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Conserved domains on  [gi|295321673|pdb|3HST|B]
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Chain B, Protein Rv2228c/MT2287

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07238 super family cl32201
bifunctional RNase H/acid phosphatase; Provisional
 3-128 2.71e-86

bifunctional RNase H/acid phosphatase; Provisional


The actual alignment was detected with superfamily member PRK07238:

Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 256.44  E-value: 2.71e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:PRK07238   2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
3HST_B        83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:PRK07238  82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLAN 127
 
Name Accession Description Interval E-value
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 3-128 2.71e-86

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 256.44  E-value: 2.71e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:PRK07238   2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
3HST_B        83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:PRK07238  82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLAN 127
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 4-128 1.20e-49

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 154.94  E-value: 1.20e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        4 VVIEADGGSRGNPGPAGYGAVVWtaDHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIY--SPGGEVLELSERLGfPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQL 78

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
3HST_B       83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:cd09279  79 NGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALAN 124
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
3-128 3.93e-39

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 128.42  E-value: 3.93e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        3 KVVIEADGGSRGNPGPAGYGAVVWTADHstvLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:COG0328   2 MIEIYTDGACRGNPGPGGWGAVIRYGGE---EKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQI 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
3HST_B       83 SG---RWK------VKHPDLLKlyvQAQALASQfRRINYEWVPRAR----NTYADRLAN 128
Cdd:COG0328  79 TGwihGWKkngwkpVKNPDLWQ---RLDELLAR-HKVTFEWVKGHAghpgNERADALAN 133
RNAseHI_Thmprot NF041175
ribonuclease HI;
15-126 1.40e-30

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 106.98  E-value: 1.40e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        15 NPGP-AGYGAVVWTADHSTV----LAESKQAIgRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVK 89
Cdd:NF041175  14 NPGGiATYGYVIYLDNKRKIegygLAAEPWSK-DSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKVK 92

                         90       100       110
                 ....*....|....*....|....*....|....*..
3HST_B        90 HPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRL 126
Cdd:NF041175  93 SPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRL 129
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 9-128 3.49e-22

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 85.01  E-value: 3.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B          9 DGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKv 88
Cdd:pfam13456   3 DGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP- 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
3HST_B         89 KHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:pfam13456  82 KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
 
Name Accession Description Interval E-value
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 3-128 2.71e-86

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 256.44  E-value: 2.71e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:PRK07238   2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
3HST_B        83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:PRK07238  82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLAN 127
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 4-128 1.20e-49

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 154.94  E-value: 1.20e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        4 VVIEADGGSRGNPGPAGYGAVVWtaDHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIY--SPGGEVLELSERLGfPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQL 78

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
3HST_B       83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:cd09279  79 NGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALAN 124
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
3-128 3.93e-39

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 128.42  E-value: 3.93e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        3 KVVIEADGGSRGNPGPAGYGAVVWTADHstvLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:COG0328   2 MIEIYTDGACRGNPGPGGWGAVIRYGGE---EKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQI 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
3HST_B       83 SG---RWK------VKHPDLLKlyvQAQALASQfRRINYEWVPRAR----NTYADRLAN 128
Cdd:COG0328  79 TGwihGWKkngwkpVKNPDLWQ---RLDELLAR-HKVTFEWVKGHAghpgNERADALAN 133
RNAseHI_Thmprot NF041175
ribonuclease HI;
15-126 1.40e-30

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 106.98  E-value: 1.40e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        15 NPGP-AGYGAVVWTADHSTV----LAESKQAIgRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVK 89
Cdd:NF041175  14 NPGGiATYGYVIYLDNKRKIegygLAAEPWSK-DSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKVK 92

                         90       100       110
                 ....*....|....*....|....*....|....*..
3HST_B        90 HPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRL 126
Cdd:NF041175  93 SPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRL 129
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 6-128 3.29e-28

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 100.47  E-value: 3.29e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        6 IEADGGSRGNPGPAGYGAVVWTADHStVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGR 85
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGG-WLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
3HST_B       86 WKVKHPdLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:cd06222  80 SFKWSP-NILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 9-128 3.49e-22

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 85.01  E-value: 3.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B          9 DGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKv 88
Cdd:pfam13456   3 DGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP- 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
3HST_B         89 KHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:pfam13456  82 KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 3-128 1.80e-17

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 73.29  E-value: 1.80e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLaesKQAIGRATNNVAEYRGLIAGLdDAVKLGAtEAAVLMDSKLVVEQM 82
Cdd:cd09278   1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKEL---SGGEPGTTNNRMELTAAIEAL-EALKEPC-PVTIYTDSQYVINGI 75

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
3HST_B       83 S---GRWK-----------VKHPDLLKLYVQaqalASQFRRINYEWVP----RARNTYADRLAN 128
Cdd:cd09278  76 TkwiKGWKkngwktadgkpVKNRDLWQELDA----LLAGHKVTWEWVKghagHPGNERADRLAN 135
rnhA PRK13907
ribonuclease H; Provisional
 9-127 2.30e-11

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 57.37  E-value: 2.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         9 DGGSRGNPGPAGYGAVVWTADHSTVLAeskQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLV---VEQMSGR 85
Cdd:PRK13907   7 DGASKGNPGPSGAGVFIKGVQPAVQLS---LPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVeraVEKEYAK 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
3HST_B        86 WKVKHPdllkLYVQAQALASQFRRINYEWVPRARNTYADRLA 127
Cdd:PRK13907  84 NKMFAP----LLEEALQYIKSFDLFFIKWIPSSQNKVADELA 121
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 4-127 2.36e-11

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 57.39  E-value: 2.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B          4 VVIEADGGSRGNPGPAGYGAVVWTaDHSTVlaeSKQAIGRATNNVAEYRGLIAGLDDAVKlgATEAAVLMDSKLVVE--- 80
Cdd:pfam00075   4 VTVYTDGSCLGNPGPGGAGAVLYR-GHENI---SAPLPGRTTNNRAELQAVIEALKALKS--PSKVNIYTDSQYVIGgit 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
3HST_B         81 QMSGRWK------------VKHPDLLKLyvqAQALASQfRRINYEWVP----RARNTYADRLA 127
Cdd:pfam00075  78 QWVHGWKkngwpttsegkpVKNKDLWQL---LKALCKK-HQVYWQWVKghagNPGNEMADRLA 136
PRK07708 PRK07708
hypothetical protein; Validated
 4-128 4.30e-09

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 52.73  E-value: 4.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         4 VVIEADGGSRGNPGPAGYGAVVW--TADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLM--DSKLVV 79
Cdd:PRK07708  74 ILVYFDGGFDKETKLAGLGIVIYykQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFrgDSQVVL 153

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
3HST_B        80 EQMSGRWKVKHPDLLKLYVQAQALASQFR-RINYEWVPRARNTYADRLAN 128
Cdd:PRK07708 154 NQLAGEWPCYDEHLNHWLDRIEQKLKQLKlTPVYEPISRKQNKEADQLAT 203
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 5-128 6.42e-07

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 45.65  E-value: 6.42e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        5 VIEADGGSRGNPGP---AGYGaVVW----TADHSTVLAESkqAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVL----- 72
Cdd:cd13934   1 LVYIDGACRNNGRPdarAGYG-VYFgpdsSYNVSGRLEDT--GGHPQTSQRAELRAAIAALRFRSWIIDPDGEGLktvvi 77

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
3HST_B       73 -MDSKLVVEQMSG---RWK-----------VKHPDLLK-LYVQAQALASQFRRINYEWVPRARNTYADRLAN 128
Cdd:cd13934  78 aTDSEYVVKGATEwipKWKrngwrtskgkpVKNRDLFElLLDEIEDLEEGGVEVQFWHVPRELNKEADRLAK 149
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 9-128 1.35e-06

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 44.86  E-value: 1.35e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B        9 DGGSRGNPGP---AGYGaVVWTADHStvLAESKQAIGRA-TNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM-- 82
Cdd:cd09280   5 DGSCLNNGKPgarAGIG-VYFGPGDP--RNVSEPLPGRKqTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINCItk 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
3HST_B       83 ------------SGRWKVKHPDLLKLYVqaQALASQFRRINYEWVP----RARNTYADRLAN 128
Cdd:cd09280  82 wipkwkkngwktSKGKPVKNQDLIKELD--KLLRKRGIKVKFEHVKghsgDPGNEEADRLAR 141
rnhA PRK00203
ribonuclease H; Reviewed
 3-128 6.05e-06

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 43.28  E-value: 6.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         3 KVVIEADGGSRGNPGPAGYGAVVWTADHstvlaESKQAIGRA--TNNVAEYRGLIAGLdDAVKlGATEAAVLMDSKLVVE 80
Cdd:PRK00203   3 QVEIYTDGACLGNPGPGGWGAILRYKGH-----EKELSGGEAltTNNRMELMAAIEAL-EALK-EPCEVTLYTDSQYVRQ 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
3HST_B        81 QMSG---RWK-----------VKHPDLLKLYVQaqalASQFRRINYEWVP----RARNTYADRLAN 128
Cdd:PRK00203  76 GITEwihGWKkngwktadkkpVKNVDLWQRLDA----ALKRHQIKWHWVKghagHPENERCDELAR 137
PRK06548 PRK06548
ribonuclease H; Provisional
 3-127 1.30e-03

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 37.10  E-value: 1.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3HST_B         3 KVVIEADGGSRGNPGPAGYGavvWTADHSTvlaESKQAIGRATNNVAEYRGlIAGLDDAVKLGATEAAVLMDSKLVVEQM 82
Cdd:PRK06548   5 EIIAATDGSSLANPGPSGWA---WYVDENT---WDSGGWDIATNNIAELTA-VRELLIATRHTDRPILILSDSKYVINSL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
3HST_B        83 SG---RWKVK-------HPDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLA 127
Cdd:PRK06548  78 TKwvySWKMRkwrkadgKPVLNQEIIQEIDSLMENRNIRMSWVNahtgHPLNEAADSLA 136
 
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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