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Conserved domains on  [gi|1256763246|gb|PEE35281|]
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hypothetical protein CON59_16600 [Bacillus cereus]

Protein Classification

ribonuclease H family protein( domain architecture ID 11482853)

ribonuclease H family protein similar to Bacillus subtilis uncharacterized protein YpeP

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07708 PRK07708
hypothetical protein; Validated
 1-219 4.44e-134

hypothetical protein; Validated


:

Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 375.14  E-value: 4.44e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246   1 MKYKIHWLYKTKRGLQTELTTEYMNIEEVLQFAEDFEKTGRVKEISFYDEMDAEWSLKEMKKLSKQVEEDPQEILVYFDG 80
Cdd:PRK07708    1 MKYRIHWTYKTKKGLQTELTSDWMNIEEALQLAEDFEKTGRVKELEFYDEMDTEWSLKELKKLSKEVEEEPHEILVYFDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  81 GYDVQTKEAGVGICVYYKKGNTNYRIRRNAYIEGIYDNNEAEYASLLYGMNILEELGVKYEAVTLHGDSQVVLQQLAGEW 160
Cdd:PRK07708   81 GFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEW 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1256763246 161 PCYDEHLNHYLDQIEQKAKQMKLKLICEPISRKQNKEAHQLATQALEGTVIDSHKEITE 219
Cdd:PRK07708  161 PCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGTVIESHKELTE 219
 
Name Accession Description Interval E-value
PRK07708 PRK07708
hypothetical protein; Validated
 1-219 4.44e-134

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 375.14  E-value: 4.44e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246   1 MKYKIHWLYKTKRGLQTELTTEYMNIEEVLQFAEDFEKTGRVKEISFYDEMDAEWSLKEMKKLSKQVEEDPQEILVYFDG 80
Cdd:PRK07708    1 MKYRIHWTYKTKKGLQTELTSDWMNIEEALQLAEDFEKTGRVKELEFYDEMDTEWSLKELKKLSKEVEEEPHEILVYFDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  81 GYDVQTKEAGVGICVYYKKGNTNYRIRRNAYIEGIYDNNEAEYASLLYGMNILEELGVKYEAVTLHGDSQVVLQQLAGEW 160
Cdd:PRK07708   81 GFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEW 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1256763246 161 PCYDEHLNHYLDQIEQKAKQMKLKLICEPISRKQNKEAHQLATQALEGTVIDSHKEITE 219
Cdd:PRK07708  161 PCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGTVIESHKELTE 219
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 74-206 3.35e-39

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: 131.44  E-value: 3.35e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  74 ILVYFDGGYDVQTKEAGVGICVYYKKGntnYRIRRNAYIEGIYDNNEAEYASLLYGMNILEELGVkyEAVTLHGDSQVVL 153
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGG---EVLELSERLGFPATNNEAEYEALIAGLELALELGA--EKLEIYGDSQLVV 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1256763246 154 QQLAGEWPCYDEHLNHYLDQIEQKAKQmKLKLICEPISRKQNKEAHQLATQAL 206
Cdd:cd09279    76 NQLNGEYKVKNERLKPLLEKVLELLAK-FELVELKWIPREQNKEADALANQAL 127
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
73-206 6.81e-18

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 76.42  E-value: 6.81e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  73 EILVYFDGGYDVQTKEAGVGICVYYKKgntnYRIRRNAYiEGIYDNNEAEYASLLYGMNILEELGVkyEAVTLHGDSQVV 152
Cdd:COG0328     2 MIEIYTDGACRGNPGPGGWGAVIRYGG----EEKELSGG-LGDTTNNRAELTALIAALEALKELGP--CEVEIYTDSQYV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1256763246 153 LQQLAGEWP-----CYDEHLN-HYLDQIEQKAKQMKLKLicEPISRKQ----NKEAHQLATQAL 206
Cdd:COG0328    75 VNQITGWIHgwkknGWKPVKNpDLWQRLDELLARHKVTF--EWVKGHAghpgNERADALANKAL 136
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 78-205 6.03e-10

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: 54.96  E-value: 6.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  78 FDGGYDVQTKEAGVGICVYYKKGN----TNYRIRRNAYIEgiydnnEAEYASLLYGMNILEELGVKYeaVTLHGDSQVVL 153
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNvllaGQKKLGPGASVL------EAEAQALIIGLQLAWKLGIRH--LIVEGDSATVV 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1256763246 154 QQLAGEWPCyDEHLNHYLDQIEQKAKQM---KLKLicepISRKQNKEAHQLATQA 205
Cdd:pfam13456  74 QLINGRSPK-QSKLANLLDEIRKLLKRFesvSFEH----IPREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
PRK07708 PRK07708
hypothetical protein; Validated
 1-219 4.44e-134

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 375.14  E-value: 4.44e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246   1 MKYKIHWLYKTKRGLQTELTTEYMNIEEVLQFAEDFEKTGRVKEISFYDEMDAEWSLKEMKKLSKQVEEDPQEILVYFDG 80
Cdd:PRK07708    1 MKYRIHWTYKTKKGLQTELTSDWMNIEEALQLAEDFEKTGRVKELEFYDEMDTEWSLKELKKLSKEVEEEPHEILVYFDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  81 GYDVQTKEAGVGICVYYKKGNTNYRIRRNAYIEGIYDNNEAEYASLLYGMNILEELGVKYEAVTLHGDSQVVLQQLAGEW 160
Cdd:PRK07708   81 GFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEW 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1256763246 161 PCYDEHLNHYLDQIEQKAKQMKLKLICEPISRKQNKEAHQLATQALEGTVIDSHKEITE 219
Cdd:PRK07708  161 PCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGTVIESHKELTE 219
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 74-206 3.35e-39

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: 131.44  E-value: 3.35e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  74 ILVYFDGGYDVQTKEAGVGICVYYKKGntnYRIRRNAYIEGIYDNNEAEYASLLYGMNILEELGVkyEAVTLHGDSQVVL 153
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGG---EVLELSERLGFPATNNEAEYEALIAGLELALELGA--EKLEIYGDSQLVV 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1256763246 154 QQLAGEWPCYDEHLNHYLDQIEQKAKQmKLKLICEPISRKQNKEAHQLATQAL 206
Cdd:cd09279    76 NQLNGEYKVKNERLKPLLEKVLELLAK-FELVELKWIPREQNKEADALANQAL 127
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
73-206 6.81e-18

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 76.42  E-value: 6.81e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  73 EILVYFDGGYDVQTKEAGVGICVYYKKgntnYRIRRNAYiEGIYDNNEAEYASLLYGMNILEELGVkyEAVTLHGDSQVV 152
Cdd:COG0328     2 MIEIYTDGACRGNPGPGGWGAVIRYGG----EEKELSGG-LGDTTNNRAELTALIAALEALKELGP--CEVEIYTDSQYV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1256763246 153 LQQLAGEWP-----CYDEHLN-HYLDQIEQKAKQMKLKLicEPISRKQ----NKEAHQLATQAL 206
Cdd:COG0328    75 VNQITGWIHgwkknGWKPVKNpDLWQRLDELLARHKVTF--EWVKGHAghpgNERADALANKAL 136
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 76-202 1.36e-10

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: 56.94  E-value: 1.36e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  76 VYFDGGYDVQTKEAGVGICVyykKGNTNYRIRRNAYIEGIYDNNEAEYASLLYGMNILEELGVKYeaVTLHGDSQVVLQQ 155
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVL---RDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLK--VIIESDSKYVVDL 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1256763246 156 LAGEWPCYDEHLNHYLDQIEQKAKQMKLKLICEPisRKQNKEAHQLA 202
Cdd:cd06222    76 INSGSFKWSPNILLIEDILLLLSRFWSVKISHVP--REGNQVADALA 120
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 78-205 6.03e-10

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: 54.96  E-value: 6.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1256763246  78 FDGGYDVQTKEAGVGICVYYKKGN----TNYRIRRNAYIEgiydnnEAEYASLLYGMNILEELGVKYeaVTLHGDSQVVL 153
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNvllaGQKKLGPGASVL------EAEAQALIIGLQLAWKLGIRH--LIVEGDSATVV 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1256763246 154 QQLAGEWPCyDEHLNHYLDQIEQKAKQM---KLKLicepISRKQNKEAHQLATQA 205
Cdd:pfam13456  74 QLINGRSPK-QSKLANLLDEIRKLLKRFesvSFEH----IPREQNRVADTLAKMA 123
 
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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