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Conserved domains on  [gi|22550094|ref|NP_032950|]
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cAMP-dependent protein kinase type II-alpha regulatory subunit [Mus musculus]

Protein Classification

cyclic nucleotide-binding domain-containing protein( domain architecture ID 10186680)

cyclic nucleotide-binding domain-containing protein binds cyclic nucleotides (cAMP or cGMP) where binding of the effector leads to conformational changes; may be involved in regulating transcription, be present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK), or be part of vertebrate cyclic nucleotide-gated ion-channels.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 259-380 3.55e-31

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


:

Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 115.12  E-value: 3.55e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 259 LFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSILIRsktksnkNGGNQEVEIAHCHKGQYFGELA 338
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKL-------DEDGREQIVGFLGPGDLFGELA 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 22550094 339 LVTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNI 380
Cdd:cd00038  74 LLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 137-249 4.76e-25

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


:

Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 98.55  E-value: 4.76e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 137 LFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRG-SFGELALMYNTPR 215
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGdLFGELALLGNGPR 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 22550094 216 AATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKM 249
Cdd:cd00038  81 SATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
DD_RIIalpha_PKA cd12103
dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent ...
 4-44 8.12e-22

dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent protein kinase; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIalpha plays a role in the association and dissociation of PKA with the centrosome during interphase and mitosis, respectively. It is also involved in endosome-to-Golgi and Golgi-to-ER transport. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.


:

Pssm-ID: 438524  Cd Length: 41  Bit Score: 87.58  E-value: 8.12e-22
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR 44
Cdd:cd12103   1 IQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 41
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 259-380 3.55e-31

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 115.12  E-value: 3.55e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 259 LFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSILIRsktksnkNGGNQEVEIAHCHKGQYFGELA 338
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKL-------DEDGREQIVGFLGPGDLFGELA 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 22550094 339 LVTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNI 380
Cdd:cd00038  74 LLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 259-380 2.05e-25

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 99.78  E-value: 2.05e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094    259 LFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSIlirskTKSNKNGGnqEVEIAHCHKGQYFGELA 338
Cdd:smart00100   1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEV-----YKVLEDGE--EQIVGTLGPGDFFGELA 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 22550094    339 LVTNKPRAASAYAV--GDVKCLVMDVQAFERLLGPCMDIMKRNI 380
Cdd:smart00100  74 LLTNSRRAASAAAValELATLLRIDFRDFLQLLPELPQLLLELL 117
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 137-249 4.76e-25

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 98.55  E-value: 4.76e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 137 LFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRG-SFGELALMYNTPR 215
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGdLFGELALLGNGPR 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 22550094 216 AATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKM 249
Cdd:cd00038  81 SATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 137-255 4.75e-22

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 90.54  E-value: 4.75e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094    137 LFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDIL-VTKDNQTRSVGQYDNRGSFGELALMYNTPR 215
Cdd:smart00100   1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYkVLEDGEEQIVGTLGPGDFFGELALLTNSRR 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 22550094    216 AATIIATSEgSLWGLDRVTFRRIIVKNNAKKRKMFESFIE 255
Cdd:smart00100  81 AASAAAVAL-ELATLLRIDFRDFLQLLPELPQLLLELLLE 119
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 277-369 5.57e-22

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 89.21  E-value: 5.57e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094   277 EKIYKDGERIIAQGEKADSFYIIESGEVSIlirskTKSNKNGgnQEVEIAHCHKGQYFGELALVTNKPRAASAYAVGDVK 356
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKV-----YRTLEDG--REQILAVLGPGDFFGELALLGGEPRSATVVALTDSE 73

                          90
                  ....*....|...
gi 22550094   357 CLVMDVQAFERLL 369
Cdd:pfam00027  74 LLVIPREDFLELL 86
DD_RIIalpha_PKA cd12103
dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent ...
 4-44 8.12e-22

dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent protein kinase; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIalpha plays a role in the association and dissociation of PKA with the centrosome during interphase and mitosis, respectively. It is also involved in endosome-to-Golgi and Golgi-to-ER transport. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.


Pssm-ID: 438524  Cd Length: 41  Bit Score: 87.58  E-value: 8.12e-22
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR 44
Cdd:cd12103   1 IQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 41
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 260-390 2.89e-19

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 85.42  E-value: 2.89e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 260 FKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSIlirskTKSNKNGgnQEVEIAHCHKGQYFGELAL 339
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKL-----YRISEDG--REQILGFLGPGDFFGELSL 73

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 22550094 340 VTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNISHYEEQLVKM 390
Cdd:COG0664  74 LGGEPSPATAEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQL 124
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 155-242 8.21e-13

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 63.78  E-value: 8.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094   155 EKIVKTDEHVIDQGDDGDNFYVIERGTYDI-LVTKDNQTRSVGQYDNRGSFGELALMYNTPRAATIIATSEGSLWGLDRV 233
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVyRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ....*....
gi 22550094   234 TFRRIIVKN 242
Cdd:pfam00027  81 DFLELLERD 89
RIIa smart00394
RIIalpha, Regulatory subunit portion of type II PKA R-subunit; RIIalpha, Regulatory subunit ...
 9-45 5.95e-12

RIIalpha, Regulatory subunit portion of type II PKA R-subunit; RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).


Pssm-ID: 197697  Cd Length: 38  Bit Score: 59.65  E-value: 5.95e-12
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 22550094      9 GLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR 45
Cdd:smart00394   2 GLQALLEDLTVEVLRAQPSDLVQFAADYFEKLEEQRA 38
RIIa pfam02197
Regulatory subunit of type II PKA R-subunit;
9-44 1.03e-11

Regulatory subunit of type II PKA R-subunit;


Pssm-ID: 396669  Cd Length: 37  Bit Score: 58.87  E-value: 1.03e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 22550094     9 GLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR 44
Cdd:pfam02197   2 GLQALLEDLTVEVLRAQPSDPLQFAADYFEKLEEER 37
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 138-253 1.59e-11

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 63.08  E-value: 1.59e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 138 FKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRGS-FGELALMYNTPRA 216
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDfFGELSLLGGEPSP 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 22550094 217 ATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESF 253
Cdd:COG0664  81 ATAEALEDSELLRIPREDLEELLERNPELARALLRLL 117
PLN02868 PLN02868
acyl-CoA thioesterase family protein
 253-360 1.18e-06

acyl-CoA thioesterase family protein


Pssm-ID: 178459 [Multi-domain]  Cd Length: 413  Bit Score: 50.10  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094  253 FIESVPLFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSILIrsktkSNKNGGNQEVEIahcHKGQ 332
Cdd:PLN02868   9 FLGSVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSG-----PAEEESRPEFLL---KRYD 80

                         90       100
                 ....*....|....*....|....*...
gi 22550094  333 YFGElALVTNKpRAASAYAVGDVKCLVM 360
Cdd:PLN02868  81 YFGY-GLSGSV-HSADVVAVSELTCLVL 106
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 133-288 3.09e-03

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 39.85  E-value: 3.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094  133 KDILLFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRGSFGELALMYN 212
Cdd:PLN03192 377 EKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEVGALCC 456

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22550094  213 TPRAATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIEsvplfKSLEMSErMKIVDVIGEKIYKDGERIIA 288
Cdd:PLN03192 457 RPQSFTFRTKTLSQLLRLKTSTLIEAMQTRQEDNVVILKNFLQ-----HHKELHD-LNVGDLLGDNGGEHDDPNMA 526
cyc_nuc_ocin TIGR03896
bacteriocin-type transport-associated protein; Members of this protein family are ...
 283-352 4.37e-03

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 38.72  E-value: 4.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094   283 GERIIAQGEKADSFYIIESGEVSILIRSKTKsnkNGGNQEVEIAHCHKGQYFGELALVTNKPRAASAYAV 352
Cdd:TIGR03896  16 GTTLIEEGKAADFLFILLDGTFTVTTPQPED---NPLTRAFELARLSRGEIVGEMSLLETRPPVATIKAV 82
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 259-380 3.55e-31

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 115.12  E-value: 3.55e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 259 LFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSILIRsktksnkNGGNQEVEIAHCHKGQYFGELA 338
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKL-------DEDGREQIVGFLGPGDLFGELA 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 22550094 339 LVTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNI 380
Cdd:cd00038  74 LLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 259-380 2.05e-25

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 99.78  E-value: 2.05e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094    259 LFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSIlirskTKSNKNGGnqEVEIAHCHKGQYFGELA 338
Cdd:smart00100   1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEV-----YKVLEDGE--EQIVGTLGPGDFFGELA 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 22550094    339 LVTNKPRAASAYAV--GDVKCLVMDVQAFERLLGPCMDIMKRNI 380
Cdd:smart00100  74 LLTNSRRAASAAAValELATLLRIDFRDFLQLLPELPQLLLELL 117
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 137-249 4.76e-25

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 98.55  E-value: 4.76e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 137 LFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRG-SFGELALMYNTPR 215
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGdLFGELALLGNGPR 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 22550094 216 AATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKM 249
Cdd:cd00038  81 SATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 137-255 4.75e-22

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 90.54  E-value: 4.75e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094    137 LFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDIL-VTKDNQTRSVGQYDNRGSFGELALMYNTPR 215
Cdd:smart00100   1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYkVLEDGEEQIVGTLGPGDFFGELALLTNSRR 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 22550094    216 AATIIATSEgSLWGLDRVTFRRIIVKNNAKKRKMFESFIE 255
Cdd:smart00100  81 AASAAAVAL-ELATLLRIDFRDFLQLLPELPQLLLELLLE 119
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 277-369 5.57e-22

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 89.21  E-value: 5.57e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094   277 EKIYKDGERIIAQGEKADSFYIIESGEVSIlirskTKSNKNGgnQEVEIAHCHKGQYFGELALVTNKPRAASAYAVGDVK 356
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKV-----YRTLEDG--REQILAVLGPGDFFGELALLGGEPRSATVVALTDSE 73

                          90
                  ....*....|...
gi 22550094   357 CLVMDVQAFERLL 369
Cdd:pfam00027  74 LLVIPREDFLELL 86
DD_RIIalpha_PKA cd12103
dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent ...
 4-44 8.12e-22

dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent protein kinase; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIalpha plays a role in the association and dissociation of PKA with the centrosome during interphase and mitosis, respectively. It is also involved in endosome-to-Golgi and Golgi-to-ER transport. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.


Pssm-ID: 438524  Cd Length: 41  Bit Score: 87.58  E-value: 8.12e-22
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR 44
Cdd:cd12103   1 IQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 41
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 260-390 2.89e-19

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 85.42  E-value: 2.89e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 260 FKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSIlirskTKSNKNGgnQEVEIAHCHKGQYFGELAL 339
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKL-----YRISEDG--REQILGFLGPGDFFGELSL 73

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 22550094 340 VTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNISHYEEQLVKM 390
Cdd:COG0664  74 LGGEPSPATAEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQL 124
DD_RII_PKA cd12099
dimerization/docking (D/D) domain of the Type II Regulatory subunit of cAMP-dependent protein ...
 6-42 1.76e-17

dimerization/docking (D/D) domain of the Type II Regulatory subunit of cAMP-dependent protein kinase; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIalpha plays a role in the association and dissociation of PKA with the centrosome during interphase and mitosis, respectively. RIIbeta plays an important role in adipocytes and neuronal tissues. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.


Pssm-ID: 438520  Cd Length: 37  Bit Score: 75.20  E-value: 1.76e-17
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 22550094   6 IPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLRE 42
Cdd:cd12099   1 VPPGLTELLQDFTVAVLREQPTDLVDFAAEYFTRLRE 37
DD_RIIbeta_PKA cd12104
dimerization/docking (D/D) domain of the Type II beta Regulatory subunit of cAMP-dependent ...
 4-46 1.43e-16

dimerization/docking (D/D) domain of the Type II beta Regulatory subunit of cAMP-dependent protein kinase; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIbeta plays an important role in adipocytes and neuronal tissues. Mice deficient with RIIbeta have small fat cells, and are resistant to obesity, diet-induced diabetes, and alcohol-induced motor defects. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.


Pssm-ID: 438525  Cd Length: 43  Bit Score: 73.01  E-value: 1.43e-16
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARRQ 46
Cdd:cd12104   1 IEIPEGLTELLQGFTVEVLRNQPGDLLEFALQYFTRLKQAQSK 43
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 155-242 8.21e-13

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 63.78  E-value: 8.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094   155 EKIVKTDEHVIDQGDDGDNFYVIERGTYDI-LVTKDNQTRSVGQYDNRGSFGELALMYNTPRAATIIATSEGSLWGLDRV 233
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVyRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ....*....
gi 22550094   234 TFRRIIVKN 242
Cdd:pfam00027  81 DFLELLERD 89
RIIa smart00394
RIIalpha, Regulatory subunit portion of type II PKA R-subunit; RIIalpha, Regulatory subunit ...
 9-45 5.95e-12

RIIalpha, Regulatory subunit portion of type II PKA R-subunit; RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).


Pssm-ID: 197697  Cd Length: 38  Bit Score: 59.65  E-value: 5.95e-12
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 22550094      9 GLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR 45
Cdd:smart00394   2 GLQALLEDLTVEVLRAQPSDLVQFAADYFEKLEEQRA 38
RIIa pfam02197
Regulatory subunit of type II PKA R-subunit;
9-44 1.03e-11

Regulatory subunit of type II PKA R-subunit;


Pssm-ID: 396669  Cd Length: 37  Bit Score: 58.87  E-value: 1.03e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 22550094     9 GLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR 44
Cdd:pfam02197   2 GLQALLEDLTVEVLRAQPSDPLQFAADYFEKLEEER 37
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 138-253 1.59e-11

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 63.08  E-value: 1.59e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094 138 FKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRGS-FGELALMYNTPRA 216
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDfFGELSLLGGEPSP 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 22550094 217 ATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESF 253
Cdd:COG0664  81 ATAEALEDSELLRIPREDLEELLERNPELARALLRLL 117
DD_CrRSP7-like cd22984
dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke ...
 4-43 6.24e-11

dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 7 (RSP7) and similar proteins; Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. RSP7 is a cAMP-dependent protein kinase (PKA) RII-like protein. RSP7 contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of PKA. The D/D domain of RSP7 heterodimerizes with the D/D domain of RSP11 to form an X-type four-helix bundle within the radial spoke RS1 complex.


Pssm-ID: 438553  Cd Length: 47  Bit Score: 57.22  E-value: 6.24e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREA 43
Cdd:cd22984   8 YTIPEEFPAILKDFAREVLREQPKDIYEFGAQYFKRLAEA 47
DD_RII_PKA-like cd12084
dimerization/docking (D/D) domain of the type II Regulatory subunit of cAMP-dependent protein ...
 6-41 2.17e-10

dimerization/docking (D/D) domain of the type II Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.


Pssm-ID: 438517  Cd Length: 36  Bit Score: 55.12  E-value: 2.17e-10
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 22550094   6 IPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLR 41
Cdd:cd12084   1 VPEGLRELLEDFTREVLREQPEDVYEFAADYFEKLL 36
DD_CrRSP11-like cd22985
dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke ...
 4-40 4.89e-10

dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 11 (RSP11) and similar proteins; Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. RSP11 is a non-PKA (cAMP-dependent protein kinase) RIIa protein that contains a RII domain but lack any features required for cAMP signaling or phosphorylation. It is involved in the control of ciliary and flagellar beating. RSP11 contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of PKA. The D/D domain of RSP11 heterodimerizes with the D/D domain of RSP7 to form an X-type four-helix bundle within the radial spoke RS1 complex.


Pssm-ID: 438554  Cd Length: 49  Bit Score: 54.49  E-value: 4.89e-10
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRL 40
Cdd:cd22985   9 INIPPELPDILKNYTKEVIRAQPADLYEFSAEYFAKL 45
DD_ROP-like cd22972
dimerization/docking (D/D) domain found in the ropporin (ROP)-like subfamily; The ROP-like ...
 1-40 1.17e-09

dimerization/docking (D/D) domain found in the ropporin (ROP)-like subfamily; The ROP-like family includes ropporin-1A (ROP1A, also called cancer/testis antigen 91, CT91, or rhophilin-associated protein 1A), ropporin-1B (ROP1B, also called rhophilin-associated protein 1B), and ropporin-1-like protein (ROPN1L, also called ROPN1-like protein, AKAP-associated sperm protein, or ASP), as well as Chlamydomonas reinhardtii flagellar radial spoke proteins, RSP7 and RSP11. ROP1A, ROP1B and ROPN1L play important roles in male fertility. They are involved in fibrous sheath integrity and sperm motility and play roles in cAMP-dependent protein kinase (PKA)-dependent signaling processes required for spermatozoa capacitation. RSP7 is a PKA RII-like protein. RSP11 is a non-PKA RIIa protein that contains a RII domain but lack any features required for cAMP signaling or phosphorylation. It is involved in the control of ciliary and flagellar beating. Members of this subfamily contain a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domain of the regulatory subunit of PKA.


Pssm-ID: 438541  Cd Length: 43  Bit Score: 53.46  E-value: 1.17e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 22550094   1 MSHIQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRL 40
Cdd:cd22972   1 PEQIVIPEGLPEILKAYAKEAIRSQPEDLIQWSAKYFRAL 40
DD_CABYR_SP17 cd12100
dimerization/docking (D/D) domain of the sperm fibrous sheath proteins, Calcium-Binding ...
 3-44 1.91e-08

dimerization/docking (D/D) domain of the sperm fibrous sheath proteins, Calcium-Binding tYrosine-phosphorylation Regulated protein and Sperm Protein 17; CABYR and SP17 are naturally located in the human sperm fibrous sheath (FS). CABYR was originally isolated from spermatoza and was thought to be testis-specific, but has recently been observed in lung and brain tumors. It is a polymorphic calcium binding protein that is phosphorylated during capacitation. SP17 plays an important role in the interaction of sperm with the zona pellucida during fertilization. It also promotes cell-cell adhesion. SP17 is found in various human tumors of unrelated histological origin including metastatic squamous cell carcinoma, multiple myeloma, ovarian cancer, and primary nervous system tumors, among others. Both CABYR and SP17 contain an N-terminal dimerization/docking (D/D) domain with similarity to the D/D domain of the R subunit of cAMP-dependent protein kinase (PKA). The D/D domain of the R subunit dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. The D/D domain of CABYR and SP17 have been shown to bind to AKAP3, a protein that is also associated to the FS of mammalian spermatozoa.


Pssm-ID: 438521  Cd Length: 42  Bit Score: 49.76  E-value: 1.91e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 22550094   3 HIQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR 44
Cdd:cd12100   1 RLRLPYGLKSLLEGLSREVLREQPEDIPEFAADYFEELLKFR 42
PLN02868 PLN02868
acyl-CoA thioesterase family protein
 253-360 1.18e-06

acyl-CoA thioesterase family protein


Pssm-ID: 178459 [Multi-domain]  Cd Length: 413  Bit Score: 50.10  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094  253 FIESVPLFKSLEMSERMKIVDVIGEKIYKDGERIIAQGEKADSFYIIESGEVSILIrsktkSNKNGGNQEVEIahcHKGQ 332
Cdd:PLN02868   9 FLGSVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSG-----PAEEESRPEFLL---KRYD 80

                         90       100
                 ....*....|....*....|....*...
gi 22550094  333 YFGElALVTNKpRAASAYAVGDVKCLVM 360
Cdd:PLN02868  81 YFGY-GLSGSV-HSADVVAVSELTCLVL 106
PRK11753 PRK11753
cAMP-activated global transcriptional regulator CRP;
286-347 1.65e-05

cAMP-activated global transcriptional regulator CRP;


Pssm-ID: 236969 [Multi-domain]  Cd Length: 211  Bit Score: 45.36  E-value: 1.65e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22550094  286 IIAQGEKADSFYIIESGEVSILIRsktksNKNGgnQEVEIAHCHKGQYFGELAL-VTNKPRAA 347
Cdd:PRK11753  31 LIHAGEKAETLYYIVKGSVAVLIK-----DEEG--KEMILSYLNQGDFIGELGLfEEGQERSA 86
DD_ROP cd23019
dimerization/docking (D/D) domain found in ropporins; The ROP subfamily includes ropporin-1A ...
 4-40 7.72e-05

dimerization/docking (D/D) domain found in ropporins; The ROP subfamily includes ropporin-1A (ROP1A, also called cancer/testis antigen 91, CT91, or rhophilin-associated protein 1A), ropporin-1B (ROP1B, also called rhophilin-associated protein 1B), and ropporin-1-like protein (ROPN1L, also called ROPN1-like protein, AKAP-associated sperm protein, or ASP). ROP1A, ROP1B and ROPN1L play important roles in male fertility. They are involved in fibrous sheath integrity and sperm motility and play roles in cAMP-dependent protein kinase (PKA)-dependent signaling processes required for spermatozoa capacitation. Members of this subfamily contain a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domain of the regulatory subunit of PKA, which dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs). ROP1A and ROP1B have been shown to bind AKAP3.


Pssm-ID: 438555  Cd Length: 43  Bit Score: 39.58  E-value: 7.72e-05
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 22550094   4 IQIPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRL 40
Cdd:cd23019   4 INIPPELPDILKQFTKAAIRTQPKDLLQWSAAYFRAL 40
DD_R_PKA_DPY30-like cd22957
dimerization/docking (D/D) domains found in the cAMP-dependent protein kinase regulatory ...
 12-40 1.14e-04

dimerization/docking (D/D) domains found in the cAMP-dependent protein kinase regulatory subunit (PRKAR) and the DPY30/SDC1-like family; This hierarchy includes the dimerization/docking (D/D) domains of type I and type II cAMP-dependent protein kinase (PKA) regulatory (R) subunits, DPY30 from animals and its homologs, SDC1 from yeasts, and similar domains. PKA is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of R subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal D/D domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. Yeast SDC1 (suppressor of CDC25 protein 1) is the smallest subunit of COMPASS (COMplex of Proteins ASsociated with Set1) and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. DPY30/SDC1 contains a C-terminal helical bundle domain that directly interacts with Ash2L (in human)/Bre2 (in yeast) COMPASS through the DPY30-binding motif (DBM). The DPY30/SDC1 helical bundle domain, also called D/D domain, is formed of two alpha-helices that may be analogous to the D/D domain found in regulatory subunit of PKA.


Pssm-ID: 438526  Cd Length: 29  Bit Score: 39.02  E-value: 1.14e-04
                        10        20
                ....*....|....*....|....*....
gi 22550094  12 ELLQGYTVEVLRQQPPDLVDFAVEYFTRL 40
Cdd:cd22957   1 ELLQDAVAKLLEERPEDPVEFLAEYFEKA 29
DD_R_ScPKA-like cd12098
dimerization/docking (D/D) domain found in Saccharomyces cerevisiae cAMP-dependent protein ...
 6-48 8.10e-04

dimerization/docking (D/D) domain found in Saccharomyces cerevisiae cAMP-dependent protein kinase regulatory subunit and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. The R subunit of fungal PKA is encoded by a single gene, which is called by various names in different organisms (for example: Yarrowia lipolytica RKA1, Saccharomyces cerevisiae Bcy1, and Schizosaccharomyces pombe Cgs1). Although most characterized PKA holoenzymes are tetramers, Y. lipolytica PKA has been reported to be a dimer of RKA1 and the catalytic subunit TPK1. RKA1 is essential and promotes hyphal growth. Cgs1 is essential for sexual differentiation of S. pombe; mutants with defective Cgs1 are partially sterile. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain of metazoan R subunits dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs). The D/D domain of fungal R subunits may also serve as a dimerization domain, in the case of heterotetrameric PKAs. Fungal PKA plays a major role in controlling cell growth and metabolism in response to nutrients and stress conditions.


Pssm-ID: 438519  Cd Length: 45  Bit Score: 36.74  E-value: 8.10e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 22550094   6 IPAGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARRQES 48
Cdd:cd12098   1 LPSEYPDELNELNREVLRAQPDDILQFCANYFNRKLEEQRAFL 43
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 133-288 3.09e-03

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 39.85  E-value: 3.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094  133 KDILLFKNLDQEQLSQVLDAMFEKIVKTDEHVIDQGDDGDNFYVIERGTYDILVTKDNQTRSVGQYDNRGSFGELALMYN 212
Cdd:PLN03192 377 EKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEVGALCC 456

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22550094  213 TPRAATIIATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIEsvplfKSLEMSErMKIVDVIGEKIYKDGERIIA 288
Cdd:PLN03192 457 RPQSFTFRTKTLSQLLRLKTSTLIEAMQTRQEDNVVILKNFLQ-----HHKELHD-LNVGDLLGDNGGEHDDPNMA 526
cyc_nuc_ocin TIGR03896
bacteriocin-type transport-associated protein; Members of this protein family are ...
 283-352 4.37e-03

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 38.72  E-value: 4.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22550094   283 GERIIAQGEKADSFYIIESGEVSILIRSKTKsnkNGGNQEVEIAHCHKGQYFGELALVTNKPRAASAYAV 352
Cdd:TIGR03896  16 GTTLIEEGKAADFLFILLDGTFTVTTPQPED---NPLTRAFELARLSRGEIVGEMSLLETRPPVATIKAV 82
 
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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