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Conserved domains on  [gi|171700322|gb|ACB53303|]
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unknown [Crocosphaera subtropica ATCC 51142]

Protein Classification

RNase_H_like domain-containing protein( domain architecture ID 10603123)

RNase_H_like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 21-141 3.40e-38

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: 134.32  E-value: 3.40e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322   21 FDGEFQCDLLQGVAAAILLMPNGRRYTVSQLVSVNHKD--EAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTP 98
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASvlEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 171700322   99 vTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAKRC 141
Cdd:pfam13456  82 -KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 21-141 3.40e-38

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: 134.32  E-value: 3.40e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322   21 FDGEFQCDLLQGVAAAILLMPNGRRYTVSQLVSVNHKD--EAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTP 98
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASvlEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 171700322   99 vTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAKRC 141
Cdd:pfam13456  82 -KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 18-143 5.13e-30

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: 112.57  E-value: 5.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  18 IMLFDGEFQCDLLQGVAAAILLMPNGRRYTVSQLVSV---NHkdEAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVN 94
Cdd:cd09279    2 TLYFDGASRGNPGPAGAGVVIYSPGGEVLELSERLGFpatNN--EAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 171700322  95 GLTPVTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAKRCLS 143
Cdd:cd09279   80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
34-149 9.78e-10

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 56.39  E-value: 9.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  34 AAAILLMPNGRRYTVSQLVSV--NHkdEAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTPVTQERL---IK-- 106
Cdd:COG0328   19 GWGAVIRYGGEEKELSGGLGDttNN--RAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGWIHGWKKNGwkpVKnp 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 171700322 107 -LYRIAIKLIRSfEKISLEWISPEQNRPARSAAkrclsDALGRE 149
Cdd:COG0328   97 dLWQRLDELLAR-HKVTFEWVKGHAGHPGNERA-----DALANK 134
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 60-161 5.53e-08

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 54.21  E-value: 5.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  60 AEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTPVTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAK 139
Cdd:PRK07238  48 AEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLAN 127

                         90       100
                 ....*....|....*....|..
gi 171700322 140 RCLsDALGREKAHKPQSATLTP 161
Cdd:PRK07238 128 EAM-DAAAGGEPWGPSAAAADA 148
 
Name Accession Description Interval E-value
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 21-141 3.40e-38

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: 134.32  E-value: 3.40e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322   21 FDGEFQCDLLQGVAAAILLMPNGRRYTVSQLVSVNHKD--EAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTP 98
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASvlEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 171700322   99 vTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAKRC 141
Cdd:pfam13456  82 -KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 18-143 5.13e-30

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: 112.57  E-value: 5.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  18 IMLFDGEFQCDLLQGVAAAILLMPNGRRYTVSQLVSV---NHkdEAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVN 94
Cdd:cd09279    2 TLYFDGASRGNPGPAGAGVVIYSPGGEVLELSERLGFpatNN--EAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 171700322  95 GLTPVTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAKRCLS 143
Cdd:cd09279   80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 21-139 5.10e-11

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: 59.64  E-value: 5.10e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  21 FDGEFQCDLLQGVAAAILLMPNGRRYTV-SQLVSVNHKDEAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTPV 99
Cdd:cd06222    3 VDGSCRGNPGPAGIGGVLRDHEGGWLGGfALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGSFK 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 171700322 100 tQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAK 139
Cdd:cd06222   83 -WSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
34-149 9.78e-10

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 56.39  E-value: 9.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  34 AAAILLMPNGRRYTVSQLVSV--NHkdEAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTPVTQERL---IK-- 106
Cdd:COG0328   19 GWGAVIRYGGEEKELSGGLGDttNN--RAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGWIHGWKKNGwkpVKnp 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 171700322 107 -LYRIAIKLIRSfEKISLEWISPEQNRPARSAAkrclsDALGRE 149
Cdd:COG0328   97 dLWQRLDELLAR-HKVTFEWVKGHAGHPGNERA-----DALANK 134
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 60-161 5.53e-08

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 54.21  E-value: 5.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  60 AEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNGLTPVTQERLIKLYRIAIKLIRSFEKISLEWISPEQNRPARSAAK 139
Cdd:PRK07238  48 AEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLAN 127

                         90       100
                 ....*....|....*....|..
gi 171700322 140 RCLsDALGREKAHKPQSATLTP 161
Cdd:PRK07238 128 EAM-DAAAGGEPWGPSAAAADA 148
PRK07708 PRK07708
hypothetical protein; Validated
 13-144 8.73e-07

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 49.65  E-value: 8.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  13 PKDIpIMLFDGEFQCDLLQ-GVAAAILLMPNGRRYTV---SQLVSVNHKDEAEYTALIIGLKKAQKLGL--NTLAIKGDS 86
Cdd:PRK07708  71 PHEI-LVYFDGGFDKETKLaGLGIVIYYKQGNKRYRIrrnAYIEGIYDNNEAEYAALYYAMQELEELGVkhEPVTFRGDS 149

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 171700322  87 DLIFNQVNGLTPVTQERLIK-LYRIAIKLirsfEKISL----EWISPEQNRPARSAAKRCLSD 144
Cdd:PRK07708 150 QVVLNQLAGEWPCYDEHLNHwLDRIEQKL----KQLKLtpvyEPISRKQNKEADQLATQALEG 208
rnhA PRK13907
ribonuclease H; Provisional
 55-142 1.93e-05

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 43.89  E-value: 1.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171700322  55 NHkdEAEYTALIIGLKKAQKLGLNTLAIKGDSDLIFNQVNG-------LTPVTQErliklyriAIKLIRSFEKISLEWIS 127
Cdd:PRK13907  41 NH--EAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKeyaknkmFAPLLEE--------ALQYIKSFDLFFIKWIP 110

                         90
                 ....*....|....*
gi 171700322 128 PEQNRPARSAAKRCL 142
Cdd:PRK13907 111 SSQNKVADELARKAI 125
 
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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