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Conserved domains on  [gi|1816645995|ref|WP_163596465|]
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GAF domain-containing protein, partial [Klebsiella pneumoniae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11061 super family cl32635
phosphoenolpyruvate--protein phosphotransferase;
2-86 1.05e-55

phosphoenolpyruvate--protein phosphotransferase;


The actual alignment was detected with superfamily member PRK11061:

Pssm-ID: 182937 [Multi-domain]  Cd Length: 748  Bit Score: 182.50  E-value: 1.05e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   2 AFDEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLAT 81
Cdd:PRK11061   69 AFDEGIVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQFDESEESFLVTLAT 148


                  ....*
gi 1816645995  82 QMAAI 86
Cdd:PRK11061  149 QLAAI 153
 
Name Accession Description Interval E-value
PRK11061 PRK11061
phosphoenolpyruvate--protein phosphotransferase;
2-86 1.05e-55

phosphoenolpyruvate--protein phosphotransferase;


Pssm-ID: 182937 [Multi-domain]  Cd Length: 748  Bit Score: 182.50  E-value: 1.05e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   2 AFDEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLAT 81
Cdd:PRK11061   69 AFDEGIVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQFDESEESFLVTLAT 148


                  ....*
gi 1816645995  82 QMAAI 86
Cdd:PRK11061  149 QLAAI 153
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
2-86 2.58e-36

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 120.77  E-value: 2.58e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   2 AFDEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLAT 81
Cdd:COG3605    70 PLGEGLVGLVAERGEPLNLADAASHPRFKYFPETGEEGFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLVTLAA 149


                  ....*
gi 1816645995  82 QMAAI 86
Cdd:COG3605   150 QLAEA 154
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 4-86 2.83e-12

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: 58.16  E-value: 2.83e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995    4 DEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQREL-RQYDESEESFLVTLATQ 82
Cdd:smart00065  55 DEGLAGRVAETGRPLNIPDVEADPLFAEDLLGRYQGVRSFLAVPLVADGELVGVLALHNKKSpRPFTEEDEELLQALANQ 134


                   ....
gi 1816645995   83 MAAI 86
Cdd:smart00065 135 LAIA 138
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 5-84 1.73e-08

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


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 47.86  E-value: 1.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   5 EGSVGLVGRLAEPINLADAQKHPSF-KYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRElRQYDESEESFLVTLATQM 83
Cdd:pfam01590  51 PGTGVTVLRTGRPLVVPDAAGDPRFlDPLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHPR-PPFTEEELELLEVLADQV 129


                  .
gi 1816645995  84 A 84
Cdd:pfam01590 130 A 130
 
Name Accession Description Interval E-value
PRK11061 PRK11061
phosphoenolpyruvate--protein phosphotransferase;
2-86 1.05e-55

phosphoenolpyruvate--protein phosphotransferase;


Pssm-ID: 182937 [Multi-domain]  Cd Length: 748  Bit Score: 182.50  E-value: 1.05e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   2 AFDEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLAT 81
Cdd:PRK11061   69 AFDEGIVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQFDESEESFLVTLAT 148


                  ....*
gi 1816645995  82 QMAAI 86
Cdd:PRK11061  149 QLAAI 153
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
2-86 2.58e-36

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 120.77  E-value: 2.58e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   2 AFDEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLAT 81
Cdd:COG3605    70 PLGEGLVGLVAERGEPLNLADAASHPRFKYFPETGEEGFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLVTLAA 149


                  ....*
gi 1816645995  82 QMAAI 86
Cdd:COG3605   150 QLAEA 154
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 4-86 2.83e-12

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: 58.16  E-value: 2.83e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995    4 DEGSVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQREL-RQYDESEESFLVTLATQ 82
Cdd:smart00065  55 DEGLAGRVAETGRPLNIPDVEADPLFAEDLLGRYQGVRSFLAVPLVADGELVGVLALHNKKSpRPFTEEDEELLQALANQ 134


                   ....
gi 1816645995   83 MAAI 86
Cdd:smart00065 135 LAIA 138
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 5-84 1.73e-08

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


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 47.86  E-value: 1.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   5 EGSVGLVGRLAEPINLADAQKHPSF-KYIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRElRQYDESEESFLVTLATQM 83
Cdd:pfam01590  51 PGTGVTVLRTGRPLVVPDAAGDPRFlDPLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHPR-PPFTEEELELLEVLADQV 129


                  .
gi 1816645995  84 A 84
Cdd:pfam01590 130 A 130
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 1-86 1.92e-08

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: 47.85  E-value: 1.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   1 RAFDEGSVGLVGRLAEPINLADAQKHPSFKYIPSVkEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLA 80
Cdd:pfam13185  51 DPPGEGLVGEALRTGRPVIVNDLAADPAKKGLPAG-HAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLA 129


                  ....*.
gi 1816645995  81 TQMAAI 86
Cdd:pfam13185 130 EQAAIA 135
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 37-85 7.89e-05

FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 442823 [Multi-domain]  Cd Length: 338  Bit Score: 39.06  E-value: 7.89e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1816645995  37 EERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLATQMAA 85
Cdd:COG3604    70 ARERQLFLGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLAAV 118
GAF COG2203
GAF domain [Signal transduction mechanisms];
2-84 2.64e-04

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 37.87  E-value: 2.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816645995   2 AFDEGSVGLVGRLAEPINLADAQKHPSFK--YIPSVKEERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTL 79
Cdd:COG2203   257 PLGEGLAGRALRTGEPVVVNDASTDPRFApsLRELLLALGIRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEAL 336


                  ....*
gi 1816645995  80 ATQMA 84
Cdd:COG2203   337 ADQAA 341
GAF_3 pfam13492
GAF domain;
38-84 2.92e-04

GAF domain;


Pssm-ID: 433253 [Multi-domain]  Cd Length: 129  Bit Score: 36.96  E-value: 2.92e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1816645995  38 ERFRAFLGVPNIPRRQLLGVLVVQQRELRQYDESEESFLVTLATQMA 84
Cdd:pfam13492  78 LPDGPALVVPLVAGRRVIGVLALASSKPRAFDAEDLRLLESLAAQIA 124
 
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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