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Conserved domains on  [gi|157822587|ref|NP_001099494|]
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rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta [Rattus norvegicus]

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 6.13e-104

3'5'-cyclic nucleotide phosphodiesterase;


:

Pssm-ID: 459723  Cd Length: 238  Bit Score: 321.04  E-value: 6.13e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  556 YHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHG-SSILERHHLEFGK 634
Cdd:pfam00233   1 YHNWRHAFDVTQTMYYLLKTGKLKEVLTDLEILALLIAALCHDVDHPGTNNAFLIKTKSPLAILYNdSSVLENHHCATAF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  635 FLLAEESLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRTMFQKIVDESKNYEDKKSwveylslETTRKEIVMAMMM 714
Cdd:pfam00233  81 QILQDEECNIFSNLSDEEYKEVRKLIISLILATDMAKHFELLKKFKSLLESKKTLDFLEN-------EEDRRLLLLSMLI 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  715 TACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTvLDQQPIPMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEIL 794
Cdd:pfam00233 154 KAADISNPTRPWEISKKWADLVAEEFFRQGDLEKE-LGLPVSPLMDREKKTSLPKSQIGFIDFIVLPLFEALAKLFPELQ 232

                  ....*.
gi 157822587  795 PMFDRL 800
Cdd:pfam00233 233 PLLDQL 238
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
71-230 7.56e-25

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: 101.30  E-value: 7.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587    71 NMERVVFKVLRRLCTILHADRCSLFMYrQRNGVAELATRLFSVQPdslledclvPPDSEIVFPLDIGIVGHVAQTKKMIN 150
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLV-DENDRGELVLVAADGLT---------LPTLGIRFPLDEGLAGRVAETGRPLN 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   151 VQDVAECPhfSPFADELTDY-VTKNILSTPIMNGKDVVAVIMAVNKLDGPCFTSEDEDVFTKYLNFATLNLKIYHLSYLH 229
Cdd:smart00065  71 IPDVEADP--LFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148

                   .
gi 157822587   230 N 230
Cdd:smart00065 149 R 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
252-439 1.46e-23

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: 97.45  E-value: 1.46e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   252 DIERQFHKAFYTVRAYLNCDRYSVGLLDMtkekeffdvwpvlmgeaqpysgprtpDGREIVFYKVIDYILhgkedikviP 331
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDE--------------------------NDRGELVLVAADGLT---------L 45
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   332 TPPADHWALTSGLPTYVAESGFICNIMNASADEmfnFQEGPLDESGWVIKNVLSMPIVNkKEEIVGVATFYNRKDGKPFD 411
Cdd:smart00065  46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVEADP---LFAEDLLGRYQGVRSFLAVPLVA-DGELVGVLALHNKKSPRPFT 121
                          170       180
                   ....*....|....*....|....*...
gi 157822587   412 DQDEVLMESLTQFLGWSVLNTDTYDKMN 439
Cdd:smart00065 122 EEDEELLQALANQLAIALANAQLYEELR 149
 
Name Accession Description Interval E-value
PDEase_I pfam00233
3'5'-cyclic nucleotide phosphodiesterase;
556-800 6.13e-104

3'5'-cyclic nucleotide phosphodiesterase;


Pssm-ID: 459723  Cd Length: 238  Bit Score: 321.04  E-value: 6.13e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  556 YHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHG-SSILERHHLEFGK 634
Cdd:pfam00233   1 YHNWRHAFDVTQTMYYLLKTGKLKEVLTDLEILALLIAALCHDVDHPGTNNAFLIKTKSPLAILYNdSSVLENHHCATAF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  635 FLLAEESLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRTMFQKIVDESKNYEDKKSwveylslETTRKEIVMAMMM 714
Cdd:pfam00233  81 QILQDEECNIFSNLSDEEYKEVRKLIISLILATDMAKHFELLKKFKSLLESKKTLDFLEN-------EEDRRLLLLSMLI 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  715 TACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTvLDQQPIPMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEIL 794
Cdd:pfam00233 154 KAADISNPTRPWEISKKWADLVAEEFFRQGDLEKE-LGLPVSPLMDREKKTSLPKSQIGFIDFIVLPLFEALAKLFPELQ 232

                  ....*.
gi 157822587  795 PMFDRL 800
Cdd:pfam00233 233 PLLDQL 238
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
71-230 7.56e-25

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: 101.30  E-value: 7.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587    71 NMERVVFKVLRRLCTILHADRCSLFMYrQRNGVAELATRLFSVQPdslledclvPPDSEIVFPLDIGIVGHVAQTKKMIN 150
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLV-DENDRGELVLVAADGLT---------LPTLGIRFPLDEGLAGRVAETGRPLN 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   151 VQDVAECPhfSPFADELTDY-VTKNILSTPIMNGKDVVAVIMAVNKLDGPCFTSEDEDVFTKYLNFATLNLKIYHLSYLH 229
Cdd:smart00065  71 IPDVEADP--LFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148

                   .
gi 157822587   230 N 230
Cdd:smart00065 149 R 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
252-439 1.46e-23

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: 97.45  E-value: 1.46e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   252 DIERQFHKAFYTVRAYLNCDRYSVGLLDMtkekeffdvwpvlmgeaqpysgprtpDGREIVFYKVIDYILhgkedikviP 331
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDE--------------------------NDRGELVLVAADGLT---------L 45
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   332 TPPADHWALTSGLPTYVAESGFICNIMNASADEmfnFQEGPLDESGWVIKNVLSMPIVNkKEEIVGVATFYNRKDGKPFD 411
Cdd:smart00065  46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVEADP---LFAEDLLGRYQGVRSFLAVPLVA-DGELVGVLALHNKKSPRPFT 121
                          170       180
                   ....*....|....*....|....*...
gi 157822587   412 DQDEVLMESLTQFLGWSVLNTDTYDKMN 439
Cdd:smart00065 122 EEDEELLQALANQLAIALANAQLYEELR 149
GAF COG2203
GAF domain [Signal transduction mechanisms];
52-210 6.16e-17

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 85.63  E-value: 6.16e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  52 QVEESAALFELVQDMQESVNMERVVFKVLRRLCTILHADRCSLFMYRQRNGVAELATRlfSVQPDSLLEDclvppdseiv 131
Cdd:COG2203  188 ELERLALLNEISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDGGELELVAA--PGLPEEELGR---------- 255
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 132 FPLDIGIVGHVAQTKKMINVQDVAECPHFSPFADE-LTDYVTKNILSTPIMNGKDVVAVIMAVNKLDGPcFTSEDEDVFT 210
Cdd:COG2203  256 LPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRElLLALGIRSLLCVPLLVDGRLIGVLALYSKEPRA-FTEEDLELLE 334
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
71-210 1.02e-12

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: 65.96  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   71 NMERVVFKVLRRLCTILHADRCSLFMYRQrNGVAELatrlfSVQPDSLLEDCLVPPdseivfpldIGIVGHVAQTKKMIN 150
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDA-DGLEYL-----PPGARWLKAAGLEIP---------PGTGVTVLRTGRPLV 65
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  151 VQDVAECPHFSPFADELTDYVTKNILSTPIMNGKDVVAVIMAVNKldGPCFTSEDEDVFT 210
Cdd:pfam01590  66 VPDAAGDPRFLDPLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHP--RPPFTEEELELLE 123
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
555-655 1.89e-08

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: 53.45  E-value: 1.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   555 TYHNWRHGFNVAQTMFTLLMTGKLksyytdLEAFAMVTAGLCHDIDHRGTNNLYQMKsqnplaklhgSSILERHHLEFGK 634
Cdd:smart00471   2 DYHVFEHSLRVAQLAAALAEELGL------LDIELLLLAALLHDIGKPGTPDSFLVK----------TSVLEDHHFIGAE 65
                           90       100
                   ....*....|....*....|....*
gi 157822587   635 FLL----AEESLNIYQNLNRRQHEH 655
Cdd:smart00471  66 ILLeeeePRILEEILRTAILSHHER 90
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
556-741 2.83e-07

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 50.80  E-value: 2.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 556 YHNWRHGFNVAQTMFTLLMTGKLksyyTDLEAFAMVTAGLCHDIDHRGTNNLYqmksqnplakLHGSSILERHHLEFGKF 635
Cdd:cd00077    1 EHRFEHSLRVAQLARRLAEELGL----SEEDIELLRLAALLHDIGKPGTPDAI----------TEEESELEKDHAIVGAE 66
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 636 LLAEESLniyqnlnrrqhEHVIHLMDIAIIATDLALYFKKRTMFqkivdesknyedkkswveYLSLETTRKEIVMAMMMT 715
Cdd:cd00077   67 ILRELLL-----------EEVIKLIDELILAVDASHHERLDGLG------------------YPDGLKGEEITLEARIVK 117
                        170       180
                 ....*....|....*....|....*...
gi 157822587 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 5.92e-07

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: 49.40  E-value: 5.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  332 TPPADHWALTSGL------PTYVAESGFICNIMNASADEMFNFQEGPLDESGwvIKNVLSMPIVNkKEEIVGVATFYNRK 405
Cdd:pfam01590  35 LPPGARWLKAAGLeippgtGVTVLRTGRPLVVPDAAGDPRFLDPLLLLRNFG--IRSLLAVPIID-DGELLGVLVLHHPR 111
                          90       100
                  ....*....|....*....|....
gi 157822587  406 DgkPFDDQDEVLMESLTQFLGWSV 429
Cdd:pfam01590 112 P--PFTEEELELLEVLADQVAIAL 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
232-444 6.65e-05

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 46.73  E-value: 6.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 232 ETRRGQVLLwSANKVFEELTDIERQFHKAFYTVRAYLNCDRYSVGLLDmtkekeffdvwpvlmgeaqpysgprtPDGREI 311
Cdd:COG2203  188 ELERLALLN-EISQALRSALDLEELLQRILELAGELLGADRGAILLVD--------------------------EDGGEL 240
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 312 VFYKVIDyilhgkedikvIPTPPADHWALTSGLPTYVAESGFICNIMNASADEMF-NFQEGPLDESGwvIKNVLSMPIVN 390
Cdd:COG2203  241 ELVAAPG-----------LPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFaPSLRELLLALG--IRSLLCVPLLV 307
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 157822587 391 KkEEIVGVATFYNRKDGkPFDDQDEVLMESLTQFLGWSVLNTDTYDKMNKLENR 444
Cdd:COG2203  308 D-GRLIGVLALYSKEPR-AFTEEDLELLEALADQAAIAIERARLYEALEAALAA 359
 
Name Accession Description Interval E-value
PDEase_I pfam00233
3'5'-cyclic nucleotide phosphodiesterase;
556-800 6.13e-104

3'5'-cyclic nucleotide phosphodiesterase;


Pssm-ID: 459723  Cd Length: 238  Bit Score: 321.04  E-value: 6.13e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  556 YHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHG-SSILERHHLEFGK 634
Cdd:pfam00233   1 YHNWRHAFDVTQTMYYLLKTGKLKEVLTDLEILALLIAALCHDVDHPGTNNAFLIKTKSPLAILYNdSSVLENHHCATAF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  635 FLLAEESLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRTMFQKIVDESKNYEDKKSwveylslETTRKEIVMAMMM 714
Cdd:pfam00233  81 QILQDEECNIFSNLSDEEYKEVRKLIISLILATDMAKHFELLKKFKSLLESKKTLDFLEN-------EEDRRLLLLSMLI 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  715 TACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTvLDQQPIPMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEIL 794
Cdd:pfam00233 154 KAADISNPTRPWEISKKWADLVAEEFFRQGDLEKE-LGLPVSPLMDREKKTSLPKSQIGFIDFIVLPLFEALAKLFPELQ 232

                  ....*.
gi 157822587  795 PMFDRL 800
Cdd:pfam00233 233 PLLDQL 238
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
71-230 7.56e-25

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: 101.30  E-value: 7.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587    71 NMERVVFKVLRRLCTILHADRCSLFMYrQRNGVAELATRLFSVQPdslledclvPPDSEIVFPLDIGIVGHVAQTKKMIN 150
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLV-DENDRGELVLVAADGLT---------LPTLGIRFPLDEGLAGRVAETGRPLN 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   151 VQDVAECPhfSPFADELTDY-VTKNILSTPIMNGKDVVAVIMAVNKLDGPCFTSEDEDVFTKYLNFATLNLKIYHLSYLH 229
Cdd:smart00065  71 IPDVEADP--LFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148

                   .
gi 157822587   230 N 230
Cdd:smart00065 149 R 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
252-439 1.46e-23

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: 97.45  E-value: 1.46e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   252 DIERQFHKAFYTVRAYLNCDRYSVGLLDMtkekeffdvwpvlmgeaqpysgprtpDGREIVFYKVIDYILhgkedikviP 331
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDE--------------------------NDRGELVLVAADGLT---------L 45
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   332 TPPADHWALTSGLPTYVAESGFICNIMNASADEmfnFQEGPLDESGWVIKNVLSMPIVNkKEEIVGVATFYNRKDGKPFD 411
Cdd:smart00065  46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVEADP---LFAEDLLGRYQGVRSFLAVPLVA-DGELVGVLALHNKKSPRPFT 121
                          170       180
                   ....*....|....*....|....*...
gi 157822587   412 DQDEVLMESLTQFLGWSVLNTDTYDKMN 439
Cdd:smart00065 122 EEDEELLQALANQLAIALANAQLYEELR 149
GAF COG2203
GAF domain [Signal transduction mechanisms];
52-210 6.16e-17

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 85.63  E-value: 6.16e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  52 QVEESAALFELVQDMQESVNMERVVFKVLRRLCTILHADRCSLFMYRQRNGVAELATRlfSVQPDSLLEDclvppdseiv 131
Cdd:COG2203  188 ELERLALLNEISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDGGELELVAA--PGLPEEELGR---------- 255
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 132 FPLDIGIVGHVAQTKKMINVQDVAECPHFSPFADE-LTDYVTKNILSTPIMNGKDVVAVIMAVNKLDGPcFTSEDEDVFT 210
Cdd:COG2203  256 LPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRElLLALGIRSLLCVPLLVDGRLIGVLALYSKEPRA-FTEEDLELLE 334
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
58-210 1.17e-16

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 78.78  E-value: 1.17e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  58 ALFELVQDMQESVNMERVVFKVLRRLCTILHADRCSLFMYRQRNGVAEL-ATRLFSvqPDSLledclvppdSEIVFPLDI 136
Cdd:COG3605    5 ALRRISEAVASALDLDEALDRIVRRIAEALGVDVCSIYLLDPDGGRLELrATEGLN--PEAV---------GKVRLPLGE 73
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157822587 137 GIVGHVAQTKKMINVQDVAECPHFSPFaDELTDYVTKNILSTPIMNGKDVVAVImAVNKLDGPCFTSEDEDVFT 210
Cdd:COG3605   74 GLVGLVAERGEPLNLADAASHPRFKYF-PETGEEGFRSFLGVPIIRRGRVLGVL-VVQSREPREFTEEEVEFLV 145
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
71-210 1.02e-12

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: 65.96  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   71 NMERVVFKVLRRLCTILHADRCSLFMYRQrNGVAELatrlfSVQPDSLLEDCLVPPdseivfpldIGIVGHVAQTKKMIN 150
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDA-DGLEYL-----PPGARWLKAAGLEIP---------PGTGVTVLRTGRPLV 65
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  151 VQDVAECPHFSPFADELTDYVTKNILSTPIMNGKDVVAVIMAVNKldGPCFTSEDEDVFT 210
Cdd:pfam01590  66 VPDAAGDPRFLDPLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHP--RPPFTEEELELLE 123
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
555-655 1.89e-08

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: 53.45  E-value: 1.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587   555 TYHNWRHGFNVAQTMFTLLMTGKLksyytdLEAFAMVTAGLCHDIDHRGTNNLYQMKsqnplaklhgSSILERHHLEFGK 634
Cdd:smart00471   2 DYHVFEHSLRVAQLAAALAEELGL------LDIELLLLAALLHDIGKPGTPDSFLVK----------TSVLEDHHFIGAE 65
                           90       100
                   ....*....|....*....|....*
gi 157822587   635 FLL----AEESLNIYQNLNRRQHEH 655
Cdd:smart00471  66 ILLeeeePRILEEILRTAILSHHER 90
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
556-741 2.83e-07

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 50.80  E-value: 2.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 556 YHNWRHGFNVAQTMFTLLMTGKLksyyTDLEAFAMVTAGLCHDIDHRGTNNLYqmksqnplakLHGSSILERHHLEFGKF 635
Cdd:cd00077    1 EHRFEHSLRVAQLARRLAEELGL----SEEDIELLRLAALLHDIGKPGTPDAI----------TEEESELEKDHAIVGAE 66
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 636 LLAEESLniyqnlnrrqhEHVIHLMDIAIIATDLALYFKKRTMFqkivdesknyedkkswveYLSLETTRKEIVMAMMMT 715
Cdd:cd00077   67 ILRELLL-----------EEVIKLIDELILAVDASHHERLDGLG------------------YPDGLKGEEITLEARIVK 117
                        170       180
                 ....*....|....*....|....*...
gi 157822587 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 5.92e-07

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: 49.40  E-value: 5.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  332 TPPADHWALTSGL------PTYVAESGFICNIMNASADEMFNFQEGPLDESGwvIKNVLSMPIVNkKEEIVGVATFYNRK 405
Cdd:pfam01590  35 LPPGARWLKAAGLeippgtGVTVLRTGRPLVVPDAAGDPRFLDPLLLLRNFG--IRSLLAVPIID-DGELLGVLVLHHPR 111
                          90       100
                  ....*....|....*....|....
gi 157822587  406 DgkPFDDQDEVLMESLTQFLGWSV 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 ...
128-210 4.41e-06

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: 47.08  E-value: 4.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587  128 SEIVFPLDIGIVGHVAQTKKMINVQDVAECPHFSPFADELTDYvtKNILSTPIMNGKDVVAVIMAVNKLDGPcFTSEDED 207
Cdd:pfam13185  47 AALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKGLPAGHAGL--RSFLSVPLVSGGRVVGVLALGSNRPGA-FDEEDLE 123

                  ...
gi 157822587  208 VFT 210
Cdd:pfam13185 124 LLE 126
GAF COG2203
GAF domain [Signal transduction mechanisms];
232-444 6.65e-05

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 46.73  E-value: 6.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 232 ETRRGQVLLwSANKVFEELTDIERQFHKAFYTVRAYLNCDRYSVGLLDmtkekeffdvwpvlmgeaqpysgprtPDGREI 311
Cdd:COG2203  188 ELERLALLN-EISQALRSALDLEELLQRILELAGELLGADRGAILLVD--------------------------EDGGEL 240
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822587 312 VFYKVIDyilhgkedikvIPTPPADHWALTSGLPTYVAESGFICNIMNASADEMF-NFQEGPLDESGwvIKNVLSMPIVN 390
Cdd:COG2203  241 ELVAAPG-----------LPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFaPSLRELLLALG--IRSLLCVPLLV 307
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 157822587 391 KkEEIVGVATFYNRKDGkPFDDQDEVLMESLTQFLGWSVLNTDTYDKMNKLENR 444
Cdd:COG2203  308 D-GRLIGVLALYSKEPR-AFTEEDLELLEALADQAAIAIERARLYEALEAALAA 359
 
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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