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Conserved domains on  [gi|71043744|ref|NP_001020797|]
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transcription elongation factor, mitochondrial [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HHH_3 super family cl48149
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 81-129 3.30e-07

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


The actual alignment was detected with superfamily member pfam12836:

Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 46.71  E-value: 3.30e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 71043744    81 LNTASDKELEAFRLLRGRKSVNIVEHRKKFGPFQSLESLIGVPLIQYKT 129
Cdd:pfam12836   6 INTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKT 54
RuvC-like super family cl21482
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 172-354 7.29e-05

Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family consists of bacterial RuvC, fungal Cruciform cutting endonuclease 1 (CCE1), bacterial YqgF and monokaryotic chloroplast 1 protein (MOC1). RuvC, CCE1 and MOC1 are Holliday junction resolvases (HJRs), endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. CCE1 is a HJR specific for 4-way junctions; it is involved in the maintenance of mitochondrial DNA. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


The actual alignment was detected with superfamily member cd16963:

Pssm-ID: 473878 [Multi-domain]  Cd Length: 288  Bit Score: 43.89  E-value: 7.29e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71043744 172 SIVSIVFGTRRIAWAHLD--------RKPTVLDWQ--QAECWKLTNKTYPSSFYLEEIS----SVVSKI---PKADLYIL 234
Cdd:cd16963  45 SILSIDMGIRNLAYCHLSlpktsphrRKPTLVDWNklDLEEKFGVSGADKLSFSPSYYArlayQLVNELllpPNPDLILI 124

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71043744 235 EK----SGLSiqNTSLFPILLHFlITEAMLYALL---NKTFAKDGQHRVLSINRNAVGKHF-------DLMIGDTRTSGR 300
Cdd:cd16963 125 ERqrfrSGGS--SAVLEWTLRVN-MLEAMLYAVLytrRQQGKSKSKADVISSSPQRMVRYWlsrldrkSSRPDVKKKKKK 201

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71043744 301 ----------ELVKQFLSESV--LKEQPRVFFPRELAVQYRQKIVKSSHRIEE----------LYDSLLQAVAFYE 354
Cdd:cd16963 202 syknskkariDLVKNWLSDSNvsPFLLLLPELSSRLRKLFNKKKSLKKTSTSDdaagvkklddLADSLLQGLAWLE 277
 
Name Accession Description Interval E-value
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 81-129 3.30e-07

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 46.71  E-value: 3.30e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 71043744    81 LNTASDKELEAFRLLRGRKSVNIVEHRKKFGPFQSLESLIGVPLIQYKT 129
Cdd:pfam12836   6 INTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKT 54
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 81-125 2.15e-06

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 44.85  E-value: 2.15e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 71043744  81 LNTASDKELEAFRLLRGRKSVNIVEHRKKFGPFQSLESLIGVPLI 125
Cdd:COG1555  15 INTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGI 59
CCE1 cd16963
fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1; ...
 172-354 7.29e-05

fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1; Saccharomyces cerevisiae Cruciform cutting endonuclease 1 (CCE1) is a Holliday junction resolvase specific for 4-way junctions. CCE1 is involved in the maintenance of mitochondrial DNA. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438563 [Multi-domain]  Cd Length: 288  Bit Score: 43.89  E-value: 7.29e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71043744 172 SIVSIVFGTRRIAWAHLD--------RKPTVLDWQ--QAECWKLTNKTYPSSFYLEEIS----SVVSKI---PKADLYIL 234
Cdd:cd16963  45 SILSIDMGIRNLAYCHLSlpktsphrRKPTLVDWNklDLEEKFGVSGADKLSFSPSYYArlayQLVNELllpPNPDLILI 124

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71043744 235 EK----SGLSiqNTSLFPILLHFlITEAMLYALL---NKTFAKDGQHRVLSINRNAVGKHF-------DLMIGDTRTSGR 300
Cdd:cd16963 125 ERqrfrSGGS--SAVLEWTLRVN-MLEAMLYAVLytrRQQGKSKSKADVISSSPQRMVRYWlsrldrkSSRPDVKKKKKK 201

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71043744 301 ----------ELVKQFLSESV--LKEQPRVFFPRELAVQYRQKIVKSSHRIEE----------LYDSLLQAVAFYE 354
Cdd:cd16963 202 syknskkariDLVKNWLSDSNvsPFLLLLPELSSRLRKLFNKKKSLKKTSTSDdaagvkklddLADSLLQGLAWLE 277
 
Name Accession Description Interval E-value
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 81-129 3.30e-07

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 46.71  E-value: 3.30e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 71043744    81 LNTASDKELEAFRLLRGRKSVNIVEHRKKFGPFQSLESLIGVPLIQYKT 129
Cdd:pfam12836   6 INTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKT 54
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 81-125 2.15e-06

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 44.85  E-value: 2.15e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 71043744  81 LNTASDKELEAFRLLRGRKSVNIVEHRKKFGPFQSLESLIGVPLI 125
Cdd:COG1555  15 INTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGI 59
CCE1 cd16963
fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1; ...
 172-354 7.29e-05

fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1; Saccharomyces cerevisiae Cruciform cutting endonuclease 1 (CCE1) is a Holliday junction resolvase specific for 4-way junctions. CCE1 is involved in the maintenance of mitochondrial DNA. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438563 [Multi-domain]  Cd Length: 288  Bit Score: 43.89  E-value: 7.29e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71043744 172 SIVSIVFGTRRIAWAHLD--------RKPTVLDWQ--QAECWKLTNKTYPSSFYLEEIS----SVVSKI---PKADLYIL 234
Cdd:cd16963  45 SILSIDMGIRNLAYCHLSlpktsphrRKPTLVDWNklDLEEKFGVSGADKLSFSPSYYArlayQLVNELllpPNPDLILI 124

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71043744 235 EK----SGLSiqNTSLFPILLHFlITEAMLYALL---NKTFAKDGQHRVLSINRNAVGKHF-------DLMIGDTRTSGR 300
Cdd:cd16963 125 ERqrfrSGGS--SAVLEWTLRVN-MLEAMLYAVLytrRQQGKSKSKADVISSSPQRMVRYWlsrldrkSSRPDVKKKKKK 201

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71043744 301 ----------ELVKQFLSESV--LKEQPRVFFPRELAVQYRQKIVKSSHRIEE----------LYDSLLQAVAFYE 354
Cdd:cd16963 202 syknskkariDLVKNWLSDSNvsPFLLLLPELSSRLRKLFNKKKSLKKTSTSDdaagvkklddLADSLLQGLAWLE 277
 
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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