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Conserved domains on  [gi|1824670926|ref|NP_000274|]
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rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 1 [Homo sapiens]

Protein Classification

3',5'-cyclic nucleotide phosphodiesterase( domain architecture ID 10637639)

3',5'-cyclic nucleotide phosphodiesterase catalyzes the hydrolysis of cAMP or cGMP to produce adenosine 5'-phosphate or guanosine 5'-phosphate, respectively

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PDEase_I pfam00233
3'5'-cyclic nucleotide phosphodiesterase;
556-800 3.68e-104

3'5'-cyclic nucleotide phosphodiesterase;


:

Pssm-ID: 459723  Cd Length: 238  Bit Score: 321.42  E-value: 3.68e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 556 YHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHG-SSILERHHLEFGK 634
Cdd:pfam00233   1 YHNWRHAFDVTQTMYYLLKTGKLKEVLTDLEILALLIAALCHDVDHPGTNNAFLIKTKSPLAILYNdSSVLENHHCATAF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 635 FLLSEETLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRAMFQKIVDESKNYQDKKSwveylslETTRKEIVMAMMM 714
Cdd:pfam00233  81 QILQDEECNIFSNLSDEEYKEVRKLIISLILATDMAKHFELLKKFKSLLESKKTLDFLEN-------EEDRRLLLLSMLI 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 715 TACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTvLDQQPIPMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEIL 794
Cdd:pfam00233 154 KAADISNPTRPWEISKKWADLVAEEFFRQGDLEKE-LGLPVSPLMDREKKTSLPKSQIGFIDFIVLPLFEALAKLFPELQ 232

                  ....*.
gi 1824670926 795 PMFDRL 800
Cdd:pfam00233 233 PLLDQL 238
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
71-230 4.83e-26

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


:

Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 104.77  E-value: 4.83e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926   71 NMERVVFKVLRRLCTLLQADRCSLFMYrQRNGVAELATRLFSVQPdsvledclvPPDSEIVFPLDIGVVGHVAQTKKMVN 150
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLV-DENDRGELVLVAADGLT---------LPTLGIRFPLDEGLAGRVAETGRPLN 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  151 VEDVAECPHFssFADELTDY-KTKNMLATPIMNGKDVVAVIMAVNKLNGPFFTSEDEDVFLKYLNFATLYLKIYHLSYLH 229
Cdd:smart00065  71 IPDVEADPLF--AEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148

                   .
gi 1824670926  230 N 230
Cdd:smart00065 149 R 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
252-439 3.77e-22

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


:

Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 93.60  E-value: 3.77e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  252 DIERQFHKAFYTVRAYLNCERYSVGLLDMTKEKEffdVWSVLMGESQPysgprtpdgreivfykvidyvlhgkeeikvip 331
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGE---LVLVAADGLTL-------------------------------- 45
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  332 TPSADHWALASGLPSYVAESGFICNIMNASADEmfkFQEGALDDSGWLIKNVLSMPIVNKkEEIVGVATFYNRKDGKPFD 411
Cdd:smart00065  46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVEADP---LFAEDLLGRYQGVRSFLAVPLVAD-GELVGVLALHNKKSPRPFT 121
                          170       180
                   ....*....|....*....|....*...
gi 1824670926  412 EQDEVLMESLTQFLGWSVMNTDTYDKMN 439
Cdd:smart00065 122 EEDEELLQALANQLAIALANAQLYEELR 149
 
Name Accession Description Interval E-value
PDEase_I pfam00233
3'5'-cyclic nucleotide phosphodiesterase;
556-800 3.68e-104

3'5'-cyclic nucleotide phosphodiesterase;


Pssm-ID: 459723  Cd Length: 238  Bit Score: 321.42  E-value: 3.68e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 556 YHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHG-SSILERHHLEFGK 634
Cdd:pfam00233   1 YHNWRHAFDVTQTMYYLLKTGKLKEVLTDLEILALLIAALCHDVDHPGTNNAFLIKTKSPLAILYNdSSVLENHHCATAF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 635 FLLSEETLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRAMFQKIVDESKNYQDKKSwveylslETTRKEIVMAMMM 714
Cdd:pfam00233  81 QILQDEECNIFSNLSDEEYKEVRKLIISLILATDMAKHFELLKKFKSLLESKKTLDFLEN-------EEDRRLLLLSMLI 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 715 TACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTvLDQQPIPMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEIL 794
Cdd:pfam00233 154 KAADISNPTRPWEISKKWADLVAEEFFRQGDLEKE-LGLPVSPLMDREKKTSLPKSQIGFIDFIVLPLFEALAKLFPELQ 232

                  ....*.
gi 1824670926 795 PMFDRL 800
Cdd:pfam00233 233 PLLDQL 238
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
71-230 4.83e-26

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 104.77  E-value: 4.83e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926   71 NMERVVFKVLRRLCTLLQADRCSLFMYrQRNGVAELATRLFSVQPdsvledclvPPDSEIVFPLDIGVVGHVAQTKKMVN 150
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLV-DENDRGELVLVAADGLT---------LPTLGIRFPLDEGLAGRVAETGRPLN 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  151 VEDVAECPHFssFADELTDY-KTKNMLATPIMNGKDVVAVIMAVNKLNGPFFTSEDEDVFLKYLNFATLYLKIYHLSYLH 229
Cdd:smart00065  71 IPDVEADPLF--AEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148

                   .
gi 1824670926  230 N 230
Cdd:smart00065 149 R 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
252-439 3.77e-22

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 93.60  E-value: 3.77e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  252 DIERQFHKAFYTVRAYLNCERYSVGLLDMTKEKEffdVWSVLMGESQPysgprtpdgreivfykvidyvlhgkeeikvip 331
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGE---LVLVAADGLTL-------------------------------- 45
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  332 TPSADHWALASGLPSYVAESGFICNIMNASADEmfkFQEGALDDSGWLIKNVLSMPIVNKkEEIVGVATFYNRKDGKPFD 411
Cdd:smart00065  46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVEADP---LFAEDLLGRYQGVRSFLAVPLVAD-GELVGVLALHNKKSPRPFT 121
                          170       180
                   ....*....|....*....|....*...
gi 1824670926  412 EQDEVLMESLTQFLGWSVMNTDTYDKMN 439
Cdd:smart00065 122 EEDEELLQALANQLAIALANAQLYEELR 149
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
57-209 1.01e-17

Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 81.87  E-value: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  57 TALLELVQDMQESINMERVVFKVLRRLCTLLQADRCSLFMYRQRNGVAEL-ATRLFSvqPDSVledclvppdSEIVFPLD 135
Cdd:COG3605     4 KALRRISEAVASALDLDEALDRIVRRIAEALGVDVCSIYLLDPDGGRLELrATEGLN--PEAV---------GKVRLPLG 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1824670926 136 IGVVGHVAQTKKMVNVEDVAECPHFSSFaDELTDYKTKNMLATPIMNGKDVVAVImAVNKLNGPFFTSEDEDVF 209
Cdd:COG3605    73 EGLVGLVAERGEPLNLADAASHPRFKYF-PETGEEGFRSFLGVPIIRRGRVLGVL-VVQSREPREFTEEEVEFL 144
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
71-209 1.21e-14

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 71.36  E-value: 1.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  71 NMERVVFKVLRRLCTLLQADRCSLFMYRQrNGVAELatrlfSVQPDSVLEDCLVPPdseivfpldIGVVGHVAQTKKMVN 150
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDA-DGLEYL-----PPGARWLKAAGLEIP---------PGTGVTVLRTGRPLV 65
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1824670926 151 VEDVAECPHFSSFADELTDYKTKNMLATPIMNGKDVVAVIMAVNKlnGPFFTSEDEDVF 209
Cdd:pfam01590  66 VPDAAGDPRFLDPLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHP--RPPFTEEELELL 122
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
555-640 8.96e-09

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 54.22  E-value: 8.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  555 TYHNWRHGFNVAQTMFTLLMTGKLksyytdLEAFAMVTAGLCHDIDHRGTNNLYQMKsqnplaklhgSSILERHHLEFGK 634
Cdd:smart00471   2 DYHVFEHSLRVAQLAAALAEELGL------LDIELLLLAALLHDIGKPGTPDSFLVK----------TSVLEDHHFIGAE 65

                   ....*.
gi 1824670926  635 FLLSEE 640
Cdd:smart00471  66 ILLEEE 71
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
556-741 1.87e-07

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 51.19  E-value: 1.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 556 YHNWRHGFNVAQTMFTLLMtgklKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYqmksqnplakLHGSSILERHHLEFGKF 635
Cdd:cd00077     1 EHRFEHSLRVAQLARRLAE----ELGLSEEDIELLRLAALLHDIGKPGTPDAI----------TEEESELEKDHAIVGAE 66
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 636 LLSEETLniyqnlnrrqhEHVIHLMDIAIIATDlALYFKKRAMFQKIVDESKNYQDKkswveylslettrkeivMAMMMT 715
Cdd:cd00077    67 ILRELLL-----------EEVIKLIDELILAVD-ASHHERLDGLGYPDGLKGEEITL-----------------EARIVK 117
                         170       180
                  ....*....|....*....|....*...
gi 1824670926 716 ACDLSAITK--PWEVQSKVALLVAAEFW 741
Cdd:cd00077   118 LADRLDALRrdSREKRRRIAEEDLEELL 145
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
332-429 3.79e-06

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 47.09  E-value: 3.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 332 TPSADHWALASGL------PSYVAESGFICNIMNASADEMFKFQEGALDDSGwlIKNVLSMPIVNKkEEIVGVATFYNRK 405
Cdd:pfam01590  35 LPPGARWLKAAGLeippgtGVTVLRTGRPLVVPDAAGDPRFLDPLLLLRNFG--IRSLLAVPIIDD-GELLGVLVLHHPR 111
                          90       100
                  ....*....|....*....|....
gi 1824670926 406 DgkPFDEQDEVLMESLTQFLGWSV 429
Cdd:pfam01590 112 P--PFTEEELELLEVLADQVAIAL 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
330-444 7.74e-05

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 46.34  E-value: 7.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 330 IPTPSADHWALASGLPSYVAESGFICNIMNASADEMFK-FQEGALDDSGwlIKNVLSMPIVNKkEEIVGVATFYNRKDGk 408
Cdd:COG2203   248 LPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFApSLRELLLALG--IRSLLCVPLLVD-GRLIGVLALYSKEPR- 323
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1824670926 409 PFDEQDEVLMESLTQFLGWSVMNTDTYDKMNKLENR 444
Cdd:COG2203   324 AFTEEDLELLEALADQAAIAIERARLYEALEAALAA 359
 
Name Accession Description Interval E-value
PDEase_I pfam00233
3'5'-cyclic nucleotide phosphodiesterase;
556-800 3.68e-104

3'5'-cyclic nucleotide phosphodiesterase;


Pssm-ID: 459723  Cd Length: 238  Bit Score: 321.42  E-value: 3.68e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 556 YHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHG-SSILERHHLEFGK 634
Cdd:pfam00233   1 YHNWRHAFDVTQTMYYLLKTGKLKEVLTDLEILALLIAALCHDVDHPGTNNAFLIKTKSPLAILYNdSSVLENHHCATAF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 635 FLLSEETLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRAMFQKIVDESKNYQDKKSwveylslETTRKEIVMAMMM 714
Cdd:pfam00233  81 QILQDEECNIFSNLSDEEYKEVRKLIISLILATDMAKHFELLKKFKSLLESKKTLDFLEN-------EEDRRLLLLSMLI 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 715 TACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTvLDQQPIPMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEIL 794
Cdd:pfam00233 154 KAADISNPTRPWEISKKWADLVAEEFFRQGDLEKE-LGLPVSPLMDREKKTSLPKSQIGFIDFIVLPLFEALAKLFPELQ 232

                  ....*.
gi 1824670926 795 PMFDRL 800
Cdd:pfam00233 233 PLLDQL 238
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
71-230 4.83e-26

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 104.77  E-value: 4.83e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926   71 NMERVVFKVLRRLCTLLQADRCSLFMYrQRNGVAELATRLFSVQPdsvledclvPPDSEIVFPLDIGVVGHVAQTKKMVN 150
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLV-DENDRGELVLVAADGLT---------LPTLGIRFPLDEGLAGRVAETGRPLN 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  151 VEDVAECPHFssFADELTDY-KTKNMLATPIMNGKDVVAVIMAVNKLNGPFFTSEDEDVFLKYLNFATLYLKIYHLSYLH 229
Cdd:smart00065  71 IPDVEADPLF--AEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148

                   .
gi 1824670926  230 N 230
Cdd:smart00065 149 R 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
252-439 3.77e-22

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 93.60  E-value: 3.77e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  252 DIERQFHKAFYTVRAYLNCERYSVGLLDMTKEKEffdVWSVLMGESQPysgprtpdgreivfykvidyvlhgkeeikvip 331
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGE---LVLVAADGLTL-------------------------------- 45
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  332 TPSADHWALASGLPSYVAESGFICNIMNASADEmfkFQEGALDDSGWLIKNVLSMPIVNKkEEIVGVATFYNRKDGKPFD 411
Cdd:smart00065  46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVEADP---LFAEDLLGRYQGVRSFLAVPLVAD-GELVGVLALHNKKSPRPFT 121
                          170       180
                   ....*....|....*....|....*...
gi 1824670926  412 EQDEVLMESLTQFLGWSVMNTDTYDKMN 439
Cdd:smart00065 122 EEDEELLQALANQLAIALANAQLYEELR 149
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
57-209 1.01e-17

Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 81.87  E-value: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  57 TALLELVQDMQESINMERVVFKVLRRLCTLLQADRCSLFMYRQRNGVAEL-ATRLFSvqPDSVledclvppdSEIVFPLD 135
Cdd:COG3605     4 KALRRISEAVASALDLDEALDRIVRRIAEALGVDVCSIYLLDPDGGRLELrATEGLN--PEAV---------GKVRLPLG 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1824670926 136 IGVVGHVAQTKKMVNVEDVAECPHFSSFaDELTDYKTKNMLATPIMNGKDVVAVImAVNKLNGPFFTSEDEDVF 209
Cdd:COG3605    73 EGLVGLVAERGEPLNLADAASHPRFKYF-PETGEEGFRSFLGVPIIRRGRVLGVL-VVQSREPREFTEEEVEFL 144
GAF COG2203
GAF domain [Signal transduction mechanisms];
52-209 3.42e-17

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 86.40  E-value: 3.42e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  52 QVEESTALLELVQDMQESINMERVVFKVLRRLCTLLQADRCSLFMYRQRNGVAELATRLFsvqpdsvledclVPPDSEIV 131
Cdd:COG2203   188 ELERLALLNEISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDGGELELVAAPG------------LPEEELGR 255
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1824670926 132 FPLDIGVVGHVAQTKKMVNVEDVAECPHFSSFADE-LTDYKTKNMLATPIMNGKDVVAVIMAVNKLNGPfFTSEDEDVF 209
Cdd:COG2203   256 LPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRElLLALGIRSLLCVPLLVDGRLIGVLALYSKEPRA-FTEEDLELL 333
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
71-209 1.21e-14

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 71.36  E-value: 1.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  71 NMERVVFKVLRRLCTLLQADRCSLFMYRQrNGVAELatrlfSVQPDSVLEDCLVPPdseivfpldIGVVGHVAQTKKMVN 150
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDA-DGLEYL-----PPGARWLKAAGLEIP---------PGTGVTVLRTGRPLV 65
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1824670926 151 VEDVAECPHFSSFADELTDYKTKNMLATPIMNGKDVVAVIMAVNKlnGPFFTSEDEDVF 209
Cdd:pfam01590  66 VPDAAGDPRFLDPLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHP--RPPFTEEELELL 122
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
555-640 8.96e-09

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 54.22  E-value: 8.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926  555 TYHNWRHGFNVAQTMFTLLMTGKLksyytdLEAFAMVTAGLCHDIDHRGTNNLYQMKsqnplaklhgSSILERHHLEFGK 634
Cdd:smart00471   2 DYHVFEHSLRVAQLAAALAEELGL------LDIELLLLAALLHDIGKPGTPDSFLVK----------TSVLEDHHFIGAE 65

                   ....*.
gi 1824670926  635 FLLSEE 640
Cdd:smart00471  66 ILLEEE 71
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
556-741 1.87e-07

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 51.19  E-value: 1.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 556 YHNWRHGFNVAQTMFTLLMtgklKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYqmksqnplakLHGSSILERHHLEFGKF 635
Cdd:cd00077     1 EHRFEHSLRVAQLARRLAE----ELGLSEEDIELLRLAALLHDIGKPGTPDAI----------TEEESELEKDHAIVGAE 66
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 636 LLSEETLniyqnlnrrqhEHVIHLMDIAIIATDlALYFKKRAMFQKIVDESKNYQDKkswveylslettrkeivMAMMMT 715
Cdd:cd00077    67 ILRELLL-----------EEVIKLIDELILAVD-ASHHERLDGLGYPDGLKGEEITL-----------------EARIVK 117
                         170       180
                  ....*....|....*....|....*...
gi 1824670926 716 ACDLSAITK--PWEVQSKVALLVAAEFW 741
Cdd:cd00077   118 LADRLDALRrdSREKRRRIAEEDLEELL 145
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
332-429 3.79e-06

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 47.09  E-value: 3.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 332 TPSADHWALASGL------PSYVAESGFICNIMNASADEMFKFQEGALDDSGwlIKNVLSMPIVNKkEEIVGVATFYNRK 405
Cdd:pfam01590  35 LPPGARWLKAAGLeippgtGVTVLRTGRPLVVPDAAGDPRFLDPLLLLRNFG--IRSLLAVPIIDD-GELLGVLVLHHPR 111
                          90       100
                  ....*....|....*....|....
gi 1824670926 406 DgkPFDEQDEVLMESLTQFLGWSV 429
Cdd:pfam01590 112 P--PFTEEELELLEVLADQVAIAL 133
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
128-209 1.29e-05

GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433019 [Multi-domain]  Cd Length: 137  Bit Score: 45.54  E-value: 1.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 128 SEIVFPLDIGVVGHVAQTKKMVNVEDVAECPHFSSFADELTDYKTknMLATPIMNGKDVVAVImAVNKLNGPFFTSEDED 207
Cdd:pfam13185  47 AALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKGLPAGHAGLRS--FLSVPLVSGGRVVGVL-ALGSNRPGAFDEEDLE 123

                  ..
gi 1824670926 208 VF 209
Cdd:pfam13185 124 LL 125
GAF COG2203
GAF domain [Signal transduction mechanisms];
330-444 7.74e-05

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 46.34  E-value: 7.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 330 IPTPSADHWALASGLPSYVAESGFICNIMNASADEMFK-FQEGALDDSGwlIKNVLSMPIVNKkEEIVGVATFYNRKDGk 408
Cdd:COG2203   248 LPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFApSLRELLLALG--IRSLLCVPLLVD-GRLIGVLALYSKEPR- 323
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1824670926 409 PFDEQDEVLMESLTQFLGWSVMNTDTYDKMNKLENR 444
Cdd:COG2203   324 AFTEEDLELLEALADQAAIAIERARLYEALEAALAA 359
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
132-213 1.14e-03

GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, Signal transduction mechanisms];


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 40.20  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670926 132 FPLDIGVVGHVAQTKKMVNVEDVAECPHFSSFadeltDYKTKNMLATPIMNGKDVVAVI-MAVNKLNgpFFTSEDEDvFL 210
Cdd:COG1956    72 IPFGKGVCGTAAAEGETQLVPDVHAFPGHIAC-----DSASRSEIVVPIFKDGEVIGVLdIDSPTPG--RFDEEDQA-GL 143

                  ...
gi 1824670926 211 KYL 213
Cdd:COG1956   144 EAL 146
 
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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