLNKLERL 172
PRK07740 PRK07740
hypothetical protein; Provisional
 1-205 1.23e-07

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 50.44  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592   1 MSEKNNPNALVNRFRGYYPVVIDVETGGFN-AKTDGLLEIAAITLKmdkdGWLSMDETLHFHVEPfeGANLEPSALAFTG 79
Cdd:PRK07740   43 QKEAKRDDVLDIPLTDLPFVVFDLETTGFSpQQGDEILSIGAVKTK----GGEVETDTFYSLVKP--KRPIPEHILELTG 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  80 IdpTNP-LRGAVSEYEALHAIFKVIrkgmkntdcNRAIIVAHNANFDHSFVmnaaeRAGLKRNPFHPFA--TFDTAALSG 156
Cdd:PRK07740  117 I--TAEdVAFAPPLAEVLHRFYAFI---------GAGVLVAHHAGHDKAFL-----RHALWRTYRQPFThrLIDTMFLTK 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1252953592 157 LVFGQTI---LAKACVSAGIPFDGKqaHGALYDTNRTALLFCEIVNKWKKLG 205
Cdd:PRK07740  181 LLAHERDfptLDDALAYYGIPIPRR--HHALGDALMTAKLWAILLVEAQQRG 230
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 20-129 4.87e-06

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 46.12  E-value: 4.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKMDKDG-WLSMDETLHFHVEPfeGANLEPSALAFTGIdpTNPL-RGAVSEYEALH 97
Cdd:PRK09182   40 VILDTETTGLDPRKDEIIEIGMVAFEYDDDGrIGDVLDTFGGLQQP--SRPIPPEITRLTGI--TDEMvAGQTIDPAAVD 115

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1252953592  98 AIfkvirkgMKNTDcnraIIVAHNANFDHSFV 129
Cdd:PRK09182  116 AL-------IAPAD----LIIAHNAGFDRPFL 136
PRK08517 PRK08517
3'-5' exonuclease;
20-138 2.11e-05

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 43.86  E-value: 2.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKMDKDgwlsmdetlhfhVEPFEG----ANLEPSALAFTGIDPtNPLRGAVSeyea 95
Cdd:PRK08517   71 CFVDIETNGSKPKKHQIIEIGAVKVKNGEI------------IDRFESfvkaKEVPEYITELTGITY-EDLENAPS---- 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1252953592  96 LHAIFKVIRKGMKNtdcnrAIIVAHNANFDHSFVMNAAERAGL 138
Cdd:PRK08517  134 LKEVLEEFRLFLGD-----SVFVAHNVNFDYNFISRSLEEIGL 171
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 20-194 3.91e-05

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 43.21  E-value: 3.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDgLLEIAAITLKmdkDGWLSMDEtlhFHVEPFEGANLEPSALAFTGIDPtNPLRGAVSEYEALHAI 99
Cdd:TIGR00573  10 TTGDNETTGLYAGHD-IIEIGAVEII---NRRITGNK---FHTYIKPDRPIDPDAIKIHGITD-DMLKDKPDFKEIAEDF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRKgmkntdcnrAIIVAHNANFDHSFVMNAAERAGLKRNPFHPFA-TFDTA--ALSGLVFGQTILAKACVSAGIPFD 176
Cdd:TIGR00573  82 ADYIRG---------AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIdTTDTLqyARPEFPGKRNTLDALCKRYEITNS 152

                         170
                  ....*....|....*...
gi 1252953592 177 GKQAHGALYDTNRTALLF 194
Cdd:TIGR00573 153 HRALHGALADAFILAKLY 170
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
 23-147 8.62e-05

N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.


Pssm-ID: 99841 [Multi-domain]  Cd Length: 183  Bit Score: 41.87  E-value: 8.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  23 DVETGGFNAKTDGLLEIAAITLKMDkdgwLSMDETLHFHVEPFEGANLEPSALAFTGIDPTNPLRGAVSEYEA---LHAI 99
Cdd:cd06138     4 DYETFGLNPSFDQILQFAAIRTDEN----FNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFiakIHRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1252953592 100 FKVirkgmKNTdcnraIIVAHNA-NFDHSFVmnaaeRAGLKRNPFHPFA 147
Cdd:cd06138    80 FNT-----PGT-----CIVGYNNiRFDDEFL-----RFAFYRNLYDPYT 113
PRK09145 PRK09145
3'-5' exonuclease;
20-103 4.50e-04

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 39.89  E-value: 4.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAITLKMDKdgwLSMDETLHFHVEPfeGANLEPSALAFTGIDPTNpLRGAVSEYEALHAI 99
Cdd:PRK09145   32 VALDCETTGLDPRRAEIVSIAAVKIRGNR---ILTSERLELLVRP--PQSLSAESIKIHRLRHQD-LEDGLSEEEALRQL 105


                  ....
gi 1252953592 100 FKVI 103
Cdd:PRK09145  106 LAFI 109
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 116-186 8.29e-04

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 38.65  E-value: 8.29e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1252953592 116 IIVAHNANFDHSFVMNAAERAGLkrnPFHPFATFDTAALSGLVFGQ---TILAKACVSAGIPFdgkQAHGALYD 186
Cdd:cd06130    79 LVVAHNASFDRSVLRAALEAYGL---PPPPYQYLCTVRLARRVWPLlpnHKLNTVAEHLGIEL---NHHDALED 146
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 115-154 2.12e-03

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


Pssm-ID: 176647 [Multi-domain]  Cd Length: 96  Bit Score: 36.26  E-value: 2.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1252953592 115 AIIVAHNANFDHSFVMNAAERAGLKrNPFHPFATFDTAAL 154
Cdd:cd06125    45 AILVGHNGSFDLPFLNNRCAELGLK-YPLLAGSWIDTIKL 83
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 20-186 2.96e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 37.50  E-value: 2.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592  20 VVIDVETGGFNAKTDGLLEIAAItlKMDKDGWLSMDETLhfhvepfeganlepsalaftgidpTNPLRGAVSEYEALHAI 99
Cdd:PRK06310   10 VCLDCETTGLDVKKDRIIEFAAI--RFTFDEVIDSVEFL------------------------INPERVVSAESQRIHHI 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1252953592 100 FKVIRKG----------MKNTDCNRAIIVAHNANFDHSFVMNAAERAGLKRNP-FHPFatFDTAALSGLvFGQT---ILA 165
Cdd:PRK06310   64 SDAMLRDkpkiaevfpqIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSkHYYI--IDTLRLAKE-YGDSpnnSLE 140

                         170       180
                  ....*....|....*....|.
gi 1252953592 166 KACVSAGIPFDGkqAHGALYD 186
Cdd:PRK06310  141 ALAVHFNVPYDG--NHRAMKD 159
 
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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