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Conserved domains on  [gi|134053959|ref|NP_078959|]
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transcription elongation factor, mitochondrial [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 77-119 1.13e-07

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


:

Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 48.32  E-value: 1.13e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 134053959  77 LNTASTKELEAFRLLRGRRSINIVEHRENFGPFQNLESLMNVP 119
Cdd:COG1555   15 INTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVK 57
RuvC-like super family cl21482
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 156-352 6.96e-06

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: 46.97  E-value: 6.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 156 KPDIERERLKAVNSIISIVFGTRRIAWAHLD--------RKLTVLDWQ---------QSDRWSLmrgIYSSSVY---LEE 215
Cdd:cd16963   32 ELASLSKKLPGPLSILSIDMGIRNLAYCHLSlpktsphrRKPTLVDWNkldleekfgVSGADKL---SFSPSYYarlAYQ 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 216 ISSIISKMPKADFYVLEK-TGLSIQNSSLFPILLHFHIMEAMLYALL---NKTFAQDGQHQVLSMNRNAVGKHFE--LMI 289
Cdd:cd16963  109 LVNELLLPPNPDLILIERqRFRSGGSSAVLEWTLRVNMLEAMLYAVLytrRQQGKSKSKADVISSSPQRMVRYWLsrLDR 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 290 GDSRTSGKELVKQ----------FLFDSILK-ADPRVFFPSDKIVH--YRQMF-------------LSTELQRVEELYDS 343
Cdd:cd16963  189 KSSRPDVKKKKKKsyknskkariDLVKNWLSdSNVSPFLLLLPELSsrLRKLFnkkkslkktstsdDAAGVKKLDDLADS 268


                 ....*....
gi 134053959 344 LLQAIAFYE 352
Cdd:cd16963  269 LLQGLAWLE 277
 
Name Accession Description Interval E-value
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 77-119 1.13e-07

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 48.32  E-value: 1.13e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 134053959  77 LNTASTKELEAFRLLRGRRSINIVEHRENFGPFQNLESLMNVP 119
Cdd:COG1555   15 INTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVK 57
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 77-124 1.84e-07

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 47.48  E-value: 1.84e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 134053959   77 LNTASTKELEAFRLLRGRRSINIVEHRENFGPFQNLESLMNVPLFKYK 124
Cdd:pfam12836   6 INTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPK 53
CCE1 cd16963
fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1; ...
 156-352 6.96e-06

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: 46.97  E-value: 6.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 156 KPDIERERLKAVNSIISIVFGTRRIAWAHLD--------RKLTVLDWQ---------QSDRWSLmrgIYSSSVY---LEE 215
Cdd:cd16963   32 ELASLSKKLPGPLSILSIDMGIRNLAYCHLSlpktsphrRKPTLVDWNkldleekfgVSGADKL---SFSPSYYarlAYQ 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 216 ISSIISKMPKADFYVLEK-TGLSIQNSSLFPILLHFHIMEAMLYALL---NKTFAQDGQHQVLSMNRNAVGKHFE--LMI 289
Cdd:cd16963  109 LVNELLLPPNPDLILIERqRFRSGGSSAVLEWTLRVNMLEAMLYAVLytrRQQGKSKSKADVISSSPQRMVRYWLsrLDR 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 290 GDSRTSGKELVKQ----------FLFDSILK-ADPRVFFPSDKIVH--YRQMF-------------LSTELQRVEELYDS 343
Cdd:cd16963  189 KSSRPDVKKKKKKsyknskkariDLVKNWLSdSNVSPFLLLLPELSsrLRKLFnkkkslkktstsdDAAGVKKLDDLADS 268


                 ....*....
gi 134053959 344 LLQAIAFYE 352
Cdd:cd16963  269 LLQGLAWLE 277
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 77-119 2.33e-03

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 36.06  E-value: 2.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 134053959   77 LNTASTKELEafRLLRG---RRSINIVEHRENFGPFQNLESLMNVP 119
Cdd:TIGR00426  10 INTATAEELQ--RAMNGvglKKAEAIVSYREEYGPFKTVEDLKQVP 53
 
Name Accession Description Interval E-value
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 77-119 1.13e-07

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 48.32  E-value: 1.13e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 134053959  77 LNTASTKELEAFRLLRGRRSINIVEHRENFGPFQNLESLMNVP 119
Cdd:COG1555   15 INTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVK 57
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 77-124 1.84e-07

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 47.48  E-value: 1.84e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 134053959   77 LNTASTKELEAFRLLRGRRSINIVEHRENFGPFQNLESLMNVPLFKYK 124
Cdd:pfam12836   6 INTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPK 53
CCE1 cd16963
fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1; ...
 156-352 6.96e-06

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: 46.97  E-value: 6.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 156 KPDIERERLKAVNSIISIVFGTRRIAWAHLD--------RKLTVLDWQ---------QSDRWSLmrgIYSSSVY---LEE 215
Cdd:cd16963   32 ELASLSKKLPGPLSILSIDMGIRNLAYCHLSlpktsphrRKPTLVDWNkldleekfgVSGADKL---SFSPSYYarlAYQ 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 216 ISSIISKMPKADFYVLEK-TGLSIQNSSLFPILLHFHIMEAMLYALL---NKTFAQDGQHQVLSMNRNAVGKHFE--LMI 289
Cdd:cd16963  109 LVNELLLPPNPDLILIERqRFRSGGSSAVLEWTLRVNMLEAMLYAVLytrRQQGKSKSKADVISSSPQRMVRYWLsrLDR 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134053959 290 GDSRTSGKELVKQ----------FLFDSILK-ADPRVFFPSDKIVH--YRQMF-------------LSTELQRVEELYDS 343
Cdd:cd16963  189 KSSRPDVKKKKKKsyknskkariDLVKNWLSdSNVSPFLLLLPELSsrLRKLFnkkkslkktstsdDAAGVKKLDDLADS 268


                 ....*....
gi 134053959 344 LLQAIAFYE 352
Cdd:cd16963  269 LLQGLAWLE 277
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 77-119 2.33e-03

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 36.06  E-value: 2.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 134053959   77 LNTASTKELEafRLLRG---RRSINIVEHRENFGPFQNLESLMNVP 119
Cdd:TIGR00426  10 INTATAEELQ--RAMNGvglKKAEAIVSYREEYGPFKTVEDLKQVP 53
 
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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