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Conserved domains on  [gi|330401303|gb|EGG80891|]
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hypothetical protein HMPREF1025_02814 [Lachnospiraceae bacterium 3_1_46FAA]

Protein Classification

LytR/AlgR family response regulator transcription factor( domain architecture ID 11461715)

LytR/AlgR family response regulator transcription factor with a signal receiver (REC) and a DNA-binding domain may be part of a two-component regulatory system

CATH:  3.40.50.2300|2.40.50.1020
Gene Ontology:  GO:0000160|GO:0000156|GO:0003677
PubMed:  11557134|27013338|18462668|31100988|20226724|16740923|12034833
SCOP:  4003632|4004734

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 1-225 1.99e-51

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms];


:

Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 166.92  E-value: 1.99e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKCLEITgMAGKCECFVSAEELLEKGnmPYALYILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:COG3279    2 MKILIVDDEPLARERLERLLEKYPDLE-VVGEASNGEEALELLEEH--KPDLVFLDIQMPGLDGFELARQLRELDPPPPI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  81 IFMTNHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREK---------RNYIRFTNKLKDMIFYYDEVECIESR 151
Cdd:COG3279   79 IFTTAYDEYALEAFEVNAVDYLLKPIDEERLAKALEKAKERLEAKaaaeaspeeKDRIFVKSGGKLVKIPLDDILYIEAE 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330401303 152 RRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERE---SVPLRSGLKVPITRTYKQEFNKA 225
Cdd:COG3279  159 GNYVKIHTKDKKYLVRKTLKELEEKLPPKQFFRVHRSYIVNLDKIKEIEKNfngEVVLKNGEEIPVSRRYKKEFKEW 235
 
Name Accession Description Interval E-value
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 1-225 1.99e-51

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms];


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 166.92  E-value: 1.99e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKCLEITgMAGKCECFVSAEELLEKGnmPYALYILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:COG3279    2 MKILIVDDEPLARERLERLLEKYPDLE-VVGEASNGEEALELLEEH--KPDLVFLDIQMPGLDGFELARQLRELDPPPPI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  81 IFMTNHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREK---------RNYIRFTNKLKDMIFYYDEVECIESR 151
Cdd:COG3279   79 IFTTAYDEYALEAFEVNAVDYLLKPIDEERLAKALEKAKERLEAKaaaeaspeeKDRIFVKSGGKLVKIPLDDILYIEAE 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330401303 152 RRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERE---SVPLRSGLKVPITRTYKQEFNKA 225
Cdd:COG3279  159 GNYVKIHTKDKKYLVRKTLKELEEKLPPKQFFRVHRSYIVNLDKIKEIEKNfngEVVLKNGEEIPVSRRYKKEFKEW 235
LytTR smart00850
LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional ...
 143-225 1.86e-20

LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern.


Pssm-ID: 197918 [Multi-domain]  Cd Length: 96  Bit Score: 82.62  E-value: 1.86e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   143 DEVECIESRRRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERES-----VPLRSGLKVPITRT 217
Cdd:smart00850   9 DDILYIEAEGNYVTVHTKDGTYLVRGTLKELEERLDPDNFFRIHRSYIVNLDHIKEIEPWFngtylLILKNGEEVPVSRR 88


                   ....*...
gi 330401303   218 YKQEFNKA 225
Cdd:smart00850  89 YLKELKER 96
LytTR pfam04397
LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional ...
 143-225 2.73e-19

LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern.


Pssm-ID: 427920 [Multi-domain]  Cd Length: 98  Bit Score: 79.56  E-value: 2.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  143 DEVECIESRRRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERE-----SVPLRSGLKVPITRT 217
Cdd:pfam04397   9 DDILYIEAEDKYVTIHTANGEYLTRGTLKELEEKLPPDGFFRCHRSYLVNLNKIKEIDPDfngtyELTLKNGEKIPVSRR 88


                  ....*...
gi 330401303  218 YKQEFNKA 225
Cdd:pfam04397  89 YLKELKEL 96
REC_LytTR_AgrA-like cd17533
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; ...
 1-125 1.97e-17

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AgrA-like group of LytTR/AlgR family response regulators are Staphylococcus aureus accessory gene regulator protein A (AgrA) and Streptococcus pneumoniae response regulator ComE, which are members of two-component regulatory systems. AgrA is a global regulator that controls the synthesis of virulence factors and other exoproteins. ComE is part of the ComD-ComE system that is part of a quorum-sensing signaling pathway that controls the development of competence, a physiological state required for genetic transformation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381088 [Multi-domain]  Cd Length: 131  Bit Score: 75.74  E-value: 1.97e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKCLEITGMAGKCECFVSAEELLE--KGNMPYALYILDVE--MKKLSGLELAEHIRTEDR 76
Cdd:cd17533    1 MNIFILEDDKIQRVRLEEIIENILKIENIEYVIELTGKTEELLEkiKERGKNGIYFLDIDikMEEKNGLEVAQKIRKYDP 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 330401303  77 NAVIIFMTNHSEMMQKAFDVQ--AFQYLVKPIDSDTAHNVIMRALRIIREK 125
Cdd:cd17533   81 YAIIIFVTTHSEFAPLTFEYKvaALDFILKPLKLEEFKKRIEECIKYAQKN 131
PRK14084 PRK14084
DNA-binding response regulator;
50-222 1.43e-14

DNA-binding response regulator;


Pssm-ID: 184495 [Multi-domain]  Cd Length: 246  Bit Score: 70.55  E-value: 1.43e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  50 YALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEMMQKAFDVQAFQYLVKPIDSDTahnvIMRALRIIREKRNYI 129
Cdd:PRK14084  47 YDIIFLDINLMDESGIELAAKIQKMKEPPAIIFATAHDQFAVKAFELNATDYILKPFEQKR----IEQAVNKVRATKAKD 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303 130 RFTNKL--KDMIFYYDEVECIESRRR-------KII----------VHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYL 190
Cdd:PRK14084 123 DNNASAiaNDMSANFDQSLPIEIDDKihmlnqqDIIaigvhngittIHTTNHKYETTEPLNRYEKRLNPTYFIRIHRSYI 202

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 330401303 191 VNLEKLREVER-----ESVPLRSGLKVPITRTYKQEF 222
Cdd:PRK14084 203 INKKHIKEVEQwfnytYQVILTNGVKMQVSRSFMKDF 239
 
Name Accession Description Interval E-value
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 1-225 1.99e-51

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms];


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 166.92  E-value: 1.99e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKCLEITgMAGKCECFVSAEELLEKGnmPYALYILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:COG3279    2 MKILIVDDEPLARERLERLLEKYPDLE-VVGEASNGEEALELLEEH--KPDLVFLDIQMPGLDGFELARQLRELDPPPPI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  81 IFMTNHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREK---------RNYIRFTNKLKDMIFYYDEVECIESR 151
Cdd:COG3279   79 IFTTAYDEYALEAFEVNAVDYLLKPIDEERLAKALEKAKERLEAKaaaeaspeeKDRIFVKSGGKLVKIPLDDILYIEAE 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330401303 152 RRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERE---SVPLRSGLKVPITRTYKQEFNKA 225
Cdd:COG3279  159 GNYVKIHTKDKKYLVRKTLKELEEKLPPKQFFRVHRSYIVNLDKIKEIEKNfngEVVLKNGEEIPVSRRYKKEFKEW 235
LytTR smart00850
LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional ...
 143-225 1.86e-20

LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern.


Pssm-ID: 197918 [Multi-domain]  Cd Length: 96  Bit Score: 82.62  E-value: 1.86e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   143 DEVECIESRRRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERES-----VPLRSGLKVPITRT 217
Cdd:smart00850   9 DDILYIEAEGNYVTVHTKDGTYLVRGTLKELEERLDPDNFFRIHRSYIVNLDHIKEIEPWFngtylLILKNGEEVPVSRR 88


                   ....*...
gi 330401303   218 YKQEFNKA 225
Cdd:smart00850  89 YLKELKER 96
LytTR pfam04397
LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional ...
 143-225 2.73e-19

LytTr DNA-binding domain; This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern.


Pssm-ID: 427920 [Multi-domain]  Cd Length: 98  Bit Score: 79.56  E-value: 2.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  143 DEVECIESRRRKIIVHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYLVNLEKLREVERE-----SVPLRSGLKVPITRT 217
Cdd:pfam04397   9 DDILYIEAEDKYVTIHTANGEYLTRGTLKELEEKLPPDGFFRCHRSYLVNLNKIKEIDPDfngtyELTLKNGEKIPVSRR 88


                  ....*...
gi 330401303  218 YKQEFNKA 225
Cdd:pfam04397  89 YLKELKEL 96
REC_LytTR_AgrA-like cd17533
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; ...
 1-125 1.97e-17

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AgrA-like group of LytTR/AlgR family response regulators are Staphylococcus aureus accessory gene regulator protein A (AgrA) and Streptococcus pneumoniae response regulator ComE, which are members of two-component regulatory systems. AgrA is a global regulator that controls the synthesis of virulence factors and other exoproteins. ComE is part of the ComD-ComE system that is part of a quorum-sensing signaling pathway that controls the development of competence, a physiological state required for genetic transformation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381088 [Multi-domain]  Cd Length: 131  Bit Score: 75.74  E-value: 1.97e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKCLEITGMAGKCECFVSAEELLE--KGNMPYALYILDVE--MKKLSGLELAEHIRTEDR 76
Cdd:cd17533    1 MNIFILEDDKIQRVRLEEIIENILKIENIEYVIELTGKTEELLEkiKERGKNGIYFLDIDikMEEKNGLEVAQKIRKYDP 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 330401303  77 NAVIIFMTNHSEMMQKAFDVQ--AFQYLVKPIDSDTAHNVIMRALRIIREK 125
Cdd:cd17533   81 YAIIIFVTTHSEFAPLTFEYKvaALDFILKPLKLEEFKKRIEECIKYAQKN 131
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 1-126 1.11e-16

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms];


Pssm-ID: 441806 [Multi-domain]  Cd Length: 418  Bit Score: 78.08  E-value: 1.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKnvekCLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:COG2204    3 ARILVVDDDPDIRRLLKE----LLERAGY--EVETAASGEEALALlREEPPDLVLLDLRMPGMDGLELLRELRALDPDLP 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 330401303  80 IIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREKR 126
Cdd:COG2204   77 VILLTGYGdvETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRRLRR 125
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-132 1.10e-15

DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal transduction mechanisms];


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 71.15  E-value: 1.10e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKCLEITgmagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:COG4565    4 IRVLIVEDDPMVAELLRRYLERLPGFE----VVGVASSGEEALALlAEHRPDLILLDIYLPDGDGLELLRELRARGPDVD 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 330401303  80 IIFMT--NHSEMMQKAFDVQAFQYLVKPIDSDTahnvIMRALRIIREKRNYIRFT 132
Cdd:COG4565   80 VIVITaaRDPETVREALRAGVVDYLIKPFTFER----LREALERYLEYRRLLRED 130
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 3-115 3.12e-15

Response regulator receiver domain; This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.


Pssm-ID: 395025 [Multi-domain]  Cd Length: 111  Bit Score: 69.10  E-value: 3.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303    3 IAICEDEEFIQnsieKNVEKCLEITGM-AGKCECFVSAEELLEKgnMPYALYILDVEMKKLSGLELAEHIRTEDRNAVII 81
Cdd:pfam00072   1 VLIVDDDPLIR----ELLRQLLEKEGYvVAEADDGKEALELLKE--ERPDLILLDINMPGMDGLELLKRIRRRDPTTPVI 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 330401303   82 FMTNHSE--MMQKAFDVQAFQYLVKPIDSDTAHNVI 115
Cdd:pfam00072  75 ILTAHGDedDAVEALEAGADDFLSKPFDPDELLAAI 110
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-120 7.37e-15

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms];


Pssm-ID: 440547 [Multi-domain]  Cd Length: 128  Bit Score: 68.72  E-value: 7.37e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKnvekCLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNA- 78
Cdd:COG0784    6 KRILVVDDNPDNRELLRR----LLERLGY--EVTTAEDGAEALELlRAGPPDLILLDINMPGMDGLELLRRIRALPRLPd 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 330401303  79 -VIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALR 120
Cdd:COG0784   80 iPIIALTAYAdeEDRERALEAGADDYLTKPVDPEELLEALRRLLA 124
PRK14084 PRK14084
DNA-binding response regulator;
50-222 1.43e-14

DNA-binding response regulator;


Pssm-ID: 184495 [Multi-domain]  Cd Length: 246  Bit Score: 70.55  E-value: 1.43e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  50 YALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEMMQKAFDVQAFQYLVKPIDSDTahnvIMRALRIIREKRNYI 129
Cdd:PRK14084  47 YDIIFLDINLMDESGIELAAKIQKMKEPPAIIFATAHDQFAVKAFELNATDYILKPFEQKR----IEQAVNKVRATKAKD 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303 130 RFTNKL--KDMIFYYDEVECIESRRR-------KII----------VHTEKRDYEFYGSLSQIEEDIKGSMFVRVHNSYL 190
Cdd:PRK14084 123 DNNASAiaNDMSANFDQSLPIEIDDKihmlnqqDIIaigvhngittIHTTNHKYETTEPLNRYEKRLNPTYFIRIHRSYI 202

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 330401303 191 VNLEKLREVER-----ESVPLRSGLKVPITRTYKQEF 222
Cdd:PRK14084 203 INKKHIKEVEQwfnytYQVILTNGVKMQVSRSFMKDF 239
PRK11697 PRK11697
two-component system response regulator BtsR;
55-222 2.67e-14

two-component system response regulator BtsR;


Pssm-ID: 236956 [Multi-domain]  Cd Length: 238  Bit Score: 69.88  E-value: 2.67e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  55 LDVEMKKLSGLELAEHIRTEDRNAvIIFMTNHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMRaLRIIREKRNY------ 128
Cdd:PRK11697  53 LDIQMPRISGLELVGMLDPEHMPY-IVFVTAFDEYAIKAFEEHAFDYLLKPIDPARLAKTLAR-LRQERSPQDVllpeaq 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303 129 --IRFT-----NKLKDMIFyyDEVECIESRRRKIIVHTEKRDYEFYGSLSQIEEdiKGSmFVRVHNSYLVNLEKLREVER 201
Cdd:PRK11697 131 ppLKHIpctghNRIKLLPL--EEVEFVSSRLSGVHVVSAEGKGFTELTLKTLEE--KTP-LLRCHRQYLVNPAAIQEIRL 205

                        170       180       190
                 ....*....|....*....|....*....|
gi 330401303 202 E-----SVPLRSGLKVPITRTY----KQEF 222
Cdd:PRK11697 206 LdngqaEIITRSGHTVPVSRRYlkslKEAL 235
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 5-105 3.01e-14

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381085 [Multi-domain]  Cd Length: 99  Bit Score: 66.48  E-value: 3.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   5 ICEDEEFIQNSIEKnvekCLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFM 83
Cdd:cd00156    2 IVDDDPAIRELLKS----LLEREGY--EVDTAADGEEALELlREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVL 75

                         90       100
                 ....*....|....*....|....
gi 330401303  84 TNHS--EMMQKAFDVQAFQYLVKP 105
Cdd:cd00156   76 TAKAdeEDAVRALELGADDYLVKP 99
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 2-105 5.47e-14

Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443786 [Multi-domain]  Cd Length: 103  Bit Score: 65.57  E-value: 5.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   2 RIAICEDEEFIQNSIEKNVEKC--LEITGMAGkcecfvSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNA 78
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEagFEVVGEAE------NGEEALELlEEHKPDLVITDINMPGMDGLELLEAIRELDPDT 74

                         90       100
                 ....*....|....*....|....*....
gi 330401303  79 VIIFMTNHS--EMMQKAFDVQAFQYLVKP 105
Cdd:COG4753   75 KIIILSGYSdfEYAQEAIKLGADDYLLKP 103
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 1-190 1.02e-13

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 67.67  E-value: 1.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKcleitgmAG-KCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNA 78
Cdd:COG0745    2 PRILVVEDDPDIRELLADALER-------EGyEVDTAADGEEALELlEEERPDLILLDLMLPGMDGLEVCRRLRARPSDI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  79 VIIFMTNHSEM--MQKAFDVQAFQYLVKPIDSDTAHNVIMRALRiiREKRNYIRFTNKL--KDMIFYYDEVECIESRRRK 154
Cdd:COG0745   75 PIIMLTARDDEedRVRGLEAGADDYLTKPFDPEELLARIRALLR--RRAAEVLRVGDLLdlAAREVTRDGEPVELTPKEF 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 330401303 155 IIVHTEKRDYEFYGSLSQIEEDIKGSMF-----VRVHNSYL 190
Cdd:COG0745  153 RLLELLMRNPGRVVSREQLLEEVWGYDYgddrtVDVHISRL 193
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 5-123 1.35e-13

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response regulators; This family is composed of uncharacterized response regulators that contain a REC domain and a AraC family helix-turn-helix (HTH) DNA-binding output domain, including Bacillus subtilis uncharacterized transcriptional regulatory protein YesN and Staphylococcus aureus uncharacterized response regulatory protein SAR0214. YesN is a member of the two-component regulatory system YesM/YesN and SAR0214 is a member of the probable two-component regulatory system SAR0215/SAR0214. Also included in this family is the AlgR-like group of LytTR/AlgR family response, which includes Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR and Bacillus subtilis sensory transduction protein LytT, among others. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381091 [Multi-domain]  Cd Length: 121  Bit Score: 65.05  E-value: 1.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   5 ICEDEEFIQNSIEKNVEKC---LEITGMAGkcecfvSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:cd17536    3 IVDDEPLIREGLKKLIDWEelgFEVVGEAE------NGEEALELiEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKI 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 330401303  81 IFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIR 123
Cdd:cd17536   77 IILSGYDdfEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEELD 121
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 1-109 3.15e-13

Two-component response regulator, PleD family, consists of two REC domains and a diguanylate cyclase (GGDEF) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 442920 [Multi-domain]  Cd Length: 179  Bit Score: 65.70  E-value: 3.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKnvekCLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNA- 78
Cdd:COG3706    2 ARILVVDDDPTNRKLLRR----LLEAAGY--EVVEAADGEEALELlQEHRPDLILLDLEMPDMDGLELCRRLRADPRTAd 75

                         90       100       110
                 ....*....|....*....|....*....|....
gi 330401303  79 -VIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSD 109
Cdd:COG3706   76 iPIIFLTALDdeEDRARALEAGADDYLTKPFDPE 109
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 15-119 4.80e-13

phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381146 [Multi-domain]  Cd Length: 116  Bit Score: 63.45  E-value: 4.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  15 SIEKNVEKCLEITGMagKCECFVSAEELLEKGN--MPYALyILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHS--EMM 90
Cdd:cd19919   11 SIRWVLERALAGAGL--TVTSFENAQEALAALAssQPDVL-ISDIRMPGMDGLALLAQIKQRHPDLPVIIMTAHSdlDSA 87

                         90       100
                 ....*....|....*....|....*....
gi 330401303  91 QKAFDVQAFQYLVKPIDSDTAHNVIMRAL 119
Cdd:cd19919   88 VSAYQGGAFEYLPKPFDIDEAVALVERAI 116
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 1-119 1.78e-12

phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381089 [Multi-domain]  Cd Length: 117  Bit Score: 62.04  E-value: 1.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKC-LEITGMAGkcecfvSAEELLEK--GNMPyALYILDVEMK-KLSGLELAEHIRtEDR 76
Cdd:cd17534    1 KKILIVEDEAIIALDLKEILESLgYEVVGIAD------SGEEAIELaeENKP-DLILMDINLKgDMDGIEAAREIR-EKF 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 330401303  77 NAVIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRAL 119
Cdd:cd17534   73 DIPVIFLTAYSdeETLERAKETNPYGYLVKPFNERELKAAIELAL 117
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 1-126 1.77e-10

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 59.02  E-value: 1.77e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKnvekCLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTED--RN 77
Cdd:COG3437    7 PTVLIVDDDPENLELLRQ----LLRTLGY--DVVTAESGEEALELlLEAPPDLILLDVRMPGMDGFELLRLLRADPstRD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 330401303  78 AVIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREKR 126
Cdd:COG3437   81 IPVIFLTALAdpEDRERALEAGADDYLTKPFDPEELLARVRNALELRRLQR 131
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 55-126 1.89e-10

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AlgR-like group of LytTR/AlgR family response regulators are Streptococcus agalactiae sensory transduction protein LytR, Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR, Bacillus subtilis sensory transduction protein LytT, and Escherichia coli transcriptional regulatory protein BtsR, which are members of two-component regulatory systems. LytR and LytT are components of regulatory systems that regulate genes involved in cell wall metabolism. AlgR positively regulates the algD gene, which codes for a GDP-mannose dehydrogenase, a key enzyme in the alginate biosynthesis pathway. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381087 [Multi-domain]  Cd Length: 118  Bit Score: 56.78  E-value: 1.89e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 330401303  55 LDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEMMQKAFDVQAFQYLVKPIDSDTahnvIMRALRIIREKR 126
Cdd:cd17532   50 LDIQMPGLDGLELAKKLSKLAKPPLIVFVTAYDEYAVEAFELNAVDYLLKPFSEER----LAEALAKLRKRL 117
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 5-105 6.42e-10

phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381116 [Multi-domain]  Cd Length: 99  Bit Score: 54.72  E-value: 6.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   5 ICEDEEFIQNSIEKNVEKcleitgmAG-KCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIF 82
Cdd:cd17574    2 VVEDDEEIAELLSDYLEK-------EGyEVDTAADGEEALELaREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIM 74

                         90       100
                 ....*....|....*....|....*...
gi 330401303  83 MTNHSEMMQKafdVQAFQ-----YLVKP 105
Cdd:cd17574   75 LTAKDEEEDK---VLGLElgaddYITKP 99
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 3-126 1.78e-09

phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins; C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381101 [Multi-domain]  Cd Length: 130  Bit Score: 54.03  E-value: 1.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   3 IAICEDEEFIQNSIEKNvekcLEITGMagKCECFVSAEELLE--KGNMPyALYILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:cd17549    1 VLLVDDDADVREALQQT----LELAGF--RVRAFADAEEALAalSPDFP-GVVISDIRMPGMDGLELLAQIRELDPDLPV 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 330401303  81 IFMTNHSE-------MMQKAFDvqafqYLVKPIDSDTAHNVIMRALriirEKR 126
Cdd:cd17549   74 ILITGHGDvpmaveaMRAGAYD-----FLEKPFDPERLLDVVRRAL----EKR 117
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 33-126 2.25e-09

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 55.11  E-value: 2.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  33 CECFVSAEELLE--KGNMPYALyILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHS------EMMQK-AFDvqafqYLV 103
Cdd:COG4566   26 VETFASAEAFLAalDPDRPGCL-LLDVRMPGMSGLELQEELAARGSPLPVIFLTGHGdvpmavRAMKAgAVD-----FLE 99

                         90       100
                 ....*....|....*....|...
gi 330401303 104 KPIDSDTAHNVIMRALRIIREKR 126
Cdd:COG4566  100 KPFDDQALLDAVRRALARDRARR 122
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 3-115 5.17e-09

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC; This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381099 [Multi-domain]  Cd Length: 113  Bit Score: 52.47  E-value: 5.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   3 IAICEDEEFIQNSIEKNVEKcleitgMAGKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAV-- 79
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEK------LGYEVDVAENGQEALELlKEEPFDLVLMDLQMPVMDGLEATRRIRELEGGGRrt 74

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 330401303  80 -IIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVI 115
Cdd:cd17546   75 pIIALTANAleEDREKCLEAGMDDYLSKPVKLDQLKEVL 113
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 14-126 6.24e-09

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 55.65  E-value: 6.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  14 NSIEKNVEKCLEITGMagKCECFVSAEELLE--KGNMPYALyILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEM-- 89
Cdd:PRK10923  13 SSIRWVLERALAGAGL--TCTTFENGNEVLEalASKTPDVL-LSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLda 89

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 330401303  90 MQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREKR 126
Cdd:PRK10923  90 AVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQEQQ 126
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 32-119 2.19e-08

phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response regulators contain an N-terminal receiver domain (REC) and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. The Sinorhizobium meliloti two-component system FixL/FixJ regulates nitrogen fixation in response to oxygen during symbiosis. Under microaerobic conditions, the kinase FixL phosphorylates the response regulator FixJ resulting in the regulation of nitrogen fixation genes such as nifA and fixK. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381092 [Multi-domain]  Cd Length: 116  Bit Score: 51.06  E-value: 2.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  32 KCECFVSAEELLE--KGNMPYALyILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSE--MMQKAFDVQAFQYLVKPID 107
Cdd:cd17537   26 AVKTFTSASAFLAaaPPDQPGCL-VLDVRMPGMSGLELQDELLARGSNIPIIFITGHGDvpMAVEAMKAGAVDFLEKPFR 104

                         90
                 ....*....|..
gi 330401303 108 SDTAHNVIMRAL 119
Cdd:cd17537  105 DQVLLDAIEQAL 116
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
2-130 4.00e-08

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 52.93  E-value: 4.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   2 RIAICEDEEfiqnSIEKNVEKCLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:PRK11361   6 RILIVDDED----NVRRMLSTAFALQGF--ETHCANNGRTALHLfADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 330401303  81 IFMTNHSEMMQ--KAFDVQAFQYLVKPIDSDTAHNVIMRALRiIREKRNYIR 130
Cdd:PRK11361  80 ILMTAYAEVETavEALRCGAFDYVIKPFDLDELNLIVQRALQ-LQSMKKEIR 130
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-126 1.78e-07

Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding antiterminator (ANTAR) domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 442921 [Multi-domain]  Cd Length: 194  Bit Score: 49.96  E-value: 1.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKC-LEITGMAGKCECFVSAEELLEkgnmpYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:COG3707    4 LRVLVVDDEPLRRADLREGLREAgYEVVAEAADGEDAVELVRELK-----PDLVIVDIDMPDRDGLEAARQISEERPAPV 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 330401303  80 IIFM-TNHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIREKR 126
Cdd:COG3707   79 ILLTaYSDPELIERALEAGVSAYLVKPLDPEDLLPALELALARFRELR 126
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 3-107 3.80e-07

phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381139 [Multi-domain]  Cd Length: 115  Bit Score: 47.48  E-value: 3.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   3 IAICEDEEFIQNSIEKNvekcLEITGMAgkCECFVS---AEELLEKGnmPYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:cd17624    1 ILLVEDDALLGDGLKTG----LRKAGYA--VDWVRTgaeAEAALASG--PYDLVILDLGLPDGDGLDLLRRWRRQGQSLP 72

                         90       100       110
                 ....*....|....*....|....*....|
gi 330401303  80 IIFMTNHSEMMQK--AFDVQAFQYLVKPID 107
Cdd:cd17624   73 VLILTARDGVDDRvaGLDAGADDYLVKPFA 102
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 3-120 1.06e-06

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 46.35  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   3 IAICEDEEFIQNSIEKNVEKCLEITgMAGKCECFVSAEELLEKGnmPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIF 82
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIE-VVGEAADGEEALALLREL--RPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIV 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 330401303  83 MTNHSE--MMQKAFDVQAFQYLVKPIDSDTahnvIMRALR 120
Cdd:cd17535   78 LTAHDDpeYVLRALKAGAAGYLLKDSSPEE----LIEAIR 113
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 1-106 1.13e-06

phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes Mycobacterium tuberculosis PdtaR, also called Rv1626, and similar proteins containing a REC domain and an ANTAR (AmiR and NasR transcription antitermination regulators) RNA-binding output domain. PdtaR is a response regulator that acts at the level of transcriptional antitermination and is a member of the PdtaR/PdtaS two-component regulatory system. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381159 [Multi-domain]  Cd Length: 118  Bit Score: 46.25  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKC-LEITGMAGKCEcfvSAEELLEKGNMPyaLYILDVEMKKLSGLELAEHIRTEdRNAV 79
Cdd:cd19932    1 VRVLIAEDEALIRMDLREMLEEAgYEVVGEASDGE---EAVELAKKHKPD--LVIMDVKMPRLDGIEAAKIITSE-NIAP 74

                         90       100
                 ....*....|....*....|....*....
gi 330401303  80 IIFMTNHS--EMMQKAFDVQAFQYLVKPI 106
Cdd:cd19932   75 IVLLTAYSqqDLVERAKEAGAMAYLVKPF 103
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 2-117 1.25e-06

phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators; This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381152 [Multi-domain]  Cd Length: 118  Bit Score: 46.08  E-value: 1.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   2 RIAICEDEEFIQNSIEKNVEKcleITG--MAGKCECFVSAEELLEKgnMPYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:cd19925    2 NVLIVEDDPMVAEIHRAYVEQ---VPGftVIGTAGTGEEALKLLKE--RQPDLILLDIYLPDGNGLDLLRELRAAGHDVD 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 330401303  80 IIFMT--NHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMR 117
Cdd:cd19925   77 VIVVTaaNDVETVREALRLGVVDYLIKPFTFERLRQRLER 116
PRK15479 PRK15479
transcriptional regulator TctD;
1-107 1.29e-06

transcriptional regulator TctD;


Pssm-ID: 185376 [Multi-domain]  Cd Length: 221  Bit Score: 47.79  E-value: 1.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEfiqnSIEKNVEKCLEITGMAGKC-ECFVSAEELLEKGNmpYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:PRK15479   1 MRLLLAEDNR----ELAHWLEKALVQNGFAVDCvFDGLAADHLLQSEM--YALAVLDINMPGMDGLEVLQRLRKRGQTLP 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 330401303  80 IIFMTNHSEMMQ--KAFDVQAFQYLVKPID 107
Cdd:PRK15479  75 VLLLTARSAVADrvKGLNVGADDYLPKPFE 104
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 1-109 3.96e-06

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and similar domains; Thermotoga maritima contains a two-component signal transduction system (TCS) composed of the ThkA sensory histidine kinase (HK) and its cognate response regulator (RR) TrrA; the specific function of the system is unknown. TCSs couple environmental stimuli to adaptive responses. TrrA is a stand-alone RR containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381106 [Multi-domain]  Cd Length: 113  Bit Score: 44.52  E-value: 3.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKnvekclEITGMAGKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:cd17554    1 KKILVVDDEENIRELYKE------ELEDEGYEVVTAGNGEEALEKlESEDPDLVILDIKMPGMDGLETLRKIREKKPDLP 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 330401303  80 IIFMTNHSEMMQKAFDVQAFQYLVKPIDSD 109
Cdd:cd17554   75 VIICTAYSEYKSDFSSWAADAYVVKSSDLT 104
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 40-119 9.63e-06

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY4 and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381110 [Multi-domain]  Cd Length: 118  Bit Score: 43.44  E-value: 9.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  40 EELLEK-GNMPYALYILDVEMKKLSGLELAEHIRT--EDRNAVIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNV 114
Cdd:cd17562   34 RDALSKaQSKKFDLIITDQNMPNMDGIELIKELRKlpAYKFTPILMLTTESsdEKKQEGKAAGATGWLVKPFDPEQLLEV 113


                 ....*
gi 330401303 115 IMRAL 119
Cdd:cd17562  114 VKKVL 118
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 38-120 1.45e-05

DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443624 [Multi-domain]  Cd Length: 177  Bit Score: 44.14  E-value: 1.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  38 SAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTahnv 114
Cdd:COG4567   36 SVEEALALlEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVLTGYAsiATAVEAIKLGADDYLAKPADADD---- 111


                 ....*.
gi 330401303 115 IMRALR 120
Cdd:COG4567  112 LLAALE 117
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 1-119 2.61e-05

phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381097 [Multi-domain]  Cd Length: 117  Bit Score: 42.27  E-value: 2.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIEKNVEKC-LEITGMAGkcecfvSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNA 78
Cdd:cd17542    1 KKVLIVDDAAFMRMMLKDILTKAgYEVVGEAA------NGEEAVEKyKELKPDLVTMDITMPEMDGIEALKEIKKIDPNA 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 330401303  79 VIIFMT--NHSEMMQKAFDVQAFQYLVKPIDSDTAHNVIMRAL 119
Cdd:cd17542   75 KVIMCSamGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117
REC_OmpR_CusR-like cd19935
phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ...
 39-105 4.70e-05

phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; Escherichia coli CusR is part of the CusS/CusR two-component system (TCS) that is involved in response to copper and silver. Other members of this subfamily include Escherichia coli PcoR, Pseudomonas syringae CopR, and Streptomyces coelicolor CutR, which are all transcriptional regulatory proteins and components of TCSs that regulate genes involved in copper resistance and/or metabolism. member of the subfamily is Escherichia coli HprR (hydrogen peroxide response regulator), previously called YdeW, which is part of the HprSR (or YedVW) TCS involved in stress response to hydrogen peroxide, as well as Cupriavidus metallidurans CzcR, which is part of the CzcS/CzcR TCS involved in the control of cobalt, zinc, and cadmium homeostasis. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381162 [Multi-domain]  Cd Length: 100  Bit Score: 41.27  E-value: 4.70e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 330401303  39 AEELLEKGnmPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEMMQKA--FDVQAFQYLVKP 105
Cdd:cd19935   34 GLHLALTN--EYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTARDSVEDRVkgLDLGADDYLVKP 100
REC_Spo0F-like cd17553
phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ...
 49-109 4.92e-05

phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone response regulator containing only a REC domain with no output/effector domain, controls sporulation in Bacillus subtilis through the exchange of a phosphoryl group. Bacillus subtilis forms spores when conditions for growth become unfavorable. The initiation of sporulation is controlled by a phosphorelay (an expanded version of the two-component system) that consists of four main components: a histidine kinase (KinA), a secondary messenger (Spo0F), a phosphotransferase (Spo0B), and a transcription factor (Spo0A). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381105 [Multi-domain]  Cd Length: 117  Bit Score: 41.77  E-value: 4.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 330401303  49 PYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSE--MMQKAFDVQAFQYLVKPIDSD 109
Cdd:cd17553   44 RPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGEldMIQESKELGALTHFAKPFDID 106
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 34-107 8.51e-05

phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a OmpR/PhoB homolog from Thermotoga maritima whose function is not yet known. This subfamily also includes Streptococcus agalactiae transcriptional regulatory protein DltR, part of the DltS/DltR two-component system (TCS), and Pseudomonas aeruginosa transcriptional activator protein PfeR, part of the PfeR/PfeS TCS, which activates expression of the ferric enterobactin receptor. The DltS/DltR TCS regulates the expression of the dlt operon, which comprises four genes (dltA, dltB, dltC, and dltD) that catalyze the incorporation of D-alanine residues into the lipoteichoic acids. Members of this subfamily belong to the OmpR/PhoB family, which comprises of two domains, an N-terminal receiver domain and a C-terminal DNA-binding winged helix-turn-helix effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381140 [Multi-domain]  Cd Length: 115  Bit Score: 40.67  E-value: 8.51e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 330401303  34 ECFVSAEELLEKGNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEMMQK--AFDVQAFQYLVKPID 107
Cdd:cd17625   26 VCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTALDAVEDRvkGLDLGADDYLPKPFS 101
REC_PA4781-like cd19920
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ...
 52-106 1.55e-04

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar domains; Pseudomonas aeruginosa cyclic di-GMP phosphodiesterase PA4781 contains an N-terminal REC domain and a C-terminal catalytic HD-GYP domain, characteristics of RpfG family response regulators. PA4781 is involved in cyclic di-3',5'-GMP (c-di-GMP) hydrolysis/degradation in a two-step reaction via the linear intermediate pGpG to produce GMP. Its unphosphorylated REC domain prevents accessibility of c-di-GMP to the active site. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381147 [Multi-domain]  Cd Length: 103  Bit Score: 39.80  E-value: 1.55e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 330401303  52 LYILDVEMKKLSGLELAEHIRTEDRNAVI--IFMTNHSEMM--QKAFDVQAFQYLVKPI 106
Cdd:cd19920   45 LILLDVMMPGMDGFEVCRRLKADPATRHIpvIFLTALTDTEdkVKGFELGAVDYITKPF 103
PRK11083 PRK11083
DNA-binding response regulator CreB; Provisional
 1-105 2.56e-04

DNA-binding response regulator CreB; Provisional


Pssm-ID: 236838 [Multi-domain]  Cd Length: 228  Bit Score: 41.10  E-value: 2.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEfiqnSIEKNVEKCLEITGMAgkCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAV 79
Cdd:PRK11083   4 PTILLVEDEQ----AIADTLVYALQSEGFT--VEWFERGLPALDKlRQQPPDLVILDVGLPDISGFELCRQLLAFHPALP 77

                         90       100
                 ....*....|....*....|....*...
gi 330401303  80 IIFMTNHSEMMQK--AFDVQAFQYLVKP 105
Cdd:PRK11083  78 VIFLTARSDEVDRlvGLEIGADDYVAKP 105
REC_NtrC1-like cd17572
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...
 49-109 2.78e-04

phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381114 [Multi-domain]  Cd Length: 121  Bit Score: 39.49  E-value: 2.78e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330401303  49 PYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHS------EMMQKAfdvqAFQYLVKPIDSD 109
Cdd:cd17572   42 PPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAHGsvdiavEAMRLG----AYDFLEKPFDAD 104
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 1-107 3.72e-04

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins; Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381103 [Multi-domain]  Cd Length: 118  Bit Score: 38.96  E-value: 3.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEfiqnsieKNVEKCLEITGMAGKCE--CFVSAEELLE--KGNmPYALYILDVEMKKLSGLELAEHIRTEDR 76
Cdd:cd17551    1 MRILIVDDNP-------TNLLLLEALLRSAGYLEvvSFTDPREALAwcREN-PPDLILLDYMMPGMDGLEFIRRLRALPG 72

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 330401303  77 NAV--IIFMTNHSEM--MQKAFDVQAFQYLVKPID 107
Cdd:cd17551   73 LEDvpIVMITADTDRevRLRALEAGATDFLTKPFD 107
REC_typeB_ARR-like cd17584
phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ...
 32-119 6.45e-04

phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and similar domains; Type-B ARRs (Arabidopsis response regulators) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-B ARRs contain a receiver (REC) domain and a large C-terminal extension that has characteristics of an effector or output domain, with a Myb-like DNA binding domain referred to as the GARP domain. The GARP domain is a motif specific to plant transcription factors. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381121 [Multi-domain]  Cd Length: 115  Bit Score: 38.38  E-value: 6.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  32 KCECFVSAEELL----EKGNMpYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHS-EMMQKAFDVQAFQYLVKPI 106
Cdd:cd17584   24 QVTTCTDAEEALsmlrENKDE-FDLVITDVHMPDMDGFEFLELIRLEMDLPVIMMSADGStSTVMKGLAHGACDYLLKPV 102

                         90
                 ....*....|...
gi 330401303 107 DSDTAHNVIMRAL 119
Cdd:cd17584  103 SIEDLKNIWQHVV 115
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 3-105 6.69e-04

phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The Mycobacterium tuberculosis PrrA is part of the PrrA/PrrB two-component system (TCS) that has been implicated in early intracellular multiplication and is essential for viability. Also included in this subfamily is Mycobacterium tuberculosis MprA, part of the MprAB TCS that regulates EspR, a key regulator of the ESX-1 secretion system, and is required for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. PrrA and MprA belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381142 [Multi-domain]  Cd Length: 116  Bit Score: 38.13  E-value: 6.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   3 IAICEDEEFIQNSIEKnvekCLEITGMagKCECFVSAEELLEK--GNMPYALyILDVEMKKLSGLELAEHIRTEDRNAVI 80
Cdd:cd17627    1 ILVVDDDRAVRESLRR----SLRFEGY--EVETAVDGAEALRVisGNRPDAV-VLDVMMPRLDGLEVCRRLRAAGNDLPI 73

                         90       100
                 ....*....|....*....|....*..
gi 330401303  81 IFMTNHSEMMQ--KAFDVQAFQYLVKP 105
Cdd:cd17627   74 LVLTARDSVSDrvAGLDAGADDYLVKP 100
PRK10643 PRK10643
two-component system response regulator PmrA;
1-105 7.54e-04

two-component system response regulator PmrA;


Pssm-ID: 182612 [Multi-domain]  Cd Length: 222  Bit Score: 39.63  E-value: 7.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIeknvEKCLEITGMAgkCECFVSAEE---LLEKGNmpYALYILDVEMKKLSGLELAEHIRTEDRN 77
Cdd:PRK10643   1 MKILIVEDDTLLLQGL----ILALQTEGYA--CDCASTAREaeaLLESGH--YSLVVLDLGLPDEDGLHLLRRWRQKKYT 72

                         90       100       110
                 ....*....|....*....|....*....|
gi 330401303  78 AVIIFMTNHSEMMQK--AFDVQAFQYLVKP 105
Cdd:PRK10643  73 LPVLILTARDTLEDRvaGLDVGADDYLVKP 102
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
50-124 8.87e-04

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 40.01  E-value: 8.87e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330401303  50 YALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALRIIRE 124
Cdd:PRK10365  50 FDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSsvETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHS 126
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 1-110 1.55e-03

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381150 [Multi-domain]  Cd Length: 119  Bit Score: 37.32  E-value: 1.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   1 MRIAICEDEEFIQNSIeKNVEKCLEITGMAgKCECFVSAEELLEKGNmpYALYILDVEMKKLSGLELAEHIRTEDR-NAV 79
Cdd:cd19923    1 MKVLVVDDFSTMRRII-KNLLKELGFNNVE-EAEDGVDALEKLKAGG--FDFVITDWNMPNMDGLELLKTIRADGAlSHL 76

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 330401303  80 IIFMTnhSEMMQKAFDVQAFQ-----YLVKPIDSDT 110
Cdd:cd19923   77 PVLMV--TAEAKKENVIAAAQagvnnYIVKPFTAAT 110
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 3-120 1.83e-03

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 37.09  E-value: 1.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   3 IAICEDEEFIQNSIEKNvekcLEITGMagKCECFVSAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVII 81
Cdd:cd17550    1 ILIVDDEEDIRESLSGI----LEDEGY--EVDTAADGEEALKLiKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVI 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 330401303  82 FMTNHS--EMMQKAFDVQAFQYLVKPIDSDTAHNVIMRALR 120
Cdd:cd17550   75 MISGHGtiETAVKATKLGAYDFIEKPLSLDRLLLTIERALE 115
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 54-114 3.51e-03

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381157 [Multi-domain]  Cd Length: 117  Bit Score: 36.10  E-value: 3.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330401303  54 ILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSE--MMQKAFDVQAFQYLVK--PID--SDTAHNV 114
Cdd:cd19930   49 ILDIEMPGRTGLEVAAELREELPDTKVLIVTTFGRpgYFRRALAAGVDGYVLKdrPIEelADAIRTV 115
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 1-59 3.63e-03

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.


Pssm-ID: 214668 [Multi-domain]  Cd Length: 55  Bit Score: 34.85  E-value: 3.63e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303     1 MRIAICEDEEFIQNSIEKNVEKcleitgMAGKCECFVSAEELLEKGN-MPYALYILDVEM 59
Cdd:smart00448   1 MRILVVDDDPLLRELLKALLEK------EGYEVDEATDGEEALELLKeEKPDLILLDIMM 54
pleD PRK09581
response regulator PleD; Reviewed
 39-126 4.12e-03

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 37.96  E-value: 4.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  39 AEELLEKGNMPYALYILDVEMKKLSGLELAEHIRTED--RNAVIIFMTNHSEMMQ--KAFDVQAFQYLVKPIDSDtahNV 114
Cdd:PRK09581 188 SEALFNAAETNYDLVIVSANFENYDPLRLCSQLRSKErtRYVPILLLVDEDDDPRlvKALELGVNDYLMRPIDKN---EL 264

                         90
                 ....*....|..
gi 330401303 115 IMRALRIIREKR 126
Cdd:PRK09581 265 LARVRTQIRRKR 276
REC_PilR cd19926
phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR ...
 17-105 4.36e-03

phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR and similar proteins; Pseudomonas aeruginosa PilR is the response regulator of the PilS/PilR two-component regulatory system (PilSR TCS) that acts in conjunction with sigma-54 to regulate the expression of type 4 pilus (T4P) major subunit PilA. In addition, the PilSR TCS regulates flagellum-dependent swimming motility and pilus-dependent twitching motility. PilR contains an N-terminal REC domain, a central sigma-54 interaction domain, and a C-terminal Fis-type helix-turn-helix DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381153 [Multi-domain]  Cd Length: 100  Bit Score: 35.59  E-value: 4.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  17 EKNVEKCLEITGMAGKCECfVSAEELLEKGNM----PYALYILDVEMKKLSGLELAEHI--RTEDRNAVIIFMTNHSEMM 90
Cdd:cd19926    7 EPDIRELLEITLGRMGLDV-RSARNVKEARELlasePYDLCLTDMRLPDGSGLELVQHIqqRLPQTPVAVITAYGSLDTA 85

                         90
                 ....*....|....*
gi 330401303  91 QKAFDVQAFQYLVKP 105
Cdd:cd19926   86 IEALKAGAFDFLTKP 100
REC_OmpR_EcPhoP-like cd19934
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...
 39-105 4.40e-03

phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; Escherichia coli PhoP (EcPhoP) is part of the PhoQ/PhoP two-component system (TCS) that regulates virulence genes and plays an essential role in the response of the bacteria to the environment of their mammalian hosts, sensing several stimuli such as extracellular magnesium limitation, low pH, the presence of cationic antimicrobial peptides, and osmotic upshift. This subfamily also includes Brucella suis FeuP, part of the FeuPQ TCS that is involved in the regulation of iron uptake, and Microchaete diplosiphon RcaC, which is required for chromatic adaptation. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381161 [Multi-domain]  Cd Length: 117  Bit Score: 36.11  E-value: 4.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  39 AEELLEKGNM-PYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEMMQK--AFDVQAFQYLVKP 105
Cdd:cd19934   31 GEEALFQGEEePYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTARDSWQDKveGLDAGADDYLTKP 100
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 17-120 6.03e-03

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains; This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381113 [Multi-domain]  Cd Length: 118  Bit Score: 35.46  E-value: 6.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  17 EKNVEKCLEITGMAGKCECFV--SAEELLEK-GNMPYALYILDVEMKKLSGLELAEHIRTEDRNAVIIFMTNHSEM--MQ 91
Cdd:cd17569    9 EPNILKALKRLLRREGYEVLTatSGEEALEIlKQEPVDVVISDQRMPGMDGAELLKRVRERYPDTVRILLTGYADLdaAI 88

                         90       100       110
                 ....*....|....*....|....*....|
gi 330401303  92 KAF-DVQAFQYLVKPIDSDTAHNVIMRALR 120
Cdd:cd17569   89 EAInEGEIYRFLTKPWDDEELKETIRQALE 118
REC_OmpR_BfmR-like cd19939
phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; ...
 2-105 6.05e-03

phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; Acinetobacter baumannii BfmR is part of the BfmR/S two-component system that functions as the master regulator of biofilm initiation. BfmR confers resistance to complement-mediated bactericidal activity, independent of capsular polysaccharide, and also increases resistance to the clinically important antimicrobials meropenem and colistin, making it a potential antimicrobial target. Its inhibition would have the dual benefit of significantly decreasing in vivo survival and increasing sensitivity to selected antimicrobials. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381166 [Multi-domain]  Cd Length: 116  Bit Score: 35.43  E-value: 6.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303   2 RIAICEDEEFIQNsIEKNVekcLEITGMAgkCECFVSAEE-LLEKGNMPYALYILDVEMKKLSGLELAEHIRtEDRNAVI 80
Cdd:cd19939    1 RILIVEDELELAR-LTRDY---LIKAGLE--VSVFTDGQRaVRRIIDEQPSLVVLDIMLPGMDGLTVCREVR-EHSHVPI 73

                         90       100
                 ....*....|....*....|....*..
gi 330401303  81 IFMTNHSEMMQK--AFDVQAFQYLVKP 105
Cdd:cd19939   74 LMLTARTEEMDRvlGLEMGADDYLCKP 100
orf27 CHL00148
Ycf27; Reviewed
 52-134 8.45e-03

Ycf27; Reviewed


Pssm-ID: 214376 [Multi-domain]  Cd Length: 240  Bit Score: 36.62  E-value: 8.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330401303  52 LYILDVEMKKLSGLELAEHIRTEDrNAVIIFMTNHSEMMQK--AFDVQAFQYLVKPIDSDTAHNVIMRALRIIREKRNYI 129
Cdd:CHL00148  53 LVILDVMMPKLDGYGVCQEIRKES-DVPIIMLTALGDVSDRitGLELGADDYVVKPFSPKELEARIRSVLRRTNKKSFSS 131


                 ....*
gi 330401303 130 RFTNK 134
Cdd:CHL00148 132 KIPNS 136
 
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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