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Conserved domains on  [gi|1273927484|gb|PIF40444|]
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transcriptional regulatory protein RtcR [Burkholderiales bacterium 23]

Protein Classification

sigma 54-dependent transcriptional regulator( domain architecture ID 11468665)

sigma 54-dependent transcriptional regulator similar to Escherichia coli transcriptional regulatory protein RtcR, which regulates the expression of the rtcAB genes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RtcR COG4650
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...
 1-534 0e+00

Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];


:

Pssm-ID: 443688 [Multi-domain]  Cd Length: 534  Bit Score: 1063.68  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   1 MEKKKVVIGFLGTQLD-SGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDI 79
Cdd:COG4650     1 MMKKTVVIGFLGTTLDrRGKGPNRWEKWRPTVSLCQQEDLLVDRLELLHDPRDRALAEQVAEDIAQVSPETEVRLHEVDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  80 ADPWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQRMGDPGSYALIDLD 159
Cdd:COG4650    81 ADPWDFEEVYAALLDFARAYPFDPEREDYLVHITTGTHVAQICWFLLTEARYLPGRLLQTSPPRKRRAGAAGSYTIIDLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 160 LSRYDVIAQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAVRSRAPILLTGPTGAGKSHLARRMYELKKARHQVQG 239
Cdd:COG4650   161 LSRYDAIASRFAQEQQEAVSFLKSGIATRNAAFNRLIEQIERVAIRSRAPILLTGPTGAGKSQLARRIYELKKARHQVSG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 240 DFVEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREV 319
Cdd:COG4650   241 RFVEVNCATLRGDGAMSALFGHVKGAFTGAVSDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEV 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 320 SSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRF 399
Cdd:COG4650   321 SSDFQLIAGTNRDLRQEVAEGRFREDLLARINLWTFRLPGLAERREDIEPNLDYELARFAREQGRRVRFNKEARARYLAF 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 400 ARSPEALWSGNFRDLSASMTRLATLADGGRISTALVDAEIQRLKWLWQRGDAvQPAGASLQSLLSAEVLEPLDLFDRMQL 479
Cdd:COG4650   401 ATSPEALWSGNFRDLNASVTRMATLAEGGRITVALVDEEIARLRRLWQRAEA-ATGDDLLAELLGAEQAAELDLFDRVQL 479

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1273927484 480 EAVLRVCRESPSLSDAGRRLFDQSRTQRSVVNDADRLRKYLLKFGLKWDAVAGRT 534
Cdd:COG4650   480 AAVIRVCRRSRSLSEAGRTLFAVSRQQKASPNDADRLRKYLARFGLSWDQVKART 534
 
Name Accession Description Interval E-value
RtcR COG4650
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...
 1-534 0e+00

Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];


Pssm-ID: 443688 [Multi-domain]  Cd Length: 534  Bit Score: 1063.68  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   1 MEKKKVVIGFLGTQLD-SGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDI 79
Cdd:COG4650     1 MMKKTVVIGFLGTTLDrRGKGPNRWEKWRPTVSLCQQEDLLVDRLELLHDPRDRALAEQVAEDIAQVSPETEVRLHEVDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  80 ADPWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQRMGDPGSYALIDLD 159
Cdd:COG4650    81 ADPWDFEEVYAALLDFARAYPFDPEREDYLVHITTGTHVAQICWFLLTEARYLPGRLLQTSPPRKRRAGAAGSYTIIDLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 160 LSRYDVIAQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAVRSRAPILLTGPTGAGKSHLARRMYELKKARHQVQG 239
Cdd:COG4650   161 LSRYDAIASRFAQEQQEAVSFLKSGIATRNAAFNRLIEQIERVAIRSRAPILLTGPTGAGKSQLARRIYELKKARHQVSG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 240 DFVEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREV 319
Cdd:COG4650   241 RFVEVNCATLRGDGAMSALFGHVKGAFTGAVSDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEV 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 320 SSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRF 399
Cdd:COG4650   321 SSDFQLIAGTNRDLRQEVAEGRFREDLLARINLWTFRLPGLAERREDIEPNLDYELARFAREQGRRVRFNKEARARYLAF 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 400 ARSPEALWSGNFRDLSASMTRLATLADGGRISTALVDAEIQRLKWLWQRGDAvQPAGASLQSLLSAEVLEPLDLFDRMQL 479
Cdd:COG4650   401 ATSPEALWSGNFRDLNASVTRMATLAEGGRITVALVDEEIARLRRLWQRAEA-ATGDDLLAELLGAEQAAELDLFDRVQL 479

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1273927484 480 EAVLRVCRESPSLSDAGRRLFDQSRTQRSVVNDADRLRKYLLKFGLKWDAVAGRT 534
Cdd:COG4650   480 AAVIRVCRRSRSLSEAGRTLFAVSRQQKASPNDADRLRKYLARFGLSWDQVKART 534
RNA_repair_RtcR NF038308
RNA repair transcriptional activator RtcR;
2-532 0e+00

RNA repair transcriptional activator RtcR;


Pssm-ID: 468466 [Multi-domain]  Cd Length: 527  Bit Score: 942.38  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   2 EKKKVVIGFLGTQLDSGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDIAD 81
Cdd:NF038308    1 MKKTVVIGFLGTTLDQGKGAKRWQKWRPTVALCQQPDLPVDRLELLHDRRDRALAERVAADIEEVSPETEVRLVPVVLRD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  82 PWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQrmgDPGSYALIDLDLS 161
Cdd:NF038308   81 PWDFEEVYGALLDFARAYPFDTENEDYLVHITTGTHVAQICWFLLVEARYLPARLLQTSPPRDK---EEGTYEIIDLDLS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 162 RYDVIAQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAVRSRAPILLTGPTGAGKSHLARRMYELKKARHQVQGDF 241
Cdd:NF038308  158 RYDALAQRFAREQAEAVSFLKSGIATRNAAFNRLIEQIERVALRSRAPILLTGPTGAGKSFLARRIYELKKRRHQVSGPF 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 242 VEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSS 321
Cdd:NF038308  238 VEVNCATLRGDLAMSELFGHVKGAFTGAQADRAGLLRAADGGTLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSS 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 322 DFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRFAR 401
Cdd:NF038308  318 DFQLIAGTNRDLRQEVAEGRFREDLYARINLWTFRLPGLRERREDIEPNLDYELDRFARELGRQVRFNKEARFRYLAFAT 397

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 402 SPEALWSGNFRDLSASMTRLATLADGGRISTALVDAEIQRLKWLWQRGDAVQPAGAsLQSLLSAEVLEPLDLFDRMQLEA 481
Cdd:NF038308  398 SPEALWPGNFRELSASVTRMATLADGGRITEELVEEEIARLRAAWQSAPAAADDDA-LADLLGGEQLAELDLFDRVQLAA 476

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1273927484 482 VLRVCRESPSLSDAGRRLFDQSRTQRSVVNDADRLRKYLLKFGLKWDAVAG 532
Cdd:NF038308  477 VLRVCRQSRSLSAAGRRLFGVSRQQKASPNDADRLRKYLARFGLSWEDIKA 527
RtcR pfam06956
Regulator of RNA terminal phosphate cyclase; RtcR is a sigma54-dependent enhancer binding ...
 3-184 3.50e-112

Regulator of RNA terminal phosphate cyclase; RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain pfam00158 in the central region of the protein sequence.


Pssm-ID: 429211 [Multi-domain]  Cd Length: 183  Bit Score: 330.72  E-value: 3.50e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   3 KKKVVIGFLGTQLD-SGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDIAD 81
Cdd:pfam06956   1 KKTVVIGFLGTTLDrRGKGAKRWERWRPTVSLCQQPDLLVDRLELLHDRRDRALAERVRADIAQVSPETEVRLHEVNFRD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  82 PWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQRMGDPGSYALIDLDLS 161
Cdd:pfam06956  81 PWDFEEVYGALHDFARAYPFDPEQEDYLVHITTGTHVAQICWFLLTEARYIPGRLLQTSPPRRRERGAAGSYTIIDLDLS 160

                         170       180
                  ....*....|....*....|...
gi 1273927484 162 RYDVIAQRFGAEQSEAVQFLKSG 184
Cdd:pfam06956 161 RYDAIASRFAQEQQEGTSFLKSG 183
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 167-430 3.22e-48

Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, DNA interactions]


Pssm-ID: 273817 [Multi-domain]  Cd Length: 534  Bit Score: 175.29  E-value: 3.22e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 167 AQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHqvqGDFVEVNC 246
Cdd:TIGR01817 180 LRDKAPEIARRRSGKEDGIIGKSPAMRQVVDQARVVA-RSNSTVLLRGESGTGKELIAKAIHYLSPRAK---RPFVKVNC 255

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 247 ATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLV 326
Cdd:TIGR01817 256 AALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLV 335

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 327 AGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRFArspeal 406
Cdd:TIGR01817 336 AATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCK------ 409

                         250       260
                  ....*....|....*....|....
gi 1273927484 407 WSGNFRDLSASMTRLATLADGGRI 430
Cdd:TIGR01817 410 WPGNVRELENCLERTATLSRSGTI 433
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
184-430 1.65e-46

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 168.87  E-value: 1.65e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 184 GIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRM-YELKKArhqvQGDFVEVNCATLRGDGAASVLFGHK 262
Cdd:PRK11361  144 HILTNSPAMMDICKDTAKIA-LSQASVLISGESGTGKELIARAIhYNSRRA----KGPFIKVNCAALPESLLESELFGHE 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 263 KGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRF 342
Cdd:PRK11361  219 KGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTF 298

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 343 REDLFARINLWSYALPGLAGRPEDIEPNMDHLLAR-SADETGQMVRFNVEARERYLRFArspealWSGNFRDLSASMTRL 421
Cdd:PRK11361  299 REDLFYRLNVIHLILPPLRDRREDISLLANHFLQKfSSENQRDIIDIDPMAMSLLTAWS------WPGNIRELSNVIERA 372


                  ....*....
gi 1273927484 422 ATLADGGRI 430
Cdd:PRK11361  373 VVMNSGPII 381
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 193-352 6.63e-18

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 80.65  E-value: 6.63e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 193 NALIDEIERVAVRSRAPILLTGPTGAGKSHLARRM-YELKKARHqvqgDFVEVNCATLRGDGAASVLFGHkkgaftGAAA 271
Cdd:cd00009     5 EAIEALREALELPPPKNLLLYGPPGTGKTTLARAIaNELFRPGA----PFLYLNASDLLEGLVVAELFGH------FLVR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 272 DRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFypmgsDREVSSDFQLVAGTHRDLRIDvaqgrFREDLFARIN 351
Cdd:cd00009    75 LLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLND-----LRIDRENVRVIGATNRPLLGD-----LDRALYDRLD 144


                  .
gi 1273927484 352 L 352
Cdd:cd00009   145 I 145
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 209-349 3.94e-10

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 58.15  E-value: 3.94e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  209 PILLTGPTGAGKSHLARR-MYELKKArhqvQGDFVEVNCATLR---GDGAASVLFGHKKGAFTGAAADRAG--LLRSAHQ 282
Cdd:smart00382   4 VILIVGPPGSGKTTLARAlARELGPP----GGGVIYIDGEDILeevLDQLLLIIVGGKKASGSGELRLRLAlaLARKLKP 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1273927484  283 GVLFLDEIGELGLDEQAMLLKAVEEKRfypMGSDREVSSDFQLVAGTHRDLRID--VAQGRFREDLFAR 349
Cdd:smart00382  80 DVLILDEITSLLDAEQEALLLLLEELR---LLLLLKSEKNLTVILTTNDEKDLGpaLLRRRFDRRIVLL 145
 
Name Accession Description Interval E-value
RtcR COG4650
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...
 1-534 0e+00

Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];


Pssm-ID: 443688 [Multi-domain]  Cd Length: 534  Bit Score: 1063.68  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   1 MEKKKVVIGFLGTQLD-SGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDI 79
Cdd:COG4650     1 MMKKTVVIGFLGTTLDrRGKGPNRWEKWRPTVSLCQQEDLLVDRLELLHDPRDRALAEQVAEDIAQVSPETEVRLHEVDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  80 ADPWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQRMGDPGSYALIDLD 159
Cdd:COG4650    81 ADPWDFEEVYAALLDFARAYPFDPEREDYLVHITTGTHVAQICWFLLTEARYLPGRLLQTSPPRKRRAGAAGSYTIIDLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 160 LSRYDVIAQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAVRSRAPILLTGPTGAGKSHLARRMYELKKARHQVQG 239
Cdd:COG4650   161 LSRYDAIASRFAQEQQEAVSFLKSGIATRNAAFNRLIEQIERVAIRSRAPILLTGPTGAGKSQLARRIYELKKARHQVSG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 240 DFVEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREV 319
Cdd:COG4650   241 RFVEVNCATLRGDGAMSALFGHVKGAFTGAVSDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEV 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 320 SSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRF 399
Cdd:COG4650   321 SSDFQLIAGTNRDLRQEVAEGRFREDLLARINLWTFRLPGLAERREDIEPNLDYELARFAREQGRRVRFNKEARARYLAF 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 400 ARSPEALWSGNFRDLSASMTRLATLADGGRISTALVDAEIQRLKWLWQRGDAvQPAGASLQSLLSAEVLEPLDLFDRMQL 479
Cdd:COG4650   401 ATSPEALWSGNFRDLNASVTRMATLAEGGRITVALVDEEIARLRRLWQRAEA-ATGDDLLAELLGAEQAAELDLFDRVQL 479

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1273927484 480 EAVLRVCRESPSLSDAGRRLFDQSRTQRSVVNDADRLRKYLLKFGLKWDAVAGRT 534
Cdd:COG4650   480 AAVIRVCRRSRSLSEAGRTLFAVSRQQKASPNDADRLRKYLARFGLSWDQVKART 534
RNA_repair_RtcR NF038308
RNA repair transcriptional activator RtcR;
2-532 0e+00

RNA repair transcriptional activator RtcR;


Pssm-ID: 468466 [Multi-domain]  Cd Length: 527  Bit Score: 942.38  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   2 EKKKVVIGFLGTQLDSGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDIAD 81
Cdd:NF038308    1 MKKTVVIGFLGTTLDQGKGAKRWQKWRPTVALCQQPDLPVDRLELLHDRRDRALAERVAADIEEVSPETEVRLVPVVLRD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  82 PWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQrmgDPGSYALIDLDLS 161
Cdd:NF038308   81 PWDFEEVYGALLDFARAYPFDTENEDYLVHITTGTHVAQICWFLLVEARYLPARLLQTSPPRDK---EEGTYEIIDLDLS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 162 RYDVIAQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAVRSRAPILLTGPTGAGKSHLARRMYELKKARHQVQGDF 241
Cdd:NF038308  158 RYDALAQRFAREQAEAVSFLKSGIATRNAAFNRLIEQIERVALRSRAPILLTGPTGAGKSFLARRIYELKKRRHQVSGPF 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 242 VEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSS 321
Cdd:NF038308  238 VEVNCATLRGDLAMSELFGHVKGAFTGAQADRAGLLRAADGGTLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSS 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 322 DFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRFAR 401
Cdd:NF038308  318 DFQLIAGTNRDLRQEVAEGRFREDLYARINLWTFRLPGLRERREDIEPNLDYELDRFARELGRQVRFNKEARFRYLAFAT 397

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 402 SPEALWSGNFRDLSASMTRLATLADGGRISTALVDAEIQRLKWLWQRGDAVQPAGAsLQSLLSAEVLEPLDLFDRMQLEA 481
Cdd:NF038308  398 SPEALWPGNFRELSASVTRMATLADGGRITEELVEEEIARLRAAWQSAPAAADDDA-LADLLGGEQLAELDLFDRVQLAA 476

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1273927484 482 VLRVCRESPSLSDAGRRLFDQSRTQRSVVNDADRLRKYLLKFGLKWDAVAG 532
Cdd:NF038308  477 VLRVCRQSRSLSAAGRRLFGVSRQQKASPNDADRLRKYLARFGLSWEDIKA 527
RtcR pfam06956
Regulator of RNA terminal phosphate cyclase; RtcR is a sigma54-dependent enhancer binding ...
 3-184 3.50e-112

Regulator of RNA terminal phosphate cyclase; RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain pfam00158 in the central region of the protein sequence.


Pssm-ID: 429211 [Multi-domain]  Cd Length: 183  Bit Score: 330.72  E-value: 3.50e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484   3 KKKVVIGFLGTQLD-SGRGAGRWEKWRPTLSLMQHEDLVVERLELLYTPPHLALAQLLQGDIATASPETQVNLVPMDIAD 81
Cdd:pfam06956   1 KKTVVIGFLGTTLDrRGKGAKRWERWRPTVSLCQQPDLLVDRLELLHDRRDRALAERVRADIAQVSPETEVRLHEVNFRD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  82 PWDFGEVYARLFDWTQAYRFDPEREEYWTHITTGTHVAQICLFLLVESRRIPGVLAQTSPPRRQRMGDPGSYALIDLDLS 161
Cdd:pfam06956  81 PWDFEEVYGALHDFARAYPFDPEQEDYLVHITTGTHVAQICWFLLTEARYIPGRLLQTSPPRRRERGAAGSYTIIDLDLS 160

                         170       180
                  ....*....|....*....|...
gi 1273927484 162 RYDVIAQRFGAEQSEAVQFLKSG 184
Cdd:pfam06956 161 RYDAIASRFAQEQQEGTSFLKSG 183
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 164-431 2.01e-67

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: 223.69  E-value: 2.01e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 164 DVIAQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARhqvQGDFVE 243
Cdd:COG2204   112 AAVERALERRRLRRENAEDSGLIGRSPAMQEVRRLIEKVA-PSDATVLITGESGTGKELVARAIHRLSPRA---DGPFVA 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 244 VNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDF 323
Cdd:COG2204   188 VNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDV 267

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 324 QLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRFArsp 403
Cdd:COG2204   268 RVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFLARFAAELGKPVKLSPEALEALLAYD--- 344

                         250       260
                  ....*....|....*....|....*...
gi 1273927484 404 ealWSGNFRDLSASMTRLATLADGGRIS 431
Cdd:COG2204   345 ---WPGNVRELENVIERAVILADGEVIT 369
Sigma54_activat pfam00158
Sigma-54 interaction domain;
185-351 2.34e-63

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 204.56  E-value: 2.34e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 185 IATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHqvqGDFVEVNCATLRGDGAASVLFGHKKG 264
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVA-PTDAPVLITGESGTGKELFARAIHQLSPRAD---GPFVAVNCAAIPEELLESELFGHEKG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 265 AFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFRE 344
Cdd:pfam00158  77 AFTGADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFRE 156


                  ....*..
gi 1273927484 345 DLFARIN 351
Cdd:pfam00158 157 DLYYRLN 163
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 183-487 1.55e-58

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


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 200.77  E-value: 1.55e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 183 SGIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHqvqGDFVEVNCA----TLrgdgAASVL 258
Cdd:COG3829   138 DDIIGKSPAMKELLELAKRVA-KSDSTVLILGESGTGKELFARAIHNASPRRD---GPFVAVNCAaipeNL----LESEL 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 259 FGHKKGAFTGAAA-DRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDV 337
Cdd:COG3829   210 FGYEKGAFTGAKKgGKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMV 289

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 338 AQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLArsadetgqmvRFNVEARERYLRFarSPEAL-------WSGN 410
Cdd:COG3829   290 EEGRFREDLYYRLNVIPIHIPPLRERKEDIPLLAEHFLE----------KFNKKYGKNIKGI--SPEALelllaydWPGN 357

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1273927484 411 FRDLSASMTRLATLADGGRISTALVDAEIQRlkwlwQRGDAVQPAGASLQsllsaevlEPLDLFDRMQLEAVLRVCR 487
Cdd:COG3829   358 VRELENVIERAVVLSEGDVITPEHLPEYLLE-----EAEAASAAEEGSLK--------EALEEVEKELIEEALEKTG 421
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
183-487 3.73e-57

Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 201.28  E-value: 3.73e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 183 SGIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYElkkARHQVQGDFVEVNCATLRGDGAASVLFGHK 262
Cdd:COG3284   321 AALAGGDPAMRRALRRARRLA-DRDIPVLILGETGTGKELFARAIHA---ASPRADGPFVAVNCAAIPEELIESELFGYE 396

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 263 KGAFTGAAAD-RAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGR 341
Cdd:COG3284   397 PGAFTGARRKgRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTPLGGTKPIPVDVRLIAATHRDLRELVAAGR 476

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 342 FREDLFARINLWSYALPGLAGRpEDIEPNMDHLLARSADETGQmVRFNVEARERYLRFArspealWSGNFRDLSASMTRL 421
Cdd:COG3284   477 FREDLYYRLNGLTLTLPPLRER-EDLPALIEHLLRELAAGRGP-LRLSPEALALLAAYP------WPGNVRELRNVLRTA 548

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1273927484 422 ATLADGGRISTALVDAEIqrlkwlwqRGDAVQPAGASLQSLLSAEVLEpldlfdRMQLEAVLRVCR 487
Cdd:COG3284   549 LALADGGVITVEDLPDEL--------RAELAAAAPAAAAPLTSLEEAE------RDAILRALRACG 600
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 167-430 3.22e-48

Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, DNA interactions]


Pssm-ID: 273817 [Multi-domain]  Cd Length: 534  Bit Score: 175.29  E-value: 3.22e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 167 AQRFGAEQSEAVQFLKSGIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHqvqGDFVEVNC 246
Cdd:TIGR01817 180 LRDKAPEIARRRSGKEDGIIGKSPAMRQVVDQARVVA-RSNSTVLLRGESGTGKELIAKAIHYLSPRAK---RPFVKVNC 255

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 247 ATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLV 326
Cdd:TIGR01817 256 AALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLV 335

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 327 AGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRFNVEARERYLRFArspeal 406
Cdd:TIGR01817 336 AATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCK------ 409

                         250       260
                  ....*....|....*....|....
gi 1273927484 407 WSGNFRDLSASMTRLATLADGGRI 430
Cdd:TIGR01817 410 WPGNVRELENCLERTATLSRSGTI 433
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
184-430 1.65e-46

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 168.87  E-value: 1.65e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 184 GIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRM-YELKKArhqvQGDFVEVNCATLRGDGAASVLFGHK 262
Cdd:PRK11361  144 HILTNSPAMMDICKDTAKIA-LSQASVLISGESGTGKELIARAIhYNSRRA----KGPFIKVNCAALPESLLESELFGHE 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 263 KGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRF 342
Cdd:PRK11361  219 KGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTF 298

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 343 REDLFARINLWSYALPGLAGRPEDIEPNMDHLLAR-SADETGQMVRFNVEARERYLRFArspealWSGNFRDLSASMTRL 421
Cdd:PRK11361  299 REDLFYRLNVIHLILPPLRDRREDISLLANHFLQKfSSENQRDIIDIDPMAMSLLTAWS------WPGNIRELSNVIERA 372


                  ....*....
gi 1273927484 422 ATLADGGRI 430
Cdd:PRK11361  373 VVMNSGPII 381
PRK15115 PRK15115
response regulator GlrR; Provisional
 185-440 4.14e-44

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 161.93  E-value: 4.14e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 185 IATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYelkKARHQVQGDFVEVNCATLRGDGAASVLFGHKKG 264
Cdd:PRK15115  136 IVTRSPLMLRLLEQARMVA-QSDVSVLINGQSGTGKEILAQAIH---NASPRASKPFIAINCGALPEQLLESELFGHARG 211

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 265 AFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFRE 344
Cdd:PRK15115  212 AFTGAVSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFRE 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 345 DLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVR-FNVEARERYLrfarspEALWSGNFRDLSASMTRLAT 423
Cdd:PRK15115  292 DLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRaFSTDAMKRLM------TASWPGNVRQLVNVIEQCVA 365

                         250
                  ....*....|....*..
gi 1273927484 424 LADGGRISTALVDAEIQ 440
Cdd:PRK15115  366 LTSSPVISDALVEQALE 382
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
167-431 2.43e-43

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 159.81  E-value: 2.43e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 167 AQRFGAEQSeAVQFLKSGIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHQvqgDFVEVNC 246
Cdd:PRK10365  124 THSIDAETP-AVTASQFGMVGKSPAMQHLLSEIALVA-PSEATVLIHGDSGTGKELVARAIHASSARSEK---PLVTLNC 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 247 ATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLV 326
Cdd:PRK10365  199 AALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLI 278

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 327 AGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVR-FNVEARERYLRFArspea 405
Cdd:PRK10365  279 AATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKgFTPQAMDLLIHYD----- 353

                         250       260
                  ....*....|....*....|....*.
gi 1273927484 406 lWSGNFRDLSASMTRLATLADGGRIS 431
Cdd:PRK10365  354 -WPGNIRELENAVERAVVLLTGEYIS 378
ntrC TIGR01818
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...
 198-487 4.61e-43

nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, DNA interactions, Signal transduction, Two-component systems]


Pssm-ID: 273818 [Multi-domain]  Cd Length: 463  Bit Score: 159.52  E-value: 4.61e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 198 EIERVAVR-SRAPI--LLTGPTGAGKSHLARRMYELKKARhqvQGDFVEVNCATLRGDGAASVLFGHKKGAFTGAAADRA 274
Cdd:TIGR01818 145 EVFRAIGRlSRSDItvLINGESGTGKELVARALHRHSPRA---NGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQ 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 275 GLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWS 354
Cdd:TIGR01818 222 GRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIR 301

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 355 YALPGLAGRPEDIEPNMDHLLARSADETG-QMVRFNVEARERYLRFArspealWSGNFRDLSASMTRLATLADGGRISTA 433
Cdd:TIGR01818 302 IHLPPLRERREDIPRLARHFLALAARELDvEPKLLDPEALERLKQLR------WPGNVRQLENLCRWLTVMASGDEVLVS 375

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1273927484 434 LVDAEIQRLKWLWQRGDAVQPAG-------------ASLQSLLSAEVLEpldLFDRMQLEAVLRVCR 487
Cdd:TIGR01818 376 DLPAELALTGRPASAPDSDGQDSwdealeawakqalSRGEQGLLDRALP---EFERPLLEAALQHTR 439
propionate_PrpR TIGR02329
propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ...
 205-471 1.91e-41

propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR. [Regulatory functions, DNA interactions]


Pssm-ID: 274079 [Multi-domain]  Cd Length: 526  Bit Score: 156.17  E-value: 1.91e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 205 RSRAPILLTGPTGAGKSHLARRMYELKKARhqvQGDFVEVNCATLRGDGAASVLFGHKKGAFTGA-AADRAGLLRSAHQG 283
Cdd:TIGR02329 233 RSDATVLILGESGTGKELVAQAIHQLSGRR---DFPFVAINCGAIAESLLEAELFGYEEGAFTGArRGGRTGLIEAAHRG 309

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 284 VLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGR 363
Cdd:TIGR02329 310 TLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRLSILRIALPPLRER 389

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 364 PEDIEPNMDHLLARSADETGQMVRfnvEARERylRFARSPEAL----WSGNFRDLSASMTRLA---TLADGGRISTALVD 436
Cdd:TIGR02329 390 PGDILPLAAEYLVQAAAALRLPDS---EAAAQ--VLAGVADPLqrypWPGNVRELRNLVERLAlelSAMPAGALTPDVLR 464

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1273927484 437 AeiqrlkWLWQRGDAVQPAGASLQSLLSAEVLEPL 471
Cdd:TIGR02329 465 A------LAPELAEASGKGKTSALSLRERSRVEAL 493
TyrR COG3283
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...
 194-433 2.31e-41

Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid transport and metabolism];


Pssm-ID: 442513 [Multi-domain]  Cd Length: 514  Bit Score: 155.73  E-value: 2.31e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 194 ALIDEIERVAVrSRAPILLTGPTGAGKSHLARrmyelkkARHQV----QGDFVEVNCATLRGDGAASVLFGHKKGAFTGA 269
Cdd:COG3283   215 QVIRQAKKMAM-LDAPLLIQGETGTGKELLAR-------ACHLAsprgDKPFLALNCAALPDDVAESELFGYAPGAFGNA 286

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 270 AADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFAR 349
Cdd:COG3283   287 REGKKGLFEQANGGTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFREDLYYR 366

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 350 INLWSYALPGLAGRPEDIEPNMDHLLARSADETGQ-MVRFNVEARERYLRFArspealWSGNFRDLSASMTRLATLADGG 428
Cdd:COG3283   367 LNVLTLTLPPLRERKSDILPLAEHFVARFSQQLGRpRPRLSPDLVDFLQSYP------WPGNVRQLENALYRAVSLLEGD 440


                  ....*
gi 1273927484 429 RISTA 433
Cdd:COG3283   441 ELTPE 445
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 184-433 1.23e-40

PEP-CTERM-box response regulator transcription factor; Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see SP|Q06065). These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158). [Regulatory functions, DNA interactions]


Pssm-ID: 274348 [Multi-domain]  Cd Length: 445  Bit Score: 152.21  E-value: 1.23e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 184 GIATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHQvqgDFVEVNCATLRGDGAASVLFGHKK 263
Cdd:TIGR02915 140 GLITSSPGMQKICRTIEKIA-PSDITVLLLGESGTGKEVLARALHQLSDRKDK---RFVAINCAAIPENLLESELFGYEK 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 264 GAFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFR 343
Cdd:TIGR02915 216 GAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFR 295

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 344 EDLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVR-FNVEAReRYLRFARspealWSGNFRDLSASMTRLA 422
Cdd:TIGR02915 296 EDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKgFTDDAL-RALEAHA-----WPGNVRELENKVKRAV 369

                         250
                  ....*....|.
gi 1273927484 423 TLADGGRISTA 433
Cdd:TIGR02915 370 IMAEGNQITAE 380
PRK15424 PRK15424
propionate catabolism operon regulatory protein PrpR; Provisional
 205-422 2.83e-38

propionate catabolism operon regulatory protein PrpR; Provisional


Pssm-ID: 237963 [Multi-domain]  Cd Length: 538  Bit Score: 147.56  E-value: 2.83e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 205 RSRAPILLTGPTGAGKSHLARRMYELKKARH-----QVQGDFVEVNCATLRGDGAASVLFGHKKGAFTGAA-ADRAGLLR 278
Cdd:PRK15424  240 RSSAAVLIQGETGTGKELAAQAIHREYFARHdarqgKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRrGGRAGLFE 319

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 279 SAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALP 358
Cdd:PRK15424  320 IAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLP 399

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1273927484 359 GLAGRPEDIEPNMDHLLARSADETGqmVRFNVEARErylRFARSPEAL----WSGNFRDLSASMTRLA 422
Cdd:PRK15424  400 PLRERVADILPLAESFLKQSLAALS--APFSAALRQ---GLQQCETLLlhydWPGNVRELRNLMERLA 462
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
193-425 1.28e-37

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 144.93  E-value: 1.28e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 193 NALIDEIERVAVrSRAPILLTGPTGAGKSHLARRMYELKKARHQvqgDFVEVNCATLRGDGAASVLFGHKKGAFTGAAAD 272
Cdd:PRK05022  197 QQLKKEIEVVAA-SDLNVLILGETGVGKELVARAIHAASPRADK---PLVYLNCAALPESLAESELFGHVKGAFTGAISN 272

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 273 RAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINL 352
Cdd:PRK05022  273 RSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRADLYHRLSV 352

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 353 WSYALPGLAGRPEDIepnmdHLLArsadetGqmvRFNVEARERY----LRFarSPEAL-------WSGNFRDLSASMTRL 421
Cdd:PRK05022  353 FPLSVPPLRERGDDV-----LLLA------G---YFLEQNRARLglrsLRL--SPAAQaallaydWPGNVRELEHVISRA 416


                  ....
gi 1273927484 422 ATLA 425
Cdd:PRK05022  417 ALLA 420
PRK15429 PRK15429
formate hydrogenlyase transcriptional activator FlhA;
185-439 2.37e-35

formate hydrogenlyase transcriptional activator FlhA;


Pssm-ID: 237965 [Multi-domain]  Cd Length: 686  Bit Score: 140.74  E-value: 2.37e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 185 IATRNAGFNALIDEIERVAvRSRAPILLTGPTGAGKSHLARRMYELKKARHQvqgDFVEVNCATLRGDGAASVLFGHKKG 264
Cdd:PRK15429  378 IIGRSEAMYSVLKQVEMVA-QSDSTVLILGETGTGKELIARAIHNLSGRNNR---RMVKMNCAAMPAGLLESDLFGHERG 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 265 AFTGAAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFRE 344
Cdd:PRK15429  454 AFTGASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREFRS 533

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 345 DLFARINLWSYALPGLAGRPEDIEPNMDHLLARSADETGQMVRfNVEAREryLRFARSPEalWSGNFRDLSASMTRLATL 424
Cdd:PRK15429  534 DLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNID-SIPAET--LRTLSNME--WPGNVRELENVIERAVLL 608

                         250
                  ....*....|....*
gi 1273927484 425 ADGGRISTALVDAEI 439
Cdd:PRK15429  609 TRGNVLQLSLPDITL 623
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 205-439 6.60e-35

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 136.92  E-value: 6.60e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 205 RSRAPILLTGPTGAGKSHLARRMYelkkaRH--QVQGDFVEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQ 282
Cdd:PRK10923  159 RSSISVLINGESGTGKELVAHALH-----RHspRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADG 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 283 GVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAG 362
Cdd:PRK10923  234 GTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRE 313

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1273927484 363 RPEDIEPNMDHLLARSADETGqmVRFNVEARERYLRFARSPealWSGNFRDLSASMTRLATLADGGRISTALVDAEI 439
Cdd:PRK10923  314 RREDIPRLARHFLQVAARELG--VEAKLLHPETEAALTRLA---WPGNVRQLENTCRWLTVMAAGQEVLIQDLPGEL 385
PRK10820 PRK10820
transcriptional regulator TyrR;
208-427 1.00e-30

transcriptional regulator TyrR;


Pssm-ID: 236769 [Multi-domain]  Cd Length: 520  Bit Score: 125.57  E-value: 1.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 208 APILLTGPTGAGKSHLARRMYeLKKARHQVQgdFVEVNCATLRGDGAASVLFGHKKGAFTGAAADRAGLLRSAHQGVLFL 287
Cdd:PRK10820  228 APLLITGDTGTGKDLLAYACH-LRSPRGKKP--FLALNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLL 304

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 288 DEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAGRPEDI 367
Cdd:PRK10820  305 DEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPPLRDRPQDI 384

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1273927484 368 EPNMDHLLARSADETG-QMVRFNVEARERYLRFArspealWSGNFRDLSASMTRLATLADG 427
Cdd:PRK10820  385 MPLTELFVARFADEQGvPRPKLAADLNTVLTRYG------WPGNVRQLKNAIYRALTQLEG 439
PRK11388 PRK11388
DNA-binding transcriptional regulator DhaR; Provisional
 201-487 4.94e-26

DNA-binding transcriptional regulator DhaR; Provisional


Pssm-ID: 183114 [Multi-domain]  Cd Length: 638  Bit Score: 112.08  E-value: 4.94e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 201 RVAVRSRAPILLTGPTGAGKSHLARRMYelkKARHQVQGDFVEVNCATLRGDGAASVLFGhkkGAFTGAAADRAGLLRSA 280
Cdd:PRK11388  342 RQAAKSSFPVLLCGEEGVGKALLAQAIH---NESERAAGPYIAVNCQLYPDEALAEEFLG---SDRTDSENGRLSKFELA 415

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 281 HQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGL 360
Cdd:PRK11388  416 HGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPL 495

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 361 AGRPEDIEPNMDHLLarsadeTGQMVRFNVearerylRFARSPEAL-------WSGNFRDLSASMTRLATLADGGRISTA 433
Cdd:PRK11388  496 RMRREDIPALVNNKL------RSLEKRFST-------RLKIDDDALarlvsyrWPGNDFELRSVIENLALSSDNGRIRLS 562

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1273927484 434 LVDAEIQrlkwlwQRGDAVQPAGASLQSLLSAEVLEpldlfdRMQLEAVLRVCR 487
Cdd:PRK11388  563 DLPEHLF------TEQATDDVSATRLSTSLSLAELE------KEAIINAAQVCG 604
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 209-329 1.17e-24

Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];


Pssm-ID: 440834 [Multi-domain]  Cd Length: 835  Bit Score: 108.27  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 209 PILLTGPTGAGKSHLARRMYELkkARHQVQGD----FVEVNCAtlrgDGA------ASVLFGHKKGAFTGAAADRAGLLR 278
Cdd:COG1221   132 HTLILGPTGVGKSFFAELMYEY--AIEIGVLPedapFVVFNCA----DYAnnpqllMSQLFGYVKGAFTGADKDKEGLIE 205

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1273927484 279 SAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMG-SDREVSSDFQLVAGT 329
Cdd:COG1221   206 KADGGILFLDEVHRLPPEGQEMLFTFMDKGIYRRLGeTEKTRKANVRIIFAT 257
pspF PRK11608
phage shock protein operon transcriptional activator; Provisional
 193-414 4.02e-23

phage shock protein operon transcriptional activator; Provisional


Pssm-ID: 236936 [Multi-domain]  Cd Length: 326  Bit Score: 100.13  E-value: 4.02e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 193 NALIDEIERVAVRSR--APILLTGPTGAGKSHLARRMYELKKarhQVQGDFVEVNCATLRGDGAASVLFGHKKGAFTGAA 270
Cdd:PRK11608   13 NSFLEVLEQVSRLAPldKPVLIIGERGTGKELIASRLHYLSS---RWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQ 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 271 ADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARI 350
Cdd:PRK11608   90 KRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRL 169

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1273927484 351 NLWSYALPGLAGRPEDIEPNMDHLLArsadetgQMVR---------FNVEARERYLRFArspealWSGNFRDL 414
Cdd:PRK11608  170 AFDVVQLPPLRERQSDIMLMAEHFAI-------QMCRelglplfpgFTERARETLLNYR------WPGNIREL 229
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 203-430 4.81e-21

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: 94.53  E-value: 4.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 203 AVRSRAPILLTGPTGAGKSHLARRMYELKkARHQvqGDFVEVNCATLRGDgaasvlfghkkgaftgaaadragllrsahq 282
Cdd:COG3604   111 TLASLAAVAILGETGTGKELVANAIHELS-PRAD--KPFVKVNCAALPES------------------------------ 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 283 gvlfldeigelgldeqamLLKAVEEKRFYPMGSDREVSSDFQLVAGTHRDLRIDVAQGRFREDLFARINLWSYALPGLAG 362
Cdd:COG3604   158 ------------------LLESLQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNVFPIRLPPLRE 219

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1273927484 363 RPEDIEPNMDHLLARSADETG-QMVRFNVEARERYLRFArspealWSGNFRDLSASMTRLATLADGGRI 430
Cdd:COG3604   220 RREDIPLLAEHFLEKFSRRLGkPILRLSPEALEALMAYP------WPGNVRELENVIERAVILAEGGVL 282
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 193-352 6.63e-18

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 80.65  E-value: 6.63e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 193 NALIDEIERVAVRSRAPILLTGPTGAGKSHLARRM-YELKKARHqvqgDFVEVNCATLRGDGAASVLFGHkkgaftGAAA 271
Cdd:cd00009     5 EAIEALREALELPPPKNLLLYGPPGTGKTTLARAIaNELFRPGA----PFLYLNASDLLEGLVVAELFGH------FLVR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 272 DRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVEEKRFypmgsDREVSSDFQLVAGTHRDLRIDvaqgrFREDLFARIN 351
Cdd:cd00009    75 LLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLND-----LRIDRENVRVIGATNRPLLGD-----LDRALYDRLD 144


                  .
gi 1273927484 352 L 352
Cdd:cd00009   145 I 145
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 209-349 3.94e-10

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 58.15  E-value: 3.94e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484  209 PILLTGPTGAGKSHLARR-MYELKKArhqvQGDFVEVNCATLR---GDGAASVLFGHKKGAFTGAAADRAG--LLRSAHQ 282
Cdd:smart00382   4 VILIVGPPGSGKTTLARAlARELGPP----GGGVIYIDGEDILeevLDQLLLIIVGGKKASGSGELRLRLAlaLARKLKP 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1273927484  283 GVLFLDEIGELGLDEQAMLLKAVEEKRfypMGSDREVSSDFQLVAGTHRDLRID--VAQGRFREDLFAR 349
Cdd:smart00382  80 DVLILDEITSLLDAEQEALLLLLEELR---LLLLLKSEKNLTVILTTNDEKDLGpaLLRRRFDRRIVLL 145
Sigma54_activ_2 pfam14532
Sigma-54 interaction domain;
191-360 2.32e-07

Sigma-54 interaction domain;


Pssm-ID: 434021 [Multi-domain]  Cd Length: 138  Bit Score: 50.03  E-value: 2.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 191 GFNALIDEIER---VAVRSRAPILLTGPTGAGKSHLARrmyelkkARHQVQGDFVE-VNCATLrgdgaasvlfghkkgaf 266
Cdd:pfam14532   2 GASAAIQEIKRrleQAAQSTLPVFLTGEPGSGKEFCAR-------YLHNPSTPWVQpFDIEYL----------------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 267 tgaAADRAGLLRSAHQGVLFLDEIGELGLDEQAMLLKAVeekrfypmgsDREVSSDFQLVAGTHRDLRIDVAQGRFREDL 346
Cdd:pfam14532  58 ---AHAPLELLEQAKGGTLYLKDIADLSKALQKGLLLLL----------AKAEGYRVRLVCTSSKDLPQLAAAGLFDEQL 124

                         170
                  ....*....|....
gi 1273927484 347 FARINLWSYALPGL 360
Cdd:pfam14532 125 YFELSALRLHVPPL 138
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 209-331 2.35e-06

AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 46.90  E-value: 2.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 209 PILLTGPTGAGKSHLARRMyelkkARHQVQGDFVEVNC------ATLRGdgaaSVLFGHKKGAFTGAAADRAGllRSAHq 282
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERL-----AAALSNRPVFYVQLtrdtteEDLFG----RRNIDPGGASWVDGPLVRAA--REGE- 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1273927484 283 gVLFLDEIGELGLDEQAMLLKAVEEKRFYPMGSDREVSS---DFQLVAGTHR 331
Cdd:pfam07728  69 -IAVLDEINRANPDVLNSLLSLLDERRLLLPDGGELVKAapdGFRLIATMNP 119
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 210-344 1.50e-03

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 39.57  E-value: 1.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 210 ILLTGPTGAGKSHLARRMyelkkARHQVqGDFVEVNCATLRGdgaASVLFGHKKgafTGAAADRAgllRSAHQGVLFLDE 289
Cdd:cd19481    29 ILLYGPPGTGKTLLAKAL-----AGELG-LPLIVVKLSSLLS---KYVGESEKN---LRKIFERA---RRLAPCILFIDE 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1273927484 290 IGELGLDEQAMLLKAVEEKRF----YPMGSDREvSSDFQLVAGTHRDLRIDVA---QGRFRE 344
Cdd:cd19481    94 IDAIGRKRDSSGESGELRRVLnqllTELDGVNS-RSKVLVIAATNRPDLLDPAllrPGRFDE 154
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
210-296 1.93e-03

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 40.25  E-value: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 210 ILLTGPTGAGKSHLARRM-YELKKArhqvqgdFVEVNCATL----RGDGAASVlfghkKGAFTGAAADRagllrsahqGV 284
Cdd:COG1223    38 ILFYGPPGTGKTMLAEALaGELKLP-------LLTVRLDSLigsyLGETARNL-----RKLFDFARRAP---------CV 96

                          90
                  ....*....|..
gi 1273927484 285 LFLDEIGELGLD 296
Cdd:COG1223    97 IFFDEFDAIAKD 108
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 165-351 4.04e-03

Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 38.31  E-value: 4.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 165 VIAQRFGAEQ-SEAVQFLKSGIATRNagfnalideiervavRSRAPILLTGPTGAGKSHLARrmyELKKARHQVQGDFVE 243
Cdd:cd19499    13 VVGQDEAVKAvSDAIRRARAGLSDPN---------------RPIGSFLFLGPTGVGKTELAK---ALAELLFGDEDNLIR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 244 VNCATLRGDGAASVLFG--------HKKGAFTGAAADRAgllrsahQGVLFLDEIGELGLDEQAMLLKAVEEKRFyPMGS 315
Cdd:cd19499    75 IDMSEYMEKHSVSRLIGappgyvgyTEGGQLTEAVRRKP-------YSVVLLDEIEKAHPDVQNLLLQVLDDGRL-TDSH 146

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1273927484 316 DREVssDFqlvagthRDLRIDVAQGRFREDLFARIN 351
Cdd:cd19499   147 GRTV--DF-------KNTIIIMTSNHFRPEFLNRID 173
AAA_22 pfam13401
AAA domain;
206-290 4.43e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 37.32  E-value: 4.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273927484 206 SRAPILLTGPTGAGKSHLARRmyeLKKARHQVQGDFVEVNCAtlRGDGAASVL------FGHKKGAFTGAAADRAGLLRS 279
Cdd:pfam13401   4 GAGILVLTGESGTGKTTLLRR---LLEQLPEVRDSVVFVDLP--SGTSPKDLLrallraLGLPLSGRLSKEELLAALQQL 78

                          90
                  ....*....|....*
gi 1273927484 280 AH----QGVLFLDEI 290
Cdd:pfam13401  79 LLalavAVVLIIDEA 93
 
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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