NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15221706|ref|NP_173835|]
View 

Paired amphipathic helix (PAH2) superfamily protein [Arabidopsis thaliana]

Protein Classification

PAH domain-containing protein( domain architecture ID 10496261)

PAH domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Sin3 super family cl35027
Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];
12-196 2.63e-11

Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];


The actual alignment was detected with superfamily member COG5602:

Pssm-ID: 227889 [Multi-domain]  Cd Length: 1163  Bit Score: 63.40  E-value: 2.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221706   12 LEDVKAYVNAVEVALQEmEPARFGMFVRLFRGFTAPRIGMPTFSARMQDLLKDHPSLCLGLNVLLPPEYQ---------- 81
Cdd:COG5602  128 VSDALSYLEKVKEQFSN-RPEIYNNFLDIMKDFKSQAIDTPGVIERVSVLFRGYPHLIEGFNTFLPSGYKiegslpqpng 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221706   82 -----------LTIPPEASEEF-----------HKVVGRS----VPVPPKVVGRSLPRPEPTIDDATSYLIAVKEAFHDE 135
Cdd:COG5602  207 srlhvttpqgpLSSPPVQSSYYvapcnhdqrtsHPTLPSDsqpePSAPSHMPSDARGKHQVDFNQAIIFVNKVKVRFQNN 286

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15221706  136 PAKYGEMLKLLKDFKARRVDAACVIARVEELMKDHLNLLFGFCVFLSATTSFTTKLKARFQ 196
Cdd:COG5602  287 PEMYYDFLDSLRTYQMKQRSIQEVYARVTKLFAEAPDLLEEFKEFLPDSSVSAEQSTANAQ 347
PAH pfam02671
Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The ...
 201-245 1.91e-06

Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.


:

Pssm-ID: 460645 [Multi-domain]  Cd Length: 45  Bit Score: 43.56  E-value: 1.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15221706   201 QVVDSVLQIMRMYGEGNKSKHDAYQEVVALVQGHDDLVMELSQIL 245
Cdd:pfam02671   1 EVYDEFLKILNDYKQEIIDIAEVIARVSELLKGHPDLLEGFNTFL 45
 
Name Accession Description Interval E-value
Sin3 COG5602
Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];
12-196 2.63e-11

Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];


Pssm-ID: 227889 [Multi-domain]  Cd Length: 1163  Bit Score: 63.40  E-value: 2.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221706   12 LEDVKAYVNAVEVALQEmEPARFGMFVRLFRGFTAPRIGMPTFSARMQDLLKDHPSLCLGLNVLLPPEYQ---------- 81
Cdd:COG5602  128 VSDALSYLEKVKEQFSN-RPEIYNNFLDIMKDFKSQAIDTPGVIERVSVLFRGYPHLIEGFNTFLPSGYKiegslpqpng 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221706   82 -----------LTIPPEASEEF-----------HKVVGRS----VPVPPKVVGRSLPRPEPTIDDATSYLIAVKEAFHDE 135
Cdd:COG5602  207 srlhvttpqgpLSSPPVQSSYYvapcnhdqrtsHPTLPSDsqpePSAPSHMPSDARGKHQVDFNQAIIFVNKVKVRFQNN 286

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15221706  136 PAKYGEMLKLLKDFKARRVDAACVIARVEELMKDHLNLLFGFCVFLSATTSFTTKLKARFQ 196
Cdd:COG5602  287 PEMYYDFLDSLRTYQMKQRSIQEVYARVTKLFAEAPDLLEEFKEFLPDSSVSAEQSTANAQ 347
PAH pfam02671
Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The ...
 137-181 8.80e-10

Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.


Pssm-ID: 460645 [Multi-domain]  Cd Length: 45  Bit Score: 52.81  E-value: 8.80e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15221706   137 AKYGEMLKLLKDFKARRVDAACVIARVEELMKDHLNLLFGFCVFL 181
Cdd:pfam02671   1 EVYDEFLKILNDYKQEIIDIAEVIARVSELLKGHPDLLEGFNTFL 45
PAH pfam02671
Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The ...
 201-245 1.91e-06

Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.


Pssm-ID: 460645 [Multi-domain]  Cd Length: 45  Bit Score: 43.56  E-value: 1.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15221706   201 QVVDSVLQIMRMYGEGNKSKHDAYQEVVALVQGHDDLVMELSQIL 245
Cdd:pfam02671   1 EVYDEFLKILNDYKQEIIDIAEVIARVSELLKGHPDLLEGFNTFL 45
HN_RTEL1 cd13932
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); ...
 109-181 4.30e-03

harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination intermediates, in a reaction dependent upon ATP hydrolysis. Human RTEL1 is implicated in the etiology of Dyskeratosis congenital (DC, is an inherited bone marrow failure and cancer predisposition syndrome). Point mutations in its helicase domains, and truncations which result in loss of its C-terminus have been discovered in DC families. RTEL1 is also a candidate gene influencing glioma susceptibility. The C-terminal domain of RTEL1, represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin.


Pssm-ID: 259826 [Multi-domain]  Cd Length: 99  Bit Score: 35.71  E-value: 4.30e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15221706 109 RSLPRPEPTIDDATSYLIAVKEAFhdEPAKYGEMLKLLKDFKaRRVDAACVIARVEELMKDH--LNLLFGFCVFL 181
Cdd:cd13932   8 SSSSGAKPAPESASAFLREVKQKL--SAAEYRQFSAALQAYK-TGDDFEQLLAVLAELFAEPerHPLLRGFRRFV 79
 
Name Accession Description Interval E-value
Sin3 COG5602
Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];
12-196 2.63e-11

Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];


Pssm-ID: 227889 [Multi-domain]  Cd Length: 1163  Bit Score: 63.40  E-value: 2.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221706   12 LEDVKAYVNAVEVALQEmEPARFGMFVRLFRGFTAPRIGMPTFSARMQDLLKDHPSLCLGLNVLLPPEYQ---------- 81
Cdd:COG5602  128 VSDALSYLEKVKEQFSN-RPEIYNNFLDIMKDFKSQAIDTPGVIERVSVLFRGYPHLIEGFNTFLPSGYKiegslpqpng 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221706   82 -----------LTIPPEASEEF-----------HKVVGRS----VPVPPKVVGRSLPRPEPTIDDATSYLIAVKEAFHDE 135
Cdd:COG5602  207 srlhvttpqgpLSSPPVQSSYYvapcnhdqrtsHPTLPSDsqpePSAPSHMPSDARGKHQVDFNQAIIFVNKVKVRFQNN 286

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15221706  136 PAKYGEMLKLLKDFKARRVDAACVIARVEELMKDHLNLLFGFCVFLSATTSFTTKLKARFQ 196
Cdd:COG5602  287 PEMYYDFLDSLRTYQMKQRSIQEVYARVTKLFAEAPDLLEEFKEFLPDSSVSAEQSTANAQ 347
Sin3 COG5602
Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];
110-181 4.59e-11

Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics];


Pssm-ID: 227889 [Multi-domain]  Cd Length: 1163  Bit Score: 62.63  E-value: 4.59e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15221706  110 SLPRPEPTIDDATSYLIAVKEAFHDEPAKYGEMLKLLKDFKARRVDAACVIARVEELMKDHLNLLFGFCVFL 181
Cdd:COG5602  120 RIPYRPLDVSDALSYLEKVKEQFSNRPEIYNNFLDIMKDFKSQAIDTPGVIERVSVLFRGYPHLIEGFNTFL 191
PAH pfam02671
Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The ...
 137-181 8.80e-10

Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.


Pssm-ID: 460645 [Multi-domain]  Cd Length: 45  Bit Score: 52.81  E-value: 8.80e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15221706   137 AKYGEMLKLLKDFKARRVDAACVIARVEELMKDHLNLLFGFCVFL 181
Cdd:pfam02671   1 EVYDEFLKILNDYKQEIIDIAEVIARVSELLKGHPDLLEGFNTFL 45
PAH pfam02671
Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The ...
 201-245 1.91e-06

Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.


Pssm-ID: 460645 [Multi-domain]  Cd Length: 45  Bit Score: 43.56  E-value: 1.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15221706   201 QVVDSVLQIMRMYGEGNKSKHDAYQEVVALVQGHDDLVMELSQIL 245
Cdd:pfam02671   1 EVYDEFLKILNDYKQEIIDIAEVIARVSELLKGHPDLLEGFNTFL 45
PAH pfam02671
Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The ...
 36-76 5.60e-06

Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.


Pssm-ID: 460645 [Multi-domain]  Cd Length: 45  Bit Score: 42.41  E-value: 5.60e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 15221706    36 MFVRLFRGFTAPRIGMPTFSARMQDLLKDHPSLCLGLNVLL 76
Cdd:pfam02671   5 EFLKILNDYKQEIIDIAEVIARVSELLKGHPDLLEGFNTFL 45
HN_RTEL1 cd13932
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); ...
 109-181 4.30e-03

harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination intermediates, in a reaction dependent upon ATP hydrolysis. Human RTEL1 is implicated in the etiology of Dyskeratosis congenital (DC, is an inherited bone marrow failure and cancer predisposition syndrome). Point mutations in its helicase domains, and truncations which result in loss of its C-terminus have been discovered in DC families. RTEL1 is also a candidate gene influencing glioma susceptibility. The C-terminal domain of RTEL1, represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin.


Pssm-ID: 259826 [Multi-domain]  Cd Length: 99  Bit Score: 35.71  E-value: 4.30e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15221706 109 RSLPRPEPTIDDATSYLIAVKEAFhdEPAKYGEMLKLLKDFKaRRVDAACVIARVEELMKDH--LNLLFGFCVFL 181
Cdd:cd13932   8 SSSSGAKPAPESASAFLREVKQKL--SAAEYRQFSAALQAYK-TGDDFEQLLAVLAELFAEPerHPLLRGFRRFV 79
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH