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Conserved domains on  [gi|446496013|ref|WP_000573867|]
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MULTISPECIES: reverse transcriptase-like protein [Bacillus]

Protein Classification

ribonuclease H family protein; reverse transcriptase/ribonuclease H family protein( domain architecture ID 10793884)

ribonuclease H (RNase H) family protein may function as an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner| reverse transcriptase (RT)/ribonuclease H (RNase H) family protein from retrotransposons catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements, and may be an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rnhA PRK13907
ribonuclease H; Provisional
 1-128 6.27e-98

ribonuclease H; Provisional


:

Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 276.55  E-value: 6.27e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   1 MIEVYIDGASKGNPGPSGAGVFIKGIQPPVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80
Cdd:PRK13907   1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446496013  81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQN 128
Cdd:PRK13907  81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQN 128
 
Name Accession Description Interval E-value
rnhA PRK13907
ribonuclease H; Provisional
 1-128 6.27e-98

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 276.55  E-value: 6.27e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   1 MIEVYIDGASKGNPGPSGAGVFIKGIQPPVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80
Cdd:PRK13907   1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446496013  81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQN 128
Cdd:PRK13907  81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQN 128
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 2-125 1.74e-50

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: 156.48  E-value: 1.74e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   2 IEVYIDGASKGNPGPSGAGVFIKG-IQPPVQLSLPLGT-MSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEK 79
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSpGGEVLELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446496013  80 EY-AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAI 125
Cdd:cd09279   81 EYkVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-125 3.79e-39

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 128.04  E-value: 3.79e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   1 MIEVYIDGASKGNPGPSGAGVFIKGIQPPVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGW 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446496013  81 YA--KNKMFAP-----LLEEALQYIKSFDLFFiKWIPSSQ----NKVADELARKAI 125
Cdd:COG0328   82 IHgwKKNGWKPvknpdLWQRLDELLARHKVTF-EWVKGHAghpgNERADALANKAL 136
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 7-124 2.11e-19

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: 77.31  E-value: 2.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013    7 DGASKGNPGPSGAGVFIK--------GIQPPVQlslplGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE 78
Cdd:pfam13456   3 DGAFKCDSGLAGAGVVIRdpngnvllAGQKKLG-----PGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLIN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 446496013   79 KEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKA 124
Cdd:pfam13456  78 GRSPKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNAseHI_Thmprot NF041175
ribonuclease HI;
41-124 1.51e-18

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 75.78  E-value: 1.51e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013  41 NHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYA-KNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADE 119
Cdd:NF041175  49 NNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKvKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADR 128


                 ....*
gi 446496013 120 LARKA 124
Cdd:NF041175 129 LSRIA 133
 
Name Accession Description Interval E-value
rnhA PRK13907
ribonuclease H; Provisional
 1-128 6.27e-98

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 276.55  E-value: 6.27e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   1 MIEVYIDGASKGNPGPSGAGVFIKGIQPPVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80
Cdd:PRK13907   1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446496013  81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQN 128
Cdd:PRK13907  81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQN 128
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 2-125 1.74e-50

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: 156.48  E-value: 1.74e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   2 IEVYIDGASKGNPGPSGAGVFIKG-IQPPVQLSLPLGT-MSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEK 79
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSpGGEVLELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446496013  80 EY-AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAI 125
Cdd:cd09279   81 EYkVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-125 3.79e-39

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 128.04  E-value: 3.79e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   1 MIEVYIDGASKGNPGPSGAGVFIKGIQPPVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGW 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446496013  81 YA--KNKMFAP-----LLEEALQYIKSFDLFFiKWIPSSQ----NKVADELARKAI 125
Cdd:COG0328   82 IHgwKKNGWKPvknpdLWQRLDELLARHKVTF-EWVKGHAghpgNERADALANKAL 136
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 4-122 1.78e-24

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: 90.45  E-value: 1.78e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   4 VYIDGASKGNPGPSGAGVFIKGIQPPVQ--LSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81
Cdd:cd06222    1 INVDGSCRGNPGPAGIGGVLRDHEGGWLggFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446496013  82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELAR 122
Cdd:cd06222   81 FKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 7-124 2.11e-19

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: 77.31  E-value: 2.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013    7 DGASKGNPGPSGAGVFIK--------GIQPPVQlslplGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE 78
Cdd:pfam13456   3 DGAFKCDSGLAGAGVVIRdpngnvllAGQKKLG-----PGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLIN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 446496013   79 KEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKA 124
Cdd:pfam13456  78 GRSPKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNAseHI_Thmprot NF041175
ribonuclease HI;
41-124 1.51e-18

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 75.78  E-value: 1.51e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013  41 NHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYA-KNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADE 119
Cdd:NF041175  49 NNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKvKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADR 128


                 ....*
gi 446496013 120 LARKA 124
Cdd:NF041175 129 LSRIA 133
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 7-124 1.16e-14

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 68.85  E-value: 1.16e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   7 DGASKGNPGPSGAGVFIK---GIQPPVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVeraVEKEYAK 83
Cdd:PRK07238   8 DGGSRGNPGPAGYGAVVWdadRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLV---VEQMSGR 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446496013  84 NKM----FAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKA 124
Cdd:PRK07238  85 WKVkhpdMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 2-125 6.32e-14

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: 63.55  E-value: 6.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013    2 IEVYIDGASKGNPGPSGAGVFIKGIQPPVQLSLPLGTmSNHEAEYHALLAALKYCTEH-NYNIvsfRTDSQLVERAVEKE 80
Cdd:pfam00075   4 VTVYTDGSCLGNPGPGGAGAVLYRGHENISAPLPGRT-TNNRAELQAVIEALKALKSPsKVNI---YTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446496013   81 YAKNKM------------FAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAI 125
Cdd:pfam00075  80 VHGWKKngwpttsegkpvKNKDLWQLLKALCKKHQVYWQWVKGhagnPGNEMADRLAKQGA 140
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1-125 6.05e-12

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: 58.65  E-value: 6.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   1 MIEVYIDGASKGNPGPSGAGVFIKGIQPPVQLS--LPLGTmsNHEAEYHALLAALKYCTEhNYNIVsFRTDSQLVERAVE 78
Cdd:cd09278    1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKELSggEPGTT--NNRMELTAAIEALEALKE-PCPVT-IYTDSQYVINGIT 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446496013  79 ---------------KEYAKNKmfaPLLEEALQYIKSFDLFFiKWIPS----SQNKVADELARKAI 125
Cdd:cd09278   77 kwikgwkkngwktadGKPVKNR---DLWQELDALLAGHKVTW-EWVKGhaghPGNERADRLANKAA 138
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 4-125 3.43e-11

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: 56.81  E-value: 3.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   4 VYIDGASKGNPGP---SGAGVFIkGIQPPVQLSLPLGTM--SNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE 78
Cdd:cd09280    2 VYTDGSCLNNGKPgarAGIGVYF-GPGDPRNVSEPLPGRkqTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINCIT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446496013  79 K---------------EYAKNKmfaPLLEEALQYIKSFDLFF-IKWIPSSQ----NKVADELARKAI 125
Cdd:cd09280   81 KwipkwkkngwktskgKPVKNQ---DLIKELDKLLRKRGIKVkFEHVKGHSgdpgNEEADRLAREGA 144
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 4-124 2.00e-06

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: 44.11  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   4 VYIDGASKGN--PGP-SGAGVFIkGIQPPVQLSLPL-----GTMSNHEAEYHALLAALKYCTEHNY-------NIVsFRT 68
Cdd:cd13934    2 VYIDGACRNNgrPDArAGYGVYF-GPDSSYNVSGRLedtggHPQTSQRAELRAAIAALRFRSWIIDpdgeglkTVV-IAT 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446496013  69 DSQ-LVE--------------RAVEKEYAKNKmfaPLLEEALQYIKSFDLFFIK---W-IPSSQNKVADELARKA 124
Cdd:cd13934   80 DSEyVVKgatewipkwkrngwRTSKGKPVKNR---DLFELLLDEIEDLEEGGVEvqfWhVPRELNKEADRLAKAA 151
PRK07708 PRK07708
hypothetical protein; Validated
 2-125 2.13e-06

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 44.64  E-value: 2.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   2 IEVYIDGASKGNPGPSGAGVFI---KG-----IQPPVQLSlplGTMSNHEAEYHALLAALKYCTEHN--YNIVSFRTDSQ 71
Cdd:PRK07708  74 ILVYFDGGFDKETKLAGLGIVIyykQGnkryrIRRNAYIE---GIYDNNEAEYAALYYAMQELEELGvkHEPVTFRGDSQ 150

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446496013  72 LVERAVEKEYaknkmfaPLLEEAL--------QYIKSFDLFFI-KWIPSSQNKVADELARKAI 125
Cdd:PRK07708 151 VVLNQLAGEW-------PCYDEHLnhwldrieQKLKQLKLTPVyEPISRKQNKEADQLATQAL 206
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 6-100 1.55e-05

RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; This family includes bacterial ribonuclease H (RNase H) enzymes. RNases 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. RNase H 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260015  Cd Length: 133  Bit Score: 41.35  E-value: 1.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   6 IDGASKGNPGP---------SGAGVFIKGiqppvqlslPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFrTDSQLVERA 76
Cdd:cd13935    7 VDAACSGNPGIveyrgvdtkTGEVLFHRG---------PFPGGTNNMGEFLAIVHALRYLKEKNSRKPIY-SDSQTAIAW 76

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446496013  77 VEKEYAK--------NKMFAPLLEEALQYIKS 100
Cdd:cd13935   77 VKKKKAKstlvrnekNAEIFKLVDRAEEWLST 108
rnhA PRK00203
ribonuclease H; Reviewed
 2-128 3.55e-04

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 37.88  E-value: 3.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446496013   2 IEVYIDGASKGNPGPSGAGVFI--KGIQPpvqlslplgTMSNHEA-------EYHALLAALKYCTEHnyNIVSFRTDSQL 72
Cdd:PRK00203   4 VEIYTDGACLGNPGPGGWGAILryKGHEK---------ELSGGEAlttnnrmELMAAIEALEALKEP--CEVTLYTDSQY 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446496013  73 VERAV---------------EKEYAKNKMFAPLLEEALQYIKsfdlffIKWI--------PssQNKVADELARKAILQN 128
Cdd:PRK00203  73 VRQGItewihgwkkngwktaDKKPVKNVDLWQRLDAALKRHQ------IKWHwvkghaghP--ENERCDELARAGAEEA 143
 
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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