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Conserved domains on  [gi|28076933|ref|NP_081526|]
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cytochrome c oxidase assembly factor 7 [Mus musculus]

Protein Classification

tetratricopeptide repeat protein( domain architecture ID 11434433)

tetratricopeptide repeat (TPR) protein may adopt a right-handed helical structure with an amphipathic channel and may function as an interaction scaffold in the formation of multi-protein complexes

CATH:  1.25.40.10
Gene Ontology:  GO:0005515
PubMed:  10517866|30708253
SCOP:  3001345

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TPR COG0790
TPR repeat [General function prediction only];
21-214 6.33e-30

TPR repeat [General function prediction only];


:

Pssm-ID: 440553 [Multi-domain]  Cd Length: 241  Bit Score: 111.56  E-value: 6.33e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  21 EVECHYQCYREKDPEGCYRLVDYLE---GIQKNFDEAAKVLKFNCEKyGHGDSCYKLGAYYVTGKGgLTQDLKAASSCFL 97
Cdd:COG0790  50 AAAAAAAAAAAGGAEAQYNLGLMYAegrGVPKDYEKALEWFEKAAEQ-GDAEAQYNLGLMYEEGLG-VPQDYAKALEWYE 127

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  98 MACEKpgkKSVESCHNVGLLAHDGqvnEDGQPDLGKARDYYSRACDGGYAASCFNLSAMFLQGApGFPKDMGLACKYSMK 177
Cdd:COG0790 128 KAAEQ---GDADAQYNLGLLYLNG---EGVPKDPAKAAEWYRKAAEQGDADAQYNLGVLYENGR-GVPKDPAKALEWYRK 200

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 28076933 178 ACDLGHVWACANASRMYKLGDGVDKDEAKAEVLKNRA 214
Cdd:COG0790 201 AAEQGDADAQYNLGRLYLNGEGVEKDLEKALRWLRKA 237
 
Name Accession Description Interval E-value
TPR COG0790
TPR repeat [General function prediction only];
21-214 6.33e-30

TPR repeat [General function prediction only];


Pssm-ID: 440553 [Multi-domain]  Cd Length: 241  Bit Score: 111.56  E-value: 6.33e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  21 EVECHYQCYREKDPEGCYRLVDYLE---GIQKNFDEAAKVLKFNCEKyGHGDSCYKLGAYYVTGKGgLTQDLKAASSCFL 97
Cdd:COG0790  50 AAAAAAAAAAAGGAEAQYNLGLMYAegrGVPKDYEKALEWFEKAAEQ-GDAEAQYNLGLMYEEGLG-VPQDYAKALEWYE 127

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  98 MACEKpgkKSVESCHNVGLLAHDGqvnEDGQPDLGKARDYYSRACDGGYAASCFNLSAMFLQGApGFPKDMGLACKYSMK 177
Cdd:COG0790 128 KAAEQ---GDADAQYNLGLLYLNG---EGVPKDPAKAAEWYRKAAEQGDADAQYNLGVLYENGR-GVPKDPAKALEWYRK 200

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 28076933 178 ACDLGHVWACANASRMYKLGDGVDKDEAKAEVLKNRA 214
Cdd:COG0790 201 AAEQGDADAQYNLGRLYLNGEGVEKDLEKALRWLRKA 237
OBF_DNA_ligase_III cd07967
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ...
 74-131 2.35e-03

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153436  Cd Length: 139  Bit Score: 36.96  E-value: 2.35e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28076933  74 LGAYYVTG-KGGLTqdlkaasSCFLMACEKPGKK---SVESCHNvgllAHDGQVNEDGQPDL 131
Cdd:cd07967  10 LGAYYGTGsKGGMM-------SVFLMGCYDPNSKkwcTVTKCGN----GHDDATLARLQKEL 60
 
Name Accession Description Interval E-value
TPR COG0790
TPR repeat [General function prediction only];
21-214 6.33e-30

TPR repeat [General function prediction only];


Pssm-ID: 440553 [Multi-domain]  Cd Length: 241  Bit Score: 111.56  E-value: 6.33e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  21 EVECHYQCYREKDPEGCYRLVDYLE---GIQKNFDEAAKVLKFNCEKyGHGDSCYKLGAYYVTGKGgLTQDLKAASSCFL 97
Cdd:COG0790  50 AAAAAAAAAAAGGAEAQYNLGLMYAegrGVPKDYEKALEWFEKAAEQ-GDAEAQYNLGLMYEEGLG-VPQDYAKALEWYE 127

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  98 MACEKpgkKSVESCHNVGLLAHDGqvnEDGQPDLGKARDYYSRACDGGYAASCFNLSAMFLQGApGFPKDMGLACKYSMK 177
Cdd:COG0790 128 KAAEQ---GDADAQYNLGLLYLNG---EGVPKDPAKAAEWYRKAAEQGDADAQYNLGVLYENGR-GVPKDPAKALEWYRK 200

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 28076933 178 ACDLGHVWACANASRMYKLGDGVDKDEAKAEVLKNRA 214
Cdd:COG0790 201 AAEQGDADAQYNLGRLYLNGEGVEKDLEKALRWLRKA 237
TPR COG0790
TPR repeat [General function prediction only];
38-214 9.24e-25

TPR repeat [General function prediction only];


Pssm-ID: 440553 [Multi-domain]  Cd Length: 241  Bit Score: 97.69  E-value: 9.24e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  38 YRLVDYLEGIQKNFDEAAKVLKFNCEKYGHGDSCYKLGAYYVTGKgGLTQDLKAASSCFLMACEkpgKKSVESCHNVGLL 117
Cdd:COG0790  33 AAAAAAAALAAAAGAAAAAAAAAAAAAAGGAEAQYNLGLMYAEGR-GVPKDYEKALEWFEKAAE---QGDAEAQYNLGLM 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933 118 AHDGQvneDGQPDLGKARDYYSRACDGGYAASCFNLSAMFLQGApGFPKDMGLACKYSMKACDLGHVWACANASRMYKLG 197
Cdd:COG0790 109 YEEGL---GVPQDYAKALEWYEKAAEQGDADAQYNLGLLYLNGE-GVPKDPAKAAEWYRKAAEQGDADAQYNLGVLYENG 184

                       170
                ....*....|....*..
gi 28076933 198 DGVDKDEAKAEVLKNRA 214
Cdd:COG0790 185 RGVPKDPAKALEWYRKA 201
TPR COG0790
TPR repeat [General function prediction only];
33-143 1.90e-10

TPR repeat [General function prediction only];


Pssm-ID: 440553 [Multi-domain]  Cd Length: 241  Bit Score: 58.79  E-value: 1.90e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076933  33 DPEGCYRLVDYL---EGIQKNFDEAAKVLKFNCEKyGHGDSCYKLGAYYVTGKGgLTQDLKAASSCFLMACEKpgkKSVE 109
Cdd:COG0790 134 DADAQYNLGLLYlngEGVPKDPAKAAEWYRKAAEQ-GDADAQYNLGVLYENGRG-VPKDPAKALEWYRKAAEQ---GDAD 208

                        90       100       110
                ....*....|....*....|....*....|....
gi 28076933 110 SCHNVGLLAHDGqvnEDGQPDLGKARDYYSRACD 143
Cdd:COG0790 209 AQYNLGRLYLNG---EGVEKDLEKALRWLRKAAE 239
TPR COG0790
TPR repeat [General function prediction only];
33-102 1.20e-04

TPR repeat [General function prediction only];


Pssm-ID: 440553 [Multi-domain]  Cd Length: 241  Bit Score: 41.84  E-value: 1.20e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28076933  33 DPEGCYRLVDYLE---GIQKNFDEAAKVLKFNCEKyGHGDSCYKLGAYYVTGKGgLTQDLKAASSCFLMACEK 102
Cdd:COG0790 170 DADAQYNLGVLYEngrGVPKDPAKALEWYRKAAEQ-GDADAQYNLGRLYLNGEG-VEKDLEKALRWLRKAAEQ 240
OBF_DNA_ligase_III cd07967
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ...
 74-131 2.35e-03

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153436  Cd Length: 139  Bit Score: 36.96  E-value: 2.35e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28076933  74 LGAYYVTG-KGGLTqdlkaasSCFLMACEKPGKK---SVESCHNvgllAHDGQVNEDGQPDL 131
Cdd:cd07967  10 LGAYYGTGsKGGMM-------SVFLMGCYDPNSKkwcTVTKCGN----GHDDATLARLQKEL 60
 
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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