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Conserved domains on  [gi|2529623216|ref|WP_289402377|]
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PRD domain-containing protein [Bacillus cereus]

Protein Classification

sigma-54-dependent transcriptional regulator( domain architecture ID 11440661)

sigma-54-dependent transcriptional regulator containing sigma-54 interaction, PRD, and PTS_IIA_man-related domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 1-799 0e+00

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: 762.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216   1 MKRIDLIFNAIQK-------GNYTEGVTASELATLLQLDRANVSSDLNKLVKDNRLLKTSTRPVRF-------------- 59
Cdd:COG1221     1 MKRKEKILNYLKEltknlslEKKSEGFTAEEIAEKLGISRNNVSHELNELVKEGKLIKINGRPVLFldkeafeeqfgtkl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  60 ---YIETNTSLETHSTKG--TSLDTFAIENTSLKIAIEKAKASILYPPNGMHTLLLGETGVGKSMFASLMHEYAIEVEQL 134
Cdd:COG1221    81 kseYSFVELLAEKENNEEeeDPFDNLIGANGSLKNAIEQAKAAILYPPKGLHTLILGPTGVGKSFFAELMYEYAIEIGVL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 135 PKDAPFIVFNCADYANNPQLLLGQLFGIKKGAYTGA-SDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRL 213
Cdd:COG1221   161 PEDAPFVVFNCADYANNPQLLMSQLFGYVKGAFTGAdKDKEGLIEKADGGILFLDEVHRLPPEGQEMLFTFMDKGIYRRL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 214 GETENERKARVLIITATTEEPNSFLLKTFTRRIPMTVTLPPLRERTHKERFALLQLFFTNEAIRLRKEIHVSPNTMRAFV 293
Cdd:COG1221   241 GETEKTRKANVRIIFATTEDPESSLLKTFLRRIPMVIKLPSLEERSLEERLELIKHFFKEEAKRLNKPIKVSKEVLKALL 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 294 FYNCPNNIGQLKTDVQIACAKAYSDFVTKKRDSVCVSSTDLPWYMKEGLFIERKSRH----LYQIPNETFVFTGDEGWSK 369
Cdd:COG1221   321 LYDCPGNIGQLKSDIQLACAKAFLNYITNKKEEIEITLSDLPENVKKGLLKLKENREeldkLSEYLEEYLIISPDTEKKL 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 370 HTIKPEGSRS-SIYDYIDYKYEELQARGIEEEELELLIENDIQSFFVQYFNQISKKTSHENVFKIVDRNIVSVCEKIAEL 448
Cdd:COG1221   401 ISEEDEYELPyNFYEIIEDKYEELKSEGLSEEEINKIISKDIESYFKKLIFKLDKSNISEELLLIVVDEVIVNVVEIFEE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 449 AEKYLSKTFDEKVFLALSLHVQTTLQRLHGGKQIHHPQLNQIRTKYREAFSVAMQCIQLLEEELQITMPIDEAGFLTMFF 528
Cdd:COG1221   481 AEKKLLRYNSSNLFIALSLHLLSTLLRIKKGKKIINPQLNEIKKKYYEEFILAAEAIKIIEEELKILIPDEEEGFILLLL 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 529 VVDPIPASQTEVK--VLILAHGNGIATEMANVANELLGIDEVTGI-DMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDM 605
Cdd:COG1221   561 IELKEEKSLSENVivVVVIAHGGAAASSSMAVVNLLLLEVAVAAIdDPPLEVVDVLIEEKTIVVIINKGKGGLLLLLDDG 640

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 606 GSLAYIGDILETEFKIPVRVLSMTSTPHALEAARKAqlgYSLDALYETVKNLTPFYLNVQEEKKKPLSPMKSVILTACLT 685
Cdd:COG1221   641 GSLFGIIIIEEEGIIIVTVVIVSTTTVLEAAARKKL---LELDLDEIIVLEELLKNPLESKKIKISTSKKKKIIVTTIAI 717

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 686 GEGSALAIQKMLENYLRFDKDLIEIIPISIVHEKDLTKMIENIKKERNIICIVTNFDVQVPCLTYHFQDIVNYTAIQPIQ 765
Cdd:COG1221   718 TTGEAGGILILILIIELLDKDLILIIIEILLIIIKEEILEKIIEEKKEVIIIVIISIIPLIIPPIILLLALKLIILIEIL 797

                         810       820       830
                  ....*....|....*....|....*....|....
gi 2529623216 766 ELITYEETYAKMADILEQQMQRNDGALLIKTIRY 799
Cdd:COG1221   798 VLLEILIDKEKIENIIKELLSLLNIIIVLLIIDI 831
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 801-885 7.82e-11

PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation.


:

Pssm-ID: 459973 [Multi-domain]  Cd Length: 90  Bit Score: 59.19  E-value: 7.82e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 801 LNTIQELISLQLTPDSL-MGVILHMSCMVDRLQKGESLlPHPDKEKRRQDEYWMYMKVKKALQPIENTFEIQIPDDEVFY 879
Cdd:pfam00874   4 IELIEKKLGITFDDDILyIRLILHLAFAIERIKEGITI-ENPLLEEIKEKYPKEFEIAKKILEILEEELGIELPEDEIGY 82


                  ....*.
gi 2529623216 880 VMDFFI 885
Cdd:pfam00874  83 IALHFL 88
 
Name Accession Description Interval E-value
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 1-799 0e+00

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: 762.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216   1 MKRIDLIFNAIQK-------GNYTEGVTASELATLLQLDRANVSSDLNKLVKDNRLLKTSTRPVRF-------------- 59
Cdd:COG1221     1 MKRKEKILNYLKEltknlslEKKSEGFTAEEIAEKLGISRNNVSHELNELVKEGKLIKINGRPVLFldkeafeeqfgtkl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  60 ---YIETNTSLETHSTKG--TSLDTFAIENTSLKIAIEKAKASILYPPNGMHTLLLGETGVGKSMFASLMHEYAIEVEQL 134
Cdd:COG1221    81 kseYSFVELLAEKENNEEeeDPFDNLIGANGSLKNAIEQAKAAILYPPKGLHTLILGPTGVGKSFFAELMYEYAIEIGVL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 135 PKDAPFIVFNCADYANNPQLLLGQLFGIKKGAYTGA-SDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRL 213
Cdd:COG1221   161 PEDAPFVVFNCADYANNPQLLMSQLFGYVKGAFTGAdKDKEGLIEKADGGILFLDEVHRLPPEGQEMLFTFMDKGIYRRL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 214 GETENERKARVLIITATTEEPNSFLLKTFTRRIPMTVTLPPLRERTHKERFALLQLFFTNEAIRLRKEIHVSPNTMRAFV 293
Cdd:COG1221   241 GETEKTRKANVRIIFATTEDPESSLLKTFLRRIPMVIKLPSLEERSLEERLELIKHFFKEEAKRLNKPIKVSKEVLKALL 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 294 FYNCPNNIGQLKTDVQIACAKAYSDFVTKKRDSVCVSSTDLPWYMKEGLFIERKSRH----LYQIPNETFVFTGDEGWSK 369
Cdd:COG1221   321 LYDCPGNIGQLKSDIQLACAKAFLNYITNKKEEIEITLSDLPENVKKGLLKLKENREeldkLSEYLEEYLIISPDTEKKL 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 370 HTIKPEGSRS-SIYDYIDYKYEELQARGIEEEELELLIENDIQSFFVQYFNQISKKTSHENVFKIVDRNIVSVCEKIAEL 448
Cdd:COG1221   401 ISEEDEYELPyNFYEIIEDKYEELKSEGLSEEEINKIISKDIESYFKKLIFKLDKSNISEELLLIVVDEVIVNVVEIFEE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 449 AEKYLSKTFDEKVFLALSLHVQTTLQRLHGGKQIHHPQLNQIRTKYREAFSVAMQCIQLLEEELQITMPIDEAGFLTMFF 528
Cdd:COG1221   481 AEKKLLRYNSSNLFIALSLHLLSTLLRIKKGKKIINPQLNEIKKKYYEEFILAAEAIKIIEEELKILIPDEEEGFILLLL 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 529 VVDPIPASQTEVK--VLILAHGNGIATEMANVANELLGIDEVTGI-DMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDM 605
Cdd:COG1221   561 IELKEEKSLSENVivVVVIAHGGAAASSSMAVVNLLLLEVAVAAIdDPPLEVVDVLIEEKTIVVIINKGKGGLLLLLDDG 640

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 606 GSLAYIGDILETEFKIPVRVLSMTSTPHALEAARKAqlgYSLDALYETVKNLTPFYLNVQEEKKKPLSPMKSVILTACLT 685
Cdd:COG1221   641 GSLFGIIIIEEEGIIIVTVVIVSTTTVLEAAARKKL---LELDLDEIIVLEELLKNPLESKKIKISTSKKKKIIVTTIAI 717

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 686 GEGSALAIQKMLENYLRFDKDLIEIIPISIVHEKDLTKMIENIKKERNIICIVTNFDVQVPCLTYHFQDIVNYTAIQPIQ 765
Cdd:COG1221   718 TTGEAGGILILILIIELLDKDLILIIIEILLIIIKEEILEKIIEEKKEVIIIVIISIIPLIIPPIILLLALKLIILIEIL 797

                         810       820       830
                  ....*....|....*....|....*....|....
gi 2529623216 766 ELITYEETYAKMADILEQQMQRNDGALLIKTIRY 799
Cdd:COG1221   798 VLLEILIDKEKIENIIKELLSLLNIIIVLLIIDI 831
Sigma54_activat pfam00158
Sigma-54 interaction domain;
83-245 5.94e-55

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 187.61  E-value: 5.94e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  83 ENTSLKIAIEKAKASILYPpngMHTLLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCADYanNPQLLLGQLFGI 162
Cdd:pfam00158   4 ESPAMQEVLEQAKRVAPTD---APVLITGESGTGKELFARAIHQLS-----PRADGPFVAVNCAAI--PEELLESELFGH 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 163 KKGAYTGA-SDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTEEPNSFLLKT 241
Cdd:pfam00158  74 EKGAFTGAdSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTK-PIKVDVRIIAATNRDLEEAVAEG 152


                  ....
gi 2529623216 242 FTRR 245
Cdd:pfam00158 153 RFRE 156
PTS_IIA_man cd00006
PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: ...
 540-660 1.63e-30

PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.


Pssm-ID: 237978 [Multi-domain]  Cd Length: 122  Bit Score: 116.55  E-value: 1.63e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 540 VKVLILAHGNgIATEMANVANELLGIDE-VTGIDMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDM--GSLAYIGDILE 616
Cdd:cd00006     1 VGIIIATHGG-FASGLLNSAEMILGEQEnVEAIDFPPGESPDDLLEKIKAALAELDSGEGVLILTDLfgGSPNNAAARLS 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2529623216 617 TEfKIPVRVLSMTSTPHALEAARKAQLGYSLDALYETVKNLTPF 660
Cdd:cd00006    80 ME-HPPVEVIAGVNLPMLLEAARARELGLSLDELVENALEAGRE 122
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 108-321 7.76e-26

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: 111.76  E-value: 7.76e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCADYANNpqLLLGQLFGIKKGAYTGASDQ-KGLIEKAHEGILF 186
Cdd:TIGR02915 166 LLLGESGTGKEVLARALHQLS-----DRKDKRFVAINCAAIPEN--LLESELFGYEKGAFTGAVKQtLGKIEYAHGGTLF 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 187 LDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERTh 260
Cdd:TIGR02915 239 LDEIGDLPLNLQAKLLRFLQERVIERLGGRE-EIPVDVRIVCATNQdlkrmiAEGTFREDLFYRIAEISITIPPLRSRD- 316

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2529623216 261 kERFALLQLFFTNE-AIRLRKEIH-VSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAYSDFVT 321
Cdd:TIGR02915 317 -GDAVLLANAFLERfARELKRKTKgFTDDALRALEAHAWPGNVRELENKVKRAVIMAEGNQIT 378
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
99-335 5.80e-21

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 97.02  E-value: 5.80e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  99 LYPPNGMHTLLLGETGVGKSMFASLMHEYAIEveqlpKDAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGASDQK-GLI 177
Cdd:PRK10365  157 LVAPSEATVLIHGDSGTGKELVARAIHASSAR-----SEKPLVTLNCA--ALNESLLESELFGHEKGAFTGADKRReGRF 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 178 EKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETENeRKARVLIITAT----TEEPNS--FLLKTFTRRIPMTVT 251
Cdd:PRK10365  230 VEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQT-ISVDVRLIAAThrdlAAEVNAgrFRQDLYYRLNVVAIE 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 252 LPPLRERthKERFALL-QLFFTNEAIRLRKEIH-VSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAYSDFVTKKRDSVCV 329
Cdd:PRK10365  309 VPSLRQR--REDIPLLaGHFLQRFAERNRKAVKgFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAI 386


                  ....*.
gi 2529623216 330 SSTDLP 335
Cdd:PRK10365  387 ASTPIP 392
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 106-248 4.99e-13

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: 67.40  E-value: 4.99e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  106 HTLLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCADY-ANNPQLLLGQLFGIKKGAYTGASDQKGLIEKAHE-- 182
Cdd:smart00382   4 VILIVGPPGSGKTTLARALAREL-----GPPGGGVIYIDGEDIlEEVLDQLLLIIVGGKKASGSGELRLRLALALARKlk 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2529623216  183 -GILFLDEVHRLPPEGQEMLFTFIDRgvYRRLGETENERKARVLIITATTEEPNSFLLK-TFTRRIPM 248
Cdd:smart00382  79 pDVLILDEITSLLDAEQEALLLLLEE--LRLLLLLKSEKNLTVILTTNDEKDLGPALLRrRFDRRIVL 144
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 801-885 7.82e-11

PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation.


Pssm-ID: 459973 [Multi-domain]  Cd Length: 90  Bit Score: 59.19  E-value: 7.82e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 801 LNTIQELISLQLTPDSL-MGVILHMSCMVDRLQKGESLlPHPDKEKRRQDEYWMYMKVKKALQPIENTFEIQIPDDEVFY 879
Cdd:pfam00874   4 IELIEKKLGITFDDDILyIRLILHLAFAIERIKEGITI-ENPLLEEIKEKYPKEFEIAKKILEILEEELGIELPEDEIGY 82


                  ....*.
gi 2529623216 880 VMDFFI 885
Cdd:pfam00874  83 IALHFL 88
BglG COG3711
Transcriptional antiterminator [Transcription];
794-880 4.63e-05

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 47.16  E-value: 4.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 794 IKTIRYALNTIQELISLQLTPDSLMGVILHMSCMVDRLQKGESLLPHPD--KEKRRQDEYWMymkVKKALQPIENTFEIQ 871
Cdd:COG3711   179 LELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGKYIKLDNPllWEIKKPKEYEI---AKEILKLIEERLGIS 255


                  ....*....
gi 2529623216 872 IPDDEVFYV 880
Cdd:COG3711   256 LPEDEIGYI 264
 
Name Accession Description Interval E-value
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 1-799 0e+00

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: 762.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216   1 MKRIDLIFNAIQK-------GNYTEGVTASELATLLQLDRANVSSDLNKLVKDNRLLKTSTRPVRF-------------- 59
Cdd:COG1221     1 MKRKEKILNYLKEltknlslEKKSEGFTAEEIAEKLGISRNNVSHELNELVKEGKLIKINGRPVLFldkeafeeqfgtkl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  60 ---YIETNTSLETHSTKG--TSLDTFAIENTSLKIAIEKAKASILYPPNGMHTLLLGETGVGKSMFASLMHEYAIEVEQL 134
Cdd:COG1221    81 kseYSFVELLAEKENNEEeeDPFDNLIGANGSLKNAIEQAKAAILYPPKGLHTLILGPTGVGKSFFAELMYEYAIEIGVL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 135 PKDAPFIVFNCADYANNPQLLLGQLFGIKKGAYTGA-SDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRL 213
Cdd:COG1221   161 PEDAPFVVFNCADYANNPQLLMSQLFGYVKGAFTGAdKDKEGLIEKADGGILFLDEVHRLPPEGQEMLFTFMDKGIYRRL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 214 GETENERKARVLIITATTEEPNSFLLKTFTRRIPMTVTLPPLRERTHKERFALLQLFFTNEAIRLRKEIHVSPNTMRAFV 293
Cdd:COG1221   241 GETEKTRKANVRIIFATTEDPESSLLKTFLRRIPMVIKLPSLEERSLEERLELIKHFFKEEAKRLNKPIKVSKEVLKALL 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 294 FYNCPNNIGQLKTDVQIACAKAYSDFVTKKRDSVCVSSTDLPWYMKEGLFIERKSRH----LYQIPNETFVFTGDEGWSK 369
Cdd:COG1221   321 LYDCPGNIGQLKSDIQLACAKAFLNYITNKKEEIEITLSDLPENVKKGLLKLKENREeldkLSEYLEEYLIISPDTEKKL 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 370 HTIKPEGSRS-SIYDYIDYKYEELQARGIEEEELELLIENDIQSFFVQYFNQISKKTSHENVFKIVDRNIVSVCEKIAEL 448
Cdd:COG1221   401 ISEEDEYELPyNFYEIIEDKYEELKSEGLSEEEINKIISKDIESYFKKLIFKLDKSNISEELLLIVVDEVIVNVVEIFEE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 449 AEKYLSKTFDEKVFLALSLHVQTTLQRLHGGKQIHHPQLNQIRTKYREAFSVAMQCIQLLEEELQITMPIDEAGFLTMFF 528
Cdd:COG1221   481 AEKKLLRYNSSNLFIALSLHLLSTLLRIKKGKKIINPQLNEIKKKYYEEFILAAEAIKIIEEELKILIPDEEEGFILLLL 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 529 VVDPIPASQTEVK--VLILAHGNGIATEMANVANELLGIDEVTGI-DMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDM 605
Cdd:COG1221   561 IELKEEKSLSENVivVVVIAHGGAAASSSMAVVNLLLLEVAVAAIdDPPLEVVDVLIEEKTIVVIINKGKGGLLLLLDDG 640

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 606 GSLAYIGDILETEFKIPVRVLSMTSTPHALEAARKAqlgYSLDALYETVKNLTPFYLNVQEEKKKPLSPMKSVILTACLT 685
Cdd:COG1221   641 GSLFGIIIIEEEGIIIVTVVIVSTTTVLEAAARKKL---LELDLDEIIVLEELLKNPLESKKIKISTSKKKKIIVTTIAI 717

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 686 GEGSALAIQKMLENYLRFDKDLIEIIPISIVHEKDLTKMIENIKKERNIICIVTNFDVQVPCLTYHFQDIVNYTAIQPIQ 765
Cdd:COG1221   718 TTGEAGGILILILIIELLDKDLILIIIEILLIIIKEEILEKIIEEKKEVIIIVIISIIPLIIPPIILLLALKLIILIEIL 797

                         810       820       830
                  ....*....|....*....|....*....|....
gi 2529623216 766 ELITYEETYAKMADILEQQMQRNDGALLIKTIRY 799
Cdd:COG1221   798 VLLEILIDKEKIENIIKELLSLLNIIIVLLIIDI 831
LevR COG3933
Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];
1-885 0e+00

Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];


Pssm-ID: 443134 [Multi-domain]  Cd Length: 916  Bit Score: 666.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216   1 MKRIDLIFNAIQKGNYTEGVTASELATLLQLDRANVSSDLNKLVKDNRLLKTSTRPVRFYIETNTSLETHSTKGTSLDTF 80
Cdd:COG3933    21 ARDLKELIKSKLLKESTGLLKLLALLLLLKRLSELLLELKKLKKEKKTLKKERSLLEKKKNKLNLKEEKKEKLDFKALIG 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  81 AIEntSLKIAIEKAKASILYPPNGMHTLLLGETGVGKSMFASLMHEYAIEVEQLPKDAPFIVFNCADYANNPQLLLGQLF 160
Cdd:COG3933   101 LSL--SLLSAAAAAKAAKPPPPLGLLTLLLGGTGGGKSAFAGYMYAFAAKIAELAAPFVFFNFANAAYNPNLLLLLLFGL 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 161 GIKKGAYTGAsDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETENERKARVLIITATTEEPNSFLLK 240
Cdd:COG3933   179 GGGAGGGAGA-DGGGLGGAAGAGGGLLDLLDELPLEGEEQEELFFLLGKGLFRGEGGESRSRRVRIIRATTETEESLLLT 257

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 241 TFTRRIPMTVTLPPLRERTHKERFALLQLFFTNEAIRLRKEIHVSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAYSDF- 319
Cdd:COG3933   258 TLTRRIRIIIILPRLPILERRERERLLLLLFEFEEEEIRIIKILIVLLLALLLLLLYVNNLGQLGLLKLLIKAAAAAALa 337

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 320 --VTKKRDSVCVSSTDLPWYMKEGLFIERKSRHLYQIPNETFVFTGDEGWSKHTIKPEgSRSSIYDYIDYKYEELQARGI 397
Cdd:COG3933   338 kaIKEATIILRLLSKLLKLLLLLLLNERLLLLELKILIEPLDIFFDSSASSDESDESE-EDENLYEIIEIKKKLLLELGI 416

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 398 EEEELELLIENDIQSFFVQYFNQISKKTSHENVFKIVDRNIVSVCEKIAELAEKYLSKTFDEKVFLALSLHVQTTLQRLH 477
Cdd:COG3933   417 DEEEINIIIEIDIDVHLLKFIYDDNKNFNKEELAKIVDEDIINVVEEILELAEKKLGRKFSENFIYALSLHLSSFIERIK 496

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 478 GGKQIHHPQLNQIRTKYREAFSVAMQCIQLLEEELQITMPIDEAGFLTMFFVVDPIPASQTEVKVLILAHGNGIATEMAN 557
Cdd:COG3933   497 EGKEIINPNLNEIKKKYPKEFKVAKEIKELIEQELDIEIPEDEVGFLTLFLVSLNENNESGKVGVIVLAHGYSTASSMAE 576

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 558 VANELLGIDEVTGIDMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDMGSLAYIGDILETEFKIPVRVLSMTSTPHALEA 637
Cdd:COG3933   577 VANRLLGTNIFEAIDMPLDMSPEDILEKLKEYVKKIDTGKGVLLLVDMGSLTTFGEIIEEETGIPVKTIDMVSTPLVLEA 656

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 638 ARKAQLGYSLDALYETVKNLTPFylNVQEEKKKPLSPMKSVILTACLTGEGSALAIQKMLENYLRFDKDLIEIIPISIVH 717
Cdd:COG3933   657 GRKALLGMSLEEIYESLKNFNPY--EKIISKNKPEKNKKKAIITTCFTGEGTAVKIKDLLEKSLPEDEDNIEIIPLDYLE 734

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 718 EKDLTKMIENIKKERNIICIVTNFDVQVPCLTY-HFQDIVNYTAIQPIQELITYEET------------YAKMADILEQQ 784
Cdd:COG3933   735 LEEFKEKIDEIFKEYEILAIVGTIDPEIPDIPFiSLEDLISGEGIEKLQKLLGGELDaeeieeinneiiKNFSLESLIES 814

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 785 MQRNDGALLIKTIRYALNTIQELISLQLTPDSLMGVILHMSCMVDRLQKGESLLPHPDKEKRRQDEYWMYMKVKKALQPI 864
Cdd:COG3933   815 LTILNPEKIINELEDFISRLENLLGIKLDNDVKIGLILHIACMIERLVTGEEILTYPNKEEFIQENESEYAVIKEAFSPI 894

                         890       900
                  ....*....|....*....|.
gi 2529623216 865 ENTFEIQIPDDEVFYVMDFFI 885
Cdd:COG3933   895 EEKYNIKIPDSEIAYIYDILK 915
Sigma54_activat pfam00158
Sigma-54 interaction domain;
83-245 5.94e-55

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 187.61  E-value: 5.94e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  83 ENTSLKIAIEKAKASILYPpngMHTLLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCADYanNPQLLLGQLFGI 162
Cdd:pfam00158   4 ESPAMQEVLEQAKRVAPTD---APVLITGESGTGKELFARAIHQLS-----PRADGPFVAVNCAAI--PEELLESELFGH 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 163 KKGAYTGA-SDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTEEPNSFLLKT 241
Cdd:pfam00158  74 EKGAFTGAdSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTK-PIKVDVRIIAATNRDLEEAVAEG 152


                  ....
gi 2529623216 242 FTRR 245
Cdd:pfam00158 153 RFRE 156
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 108-346 5.70e-36

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: 141.25  E-value: 5.70e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGA-SDQKGLIEKAHEGILF 186
Cdd:COG2204   158 LITGESGTGKELVARAIHRLS-----PRADGPFVAVNCA--AIPEELLESELFGHEKGAFTGAvARRIGKFELADGGTLF 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 187 LDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERth 260
Cdd:COG2204   231 LDEIGEMPLALQAKLLRVLQEREFERVGGNK-PIPVDVRVIAATNRdleelvEEGRFREDLYYRLNVFPIELPPLRER-- 307

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 261 KERFALLQLFFTNE-AIRLRKEIHVSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAYSDFVTKKrdsvcvsstDLPWYMK 339
Cdd:COG2204   308 REDIPLLARHFLARfAAELGKPVKLSPEALEALLAYDWPGNVRELENVIERAVILADGEVITAE---------DLPEALE 378


                  ....*..
gi 2529623216 340 EglfIER 346
Cdd:COG2204   379 E---VER 382
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
108-335 1.46e-34

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


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 140.81  E-value: 1.46e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAIeveqlPKDAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGASDQ--KGLIEKAHEGIL 185
Cdd:COG3284   348 LILGETGTGKELFARAIHAASP-----RADGPFVAVNCA--AIPEELIESELFGYEPGAFTGARRKgrPGKIEQADGGTL 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 186 FLDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATteepNSFLLK-----TFTR----RI-PMTVTLPPL 255
Cdd:COG3284   421 FLDEIGDMPLALQARLLRVLQEREVTPLGGTK-PIPVDVRLIAAT----HRDLRElvaagRFREdlyyRLnGLTLTLPPL 495

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 256 RERTHKErfALLQLFFTNEAIRlRKEIHVSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAysdfvtkkrDSVCVSSTDLP 335
Cdd:COG3284   496 REREDLP--ALIEHLLRELAAG-RGPLRLSPEALALLAAYPWPGNVRELRNVLRTALALA---------DGGVITVEDLP 563
PTS_IIA_man cd00006
PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: ...
 540-660 1.63e-30

PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.


Pssm-ID: 237978 [Multi-domain]  Cd Length: 122  Bit Score: 116.55  E-value: 1.63e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 540 VKVLILAHGNgIATEMANVANELLGIDE-VTGIDMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDM--GSLAYIGDILE 616
Cdd:cd00006     1 VGIIIATHGG-FASGLLNSAEMILGEQEnVEAIDFPPGESPDDLLEKIKAALAELDSGEGVLILTDLfgGSPNNAAARLS 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2529623216 617 TEfKIPVRVLSMTSTPHALEAARKAQLGYSLDALYETVKNLTPF 660
Cdd:cd00006    80 ME-HPPVEVIAGVNLPMLLEAARARELGLSLDELVENALEAGRE 122
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 67-305 9.34e-30

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: 123.73  E-value: 9.34e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  67 LETHSTKGTSLDTFAIENTSLKIAIEKAK------ASILyppngmhtlLLGETGVGKSMFASLMHEyaievEQLPKDAPF 140
Cdd:COG3829   127 LERGLSAKYTFDDIIGKSPAMKELLELAKrvaksdSTVL---------ILGESGTGKELFARAIHN-----ASPRRDGPF 192

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 141 IVFNCAdyANNPQLLLGQLFGIKKGAYTGAS--DQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETEn 218
Cdd:COG3829   193 VAVNCA--AIPENLLESELFGYEKGAFTGAKkgGKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTK- 269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 219 ERKARVLIITAT-------TEEpnsfllKTFtRR--------IPmtVTLPPLRERthKERFALLQLFFTNE-AIRLRKEI 282
Cdd:COG3829   270 PIPVDVRIIAATnrdleemVEE------GRF-REdlyyrlnvIP--IHIPPLRER--KEDIPLLAEHFLEKfNKKYGKNI 338

                         250       260
                  ....*....|....*....|....
gi 2529623216 283 H-VSPNTMRAFVFYNCPNNIGQLK 305
Cdd:COG3829   339 KgISPEALELLLAYDWPGNVRELE 362
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 108-321 7.76e-26

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: 111.76  E-value: 7.76e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCADYANNpqLLLGQLFGIKKGAYTGASDQ-KGLIEKAHEGILF 186
Cdd:TIGR02915 166 LLLGESGTGKEVLARALHQLS-----DRKDKRFVAINCAAIPEN--LLESELFGYEKGAFTGAVKQtLGKIEYAHGGTLF 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 187 LDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERTh 260
Cdd:TIGR02915 239 LDEIGDLPLNLQAKLLRFLQERVIERLGGRE-EIPVDVRIVCATNQdlkrmiAEGTFREDLFYRIAEISITIPPLRSRD- 316

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2529623216 261 kERFALLQLFFTNE-AIRLRKEIH-VSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAYSDFVT 321
Cdd:TIGR02915 317 -GDAVLLANAFLERfARELKRKTKgFTDDALRALEAHAWPGNVRELENKVKRAVIMAEGNQIT 378
TyrR COG3283
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...
 108-305 3.73e-21

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


Pssm-ID: 442513 [Multi-domain]  Cd Length: 514  Bit Score: 97.95  E-value: 3.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAIEveqlpKDAPFIVFNCA----DYANNpqlllgQLFGIKKGAYTGASD-QKGLIEKAHE 182
Cdd:COG3283   231 LIQGETGTGKELLARACHLASPR-----GDKPFLALNCAalpdDVAES------ELFGYAPGAFGNAREgKKGLFEQANG 299

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 183 GILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGEtENERKARVLIITATTEEpnsfLLKT----------FTRRIPMTVTL 252
Cdd:COG3283   300 GTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGE-EQEVKVDVRVICATQKD----LAELvqegefredlYYRLNVLTLTL 374

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2529623216 253 PPLRERthKERFALL-QLFFTNEAIRL-RKEIHVSPNTMRAFVFYNCPNNIGQLK 305
Cdd:COG3283   375 PPLRER--KSDILPLaEHFVARFSQQLgRPRPRLSPDLVDFLQSYPWPGNVRQLE 427
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
99-335 5.80e-21

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 97.02  E-value: 5.80e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  99 LYPPNGMHTLLLGETGVGKSMFASLMHEYAIEveqlpKDAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGASDQK-GLI 177
Cdd:PRK10365  157 LVAPSEATVLIHGDSGTGKELVARAIHASSAR-----SEKPLVTLNCA--ALNESLLESELFGHEKGAFTGADKRReGRF 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 178 EKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETENeRKARVLIITAT----TEEPNS--FLLKTFTRRIPMTVT 251
Cdd:PRK10365  230 VEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQT-ISVDVRLIAAThrdlAAEVNAgrFRQDLYYRLNVVAIE 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 252 LPPLRERthKERFALL-QLFFTNEAIRLRKEIH-VSPNTMRAFVFYNCPNNIGQLKTDVQIACAKAYSDFVTKKRDSVCV 329
Cdd:PRK10365  309 VPSLRQR--REDIPLLaGHFLQRFAERNRKAVKgFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAI 386


                  ....*.
gi 2529623216 330 SSTDLP 335
Cdd:PRK10365  387 ASTPIP 392
PRK10820 PRK10820
transcriptional regulator TyrR;
108-305 6.68e-20

transcriptional regulator TyrR;


Pssm-ID: 236769 [Multi-domain]  Cd Length: 520  Bit Score: 94.37  E-value: 6.68e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAIEVEQlpkdaPFIVFNCADYANNpqLLLGQLFGIKKGAYTGASD-QKGLIEKAHEGILF 186
Cdd:PRK10820  231 LITGDTGTGKDLLAYACHLRSPRGKK-----PFLALNCASIPDD--VVESELFGHAPGAYPNALEgKKGFFEQANGGSVL 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 187 LDEVHRLPPEGQEMLFTFIDRGVYRRLGEtENERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERTh 260
Cdd:PRK10820  304 LDEIGEMSPRMQAKLLRFLNDGTFRRVGE-DHEVHVDVRVICATQKnlvelvQKGEFREDLYYRLNVLTLNLPPLRDRP- 381

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2529623216 261 KERFALLQLF---FTNEAIRLRKEIhvSPNtMRAFVF-YNCPNNIGQLK 305
Cdd:PRK10820  382 QDIMPLTELFvarFADEQGVPRPKL--AAD-LNTVLTrYGWPGNVRQLK 427
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
82-311 1.52e-19

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 92.60  E-value: 1.52e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  82 IENTSLKIAIEKAKasilyppngmhTLLLGETGVGKSMFASlmheyAIEVEQLPKDAPFIVFNCAdyANNPQLLLGQLFG 161
Cdd:PRK11361  155 ICKDTAKIALSQAS-----------VLISGESGTGKELIAR-----AIHYNSRRAKGPFIKVNCA--ALPESLLESELFG 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 162 IKKGAYTGASDQK-GLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETENERkARVLIITATTEE------P 234
Cdd:PRK11361  217 HEKGAFTGAQTLRqGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIK-VDIRIIAATNRDlqamvkE 295

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2529623216 235 NSFLLKTFTRRIPMTVTLPPLRERthKERFALLQLFFTNE--AIRLRKEIHVSPNTMRAFVFYNCPNNIGQLKTDVQIA 311
Cdd:PRK11361  296 GTFREDLFYRLNVIHLILPPLRDR--REDISLLANHFLQKfsSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERA 372
pspF PRK11608
phage shock protein operon transcriptional activator; Provisional
 108-309 4.02e-18

phage shock protein operon transcriptional activator; Provisional


Pssm-ID: 236936 [Multi-domain]  Cd Length: 326  Bit Score: 86.65  E-value: 4.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHeYAIEVEQlpkdAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGAsdQK---GLIEKAHEGI 184
Cdd:PRK11608   33 LIIGERGTGKELIASRLH-YLSSRWQ----GPFISLNCA--ALNENLLDSELFGHEAGAFTGA--QKrhpGRFERADGGT 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 185 LFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRER 258
Cdd:PRK11608  104 LFLDELATAPMLVQEKLLRVIEYGELERVGGSQ-PLQVNVRLVCATNAdlpamvAEGKFRADLLDRLAFDVVQLPPLRER 182

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2529623216 259 thKERFALLQLFFtneAIRLRKEIHV------SPNTMRAFVFYNCPNNIGQLKTDVQ 309
Cdd:PRK11608  183 --QSDIMLMAEHF---AIQMCRELGLplfpgfTERARETLLNYRWPGNIRELKNVVE 234
PRK15424 PRK15424
propionate catabolism operon regulatory protein PrpR; Provisional
 90-305 8.26e-18

propionate catabolism operon regulatory protein PrpR; Provisional


Pssm-ID: 237963 [Multi-domain]  Cd Length: 538  Bit Score: 87.85  E-value: 8.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  90 AIEKAKASI-LYPPNGMHTLLLGETGVGKSMFASLMH-EYAIEVEQLP--KDAPFIVFNCAdyANNPQLLLGQLFGIKKG 165
Cdd:PRK15424  227 QMEQVRQTIlLYARSSAAVLIQGETGTGKELAAQAIHrEYFARHDARQgkKSHPFVAVNCG--AIAESLLEAELFGYEEG 304

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 166 AYTGA--SDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTE------EPNSF 237
Cdd:PRK15424  305 AFTGSrrGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQ-PVPVDVRVISATHCdleedvRQGRF 383

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2529623216 238 LLKTFTRRIPMTVTLPPLRERTH----------KERFALLQLFFTnEAIRLRKEIHvspntMRAFVFYNCPNNIGQLK 305
Cdd:PRK15424  384 RRDLFYRLSILRLQLPPLRERVAdilplaesflKQSLAALSAPFS-AALRQGLQQC-----ETLLLHYDWPGNVRELR 455
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 443-529 2.10e-17

PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation.


Pssm-ID: 459973 [Multi-domain]  Cd Length: 90  Bit Score: 78.06  E-value: 2.10e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 443 EKIAELAEKYLSKTF-DEKVFLALSLHVQTTLQRLHGGKQIHHPQLNQIRTKYREAFSVAMQCIQLLEEELQITMPIDEA 521
Cdd:pfam00874   1 EEIIELIEKKLGITFdDDILYIRLILHLAFAIERIKEGITIENPLLEEIKEKYPKEFEIAKKILEILEEELGIELPEDEI 80


                  ....*...
gi 2529623216 522 GFLTMFFV 529
Cdd:pfam00874  81 GYIALHFL 88
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 108-305 6.78e-16

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 81.46  E-value: 6.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAIEVEqlpkdAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGASD-QKGLIEKAHEGILF 186
Cdd:PRK10923  165 LINGESGTGKELVAHALHRHSPRAK-----APFIALNMA--AIPKDLIESELFGHEKGAFTGANTiRQGRFEQADGGTLF 237

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 187 LDEVHRLPPEGQEMLFTFIDRGVYRRLGETEnERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERTh 260
Cdd:PRK10923  238 LDEIGDMPLDVQTRLLRVLADGQFYRVGGYA-PVKVDVRIIAATHQnleqrvQEGKFREDLFHRLNVIRVHLPPLRERR- 315

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2529623216 261 kERFALLQLFFTNEAIR-LRKEIHV-SPNTMRAFVFYNCPNNIGQLK 305
Cdd:PRK10923  316 -EDIPRLARHFLQVAAReLGVEAKLlHPETEAALTRLAWPGNVRQLE 361
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 90-254 7.46e-16

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: 75.65  E-value: 7.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  90 AIEKAKASILYPPNGmHTLLLGETGVGKSMFASLMHEYAIEveqlpKDAPFIVFNCADyannpqlLLGQLFGIKKGAYTG 169
Cdd:cd00009     6 AIEALREALELPPPK-NLLLYGPPGTGKTTLARAIANELFR-----PGAPFLYLNASD-------LLEGLVVAELFGHFL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 170 ASDQKGLIEKAHEGILFLDEVHRLPPEGQEMLFTFIDRGVYRRlgetenERKARVLIITATTEEPNSFLLKTFTRRIPMT 249
Cdd:cd00009    73 VRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLR------IDRENVRVIGATNRPLLGDLDRALYDRLDIR 146


                  ....*
gi 2529623216 250 VTLPP 254
Cdd:cd00009   147 IVIPL 151
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
108-304 1.16e-15

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 80.99  E-value: 1.16e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHeyaievEQLP-KDAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGA-SDQKGLIEKAHEGIL 185
Cdd:PRK05022  214 LILGETGVGKELVARAIH------AASPrADKPLVYLNCA--ALPESLAESELFGHVKGAFTGAiSNRSGKFELADGGTL 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 186 FLDEVHRLPPEGQEMLFTFIDRGVYRRLGEtENERKARVLIITATteepNSFL----------------LKTFtrriPMT 249
Cdd:PRK05022  286 FLDEIGELPLALQAKLLRVLQYGEIQRVGS-DRSLRVDVRVIAAT----NRDLreevragrfradlyhrLSVF----PLS 356

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2529623216 250 VtlPPLRERthKERFALLQLFFTnEAIRLR---KEIHVSPNTMRAFVFYNCPNNIGQL 304
Cdd:PRK05022  357 V--PPLRER--GDDVLLLAGYFL-EQNRARlglRSLRLSPAAQAALLAYDWPGNVREL 409
PRK15115 PRK15115
response regulator GlrR; Provisional
 108-304 2.62e-15

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 79.50  E-value: 2.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAieveqlPK-DAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGA-SDQKGLIEKAHEGIL 185
Cdd:PRK15115  161 LINGQSGTGKEILAQAIHNAS------PRaSKPFIAINCG--ALPEQLLESELFGHARGAFTGAvSNREGLFQAAEGGTL 232

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 186 FLDEVHRLPPEGQEMLFTFIDRGVYRRLGETeNERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERT 259
Cdd:PRK15115  233 FLDEIGDMPAPLQVKLLRVLQERKVRPLGSN-RDIDIDVRIISATHRdlpkamARGEFREDLYYRLNVVSLKIPALAERT 311

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2529623216 260 hkERFALLqlffTNEAIRLRKEIH------VSPNTMRAFVFYNCPNNIGQL 304
Cdd:PRK15115  312 --EDIPLL----ANHLLRQAAERHkpfvraFSTDAMKRLMTASWPGNVRQL 356
PRK11388 PRK11388
DNA-binding transcriptional regulator DhaR; Provisional
 108-305 3.14e-15

DNA-binding transcriptional regulator DhaR; Provisional


Pssm-ID: 183114 [Multi-domain]  Cd Length: 638  Bit Score: 80.11  E-value: 3.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEyaiEVEQlpKDAPFIVFNCADYANNpqLLLGQLFGikKGAYTGASDQKGLIEKAHEGILFL 187
Cdd:PRK11388  352 LLCGEEGVGKALLAQAIHN---ESER--AAGPYIAVNCQLYPDE--ALAEEFLG--SDRTDSENGRLSKFELAHGGTLFL 422

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 188 DEVHRLPPEGQEMLFTFIDRGVYRRLgeteNERK---ARVLIITATTEE-PNSFLLKTFTRRIPMT-----VTLPPLRER 258
Cdd:PRK11388  423 EKVEYLSPELQSALLQVLKTGVITRL----DSRRlipVDVRVIATTTADlAMLVEQNRFSRQLYYAlhafeITIPPLRMR 498

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2529623216 259 THKERFALLQLFFTNEAiRLRKEIHVSPNTMRAFVFYNCPNNIGQLK 305
Cdd:PRK11388  499 REDIPALVNNKLRSLEK-RFSTRLKIDDDALARLVSYRWPGNDFELR 544
PRK15429 PRK15429
formate hydrogenlyase transcriptional activator FlhA;
108-311 5.91e-15

formate hydrogenlyase transcriptional activator FlhA;


Pssm-ID: 237965 [Multi-domain]  Cd Length: 686  Bit Score: 79.10  E-value: 5.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAIEveqlpKDAPFIVFNCAdyANNPQLLLGQLFGIKKGAYTGASDQK-GLIEKAHEGILF 186
Cdd:PRK15429  403 LILGETGTGKELIARAIHNLSGR-----NNRRMVKMNCA--AMPAGLLESDLFGHERGAFTGASAQRiGRFELADKSSLF 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 187 LDEVHRLPPEGQEMLFTFIDRGVYRRLGeTENERKARVLIITATTEE------PNSFLLKTFTRRIPMTVTLPPLRERth 260
Cdd:PRK15429  476 LDEVGDMPLELQPKLLRVLQEQEFERLG-SNKIIQTDVRLIAATNRDlkkmvaDREFRSDLYYRLNVFPIHLPPLRER-- 552

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2529623216 261 KERFALLQLFFTNE-AIRLRKEIHVSP-NTMRAFVFYNCPNNIGQLKTDVQIA 311
Cdd:PRK15429  553 PEDIPLLVKAFTFKiARRMGRNIDSIPaETLRTLSNMEWPGNVRELENVIERA 605
BglG COG3711
Transcriptional antiterminator [Transcription];
408-529 4.48e-13

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 72.97  E-value: 4.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 408 NDIQSFFVQYFNQISKKTSHENVF--KIVDRNIVSVCEKIAELAEKYLSKTFDEKVFLALSLHVQTTLQRLHGGKQIHHP 485
Cdd:COG3711   146 LDIRKALAELLSELLSENDLLSLLllKLIPEEDLELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGKYIKLD 225

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2529623216 486 QLNQIRTKYREAFSVAMQCIQLLEEELQITMPIDEAGFLTMFFV 529
Cdd:COG3711   226 NPLLWEIKKPKEYEIAKEILKLIEERLGISLPEDEIGYIALHLL 269
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 106-248 4.99e-13

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: 67.40  E-value: 4.99e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  106 HTLLLGETGVGKSMFASLMHEYAieveqLPKDAPFIVFNCADY-ANNPQLLLGQLFGIKKGAYTGASDQKGLIEKAHE-- 182
Cdd:smart00382   4 VILIVGPPGSGKTTLARALAREL-----GPPGGGVIYIDGEDIlEEVLDQLLLIIVGGKKASGSGELRLRLALALARKlk 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2529623216  183 -GILFLDEVHRLPPEGQEMLFTFIDRgvYRRLGETENERKARVLIITATTEEPNSFLLK-TFTRRIPM 248
Cdd:smart00382  79 pDVLILDEITSLLDAEQEALLLLLEE--LRLLLLLKSEKNLTVILTTNDEKDLGPALLRrRFDRRIVL 144
BglG COG3711
Transcriptional antiterminator [Transcription];
422-528 1.50e-12

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 71.43  E-value: 1.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 422 SKKTSHENVFKIVDRNIVSVCEKIAELAEKYLSKTFDEKVFLA--LSLHVQTTLQRLHGGKQIHHPQLNQIRTKYREAFS 499
Cdd:COG3711   271 ARLNNDNELSEIITLEITKLIKEIINIIEEELGIDLDEDSLLYerLITHLKPAINRLKYGIPIRNPLLEEIKEKYPEAFE 350

                          90       100
                  ....*....|....*....|....*....
gi 2529623216 500 VAMQCIQLLEEELQITMPIDEAGFLTMFF 528
Cdd:COG3711   351 LAKKIAKYLEKELGIEIPEDEIGYLTLHF 379
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 801-885 7.82e-11

PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation.


Pssm-ID: 459973 [Multi-domain]  Cd Length: 90  Bit Score: 59.19  E-value: 7.82e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 801 LNTIQELISLQLTPDSL-MGVILHMSCMVDRLQKGESLlPHPDKEKRRQDEYWMYMKVKKALQPIENTFEIQIPDDEVFY 879
Cdd:pfam00874   4 IELIEKKLGITFDDDILyIRLILHLAFAIERIKEGITI-ENPLLEEIKEKYPKEFEIAKKILEILEEELGIELPEDEIGY 82


                  ....*.
gi 2529623216 880 VMDFFI 885
Cdd:pfam00874  83 IALHFL 88
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 109-305 1.59e-09

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: 60.63  E-value: 1.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 109 LLGETGVGKSMFASLMHEYAIEveqlpKDAPFIVFNCADYannPQLLLGQLfgikkgaytgasdqkgliekahegilfld 188
Cdd:COG3604   120 ILGETGTGKELVANAIHELSPR-----ADKPFVKVNCAAL---PESLLESL----------------------------- 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 189 evhrlppegQEmlftfidrGVYRRLGETEnERKARVLIITATTE------EPNSFLLKTFTRRIPMTVTLPPLRERthKE 262
Cdd:COG3604   163 ---------QE--------GEFERVGGDE-TIKVDVRIIAATNRdleeevAEGRFREDLYYRLNVFPIRLPPLRER--RE 222

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2529623216 263 RFALLQLFFTNE-AIRLRKEI-HVSPNTMRAFVFYNCPNNIGQLK 305
Cdd:COG3604   223 DIPLLAEHFLEKfSRRLGKPIlRLSPEALEALMAYPWPGNVRELE 267
LevR COG3933
Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];
690-892 1.21e-08

Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];


Pssm-ID: 443134 [Multi-domain]  Cd Length: 916  Bit Score: 58.98  E-value: 1.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 690 ALAIQKMLENYLRFDKDLIEIIPISIVHEKDLTKMIENIKKERNIICIVTNFDVQVP-----CLTYHFQDIVNYTA---- 760
Cdd:COG3933   333 AAALAKAIKEATIILRLLSKLLKLLLLLLLNERLLLLELKILIEPLDIFFDSSASSDesdesEEDENLYEIIEIKKklll 412

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 761 -------IQPIQELITYEETYAKMADILEQQMQRND-----GALLIKTIRYALNTIQELISLQLTPDSLMGVILHMSCMV 828
Cdd:COG3933   413 elgideeEINIIIEIDIDVHLLKFIYDDNKNFNKEElakivDEDIINVVEEILELAEKKLGRKFSENFIYALSLHLSSFI 492

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2529623216 829 DRLQKGESLLPHPDKEKRRQ--DEYWMYMKVKKAlqpIENTFEIQIPDDEVFYVMDFFIKNQPVKS 892
Cdd:COG3933   493 ERIKEGKEIINPNLNEIKKKypKEFKVAKEIKEL---IEQELDIEIPEDEVGFLTLFLVSLNENNE 555
PRK09772 PRK09772
transcriptional antiterminator BglG; Provisional
 438-540 2.39e-06

transcriptional antiterminator BglG; Provisional


Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 50.09  E-value: 2.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 438 IVSVCEKIAELAEKYLSKtFDEKVFLALSLHVQTTLQRLHGGKQIHHPQLNQIRTKYREAFSVAMQCIQLLEEELQITMP 517
Cdd:PRK09772   72 VMATCDRIISLAQERLGK-LQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLP 150

                          90       100
                  ....*....|....*....|...
gi 2529623216 518 IDEAGFLTMFFVVDPIPASQTEV 540
Cdd:PRK09772  151 KDEVGFIAMHLVSAQMSGNMEDV 173
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 106-245 4.16e-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: 4.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 106 HTLLLGETGVGKSM----FASLMHEYAIEVEQLPKDAPfivfncADyannpqlllgQLFGIKKGAYTGASDQKG-LIEKA 180
Cdd:pfam07728   1 GVLLVGPPGTGKTElaerLAAALSNRPVFYVQLTRDTT------EE----------DLFGRRNIDPGGASWVDGpLVRAA 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2529623216 181 HEG-ILFLDEVHRLPPEGQEMLFTFIDRGVYRR--LGETENERKARVLIItATTEEPN---SFLLKTFTRR 245
Cdd:pfam07728  65 REGeIAVLDEINRANPDVLNSLLSLLDERRLLLpdGGELVKAAPDGFRLI-ATMNPLDrglNELSPALRSR 134
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 83-237 3.93e-05

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 47.00  E-value: 3.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  83 ENTSLKIAIEKAKAS--ILY-PPngmhtlllgetGVGKSMFASLMHEYAieveqlpkDAPFIVFNCAdyannpqlllgqL 159
Cdd:PRK13342   23 PGKPLRRMIEAGRLSsmILWgPP-----------GTGKTTLARIIAGAT--------DAPFEALSAV------------T 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 160 FGIKkgaytgasDQKGLIEKAHEG-------ILFLDEVHRLPPEGQEMLFTFIDRGvyrrlgetenerkaRVLIITATTE 232
Cdd:PRK13342   72 SGVK--------DLREVIEEARQRrsagrrtILFIDEIHRFNKAQQDALLPHVEDG--------------TITLIGATTE 129


                  ....*
gi 2529623216 233 EPnSF 237
Cdd:PRK13342  130 NP-SF 133
BglG COG3711
Transcriptional antiterminator [Transcription];
794-880 4.63e-05

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 47.16  E-value: 4.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 794 IKTIRYALNTIQELISLQLTPDSLMGVILHMSCMVDRLQKGESLLPHPD--KEKRRQDEYWMymkVKKALQPIENTFEIQ 871
Cdd:COG3711   179 LELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGKYIKLDNPllWEIKKPKEYEI---AKEILKLIEERLGIS 255


                  ....*....
gi 2529623216 872 IPDDEVFYV 880
Cdd:COG3711   256 LPEDEIGYI 264
EIIA-man pfam03610
PTS system fructose IIA component;
541-653 5.03e-05

PTS system fructose IIA component;


Pssm-ID: 427399 [Multi-domain]  Cd Length: 113  Bit Score: 43.39  E-value: 5.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 541 KVLILAHGNgIATEMANVANELLG-IDEVTGIDMPLHESPKDFLERVKVYMKTLQNVNGLLLLVDMGSLAYIGD-ILETE 618
Cdd:pfam03610   1 GIVIVSHGE-LAEGLLELAEMMAGeQENVIAVGGTPGESIGTSFEKIVEAIENLDSGDGVLVLVDLGGATPNNEaALELL 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2529623216 619 FKIPVRVLSMTSTPHALEAARKAQlGYSLDALYET 653
Cdd:pfam03610  80 EKERMEVITGVNLPMVEGAYAARV-SASLGELVEA 113
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 99-271 6.38e-05

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 46.44  E-value: 6.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216  99 LYPPNGMhtLLLGETGVGKSMFASLMheyAIEVeqlpkDAPFIVFNCADyannpqlLLGQlfgikkgaYTGASDQK--GL 176
Cdd:COG0464   188 LPPPRGL--LLYGPPGTGKTLLARAL---AGEL-----GLPLIEVDLSD-------LVSK--------YVGETEKNlrEV 242

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 177 IEKAHE---GILFLDEVHRLPPEGQEMLFTFIDRGVYRRLGETENERKaRVLIITATteepNSFLL--KTFTRRIPMTVT 251
Cdd:COG0464   243 FDKARGlapCVLFIDEADALAGKRGEVGDGVGRRVVNTLLTEMEELRS-DVVVIAAT----NRPDLldPALLRRFDEIIF 317

                         170       180
                  ....*....|....*....|
gi 2529623216 252 LPPLrerTHKERFALLQLFF 271
Cdd:COG0464   318 FPLP---DAEERLEIFRIHL 334
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 108-246 2.16e-04

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 41.81  E-value: 2.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFA-SLMHEYaieveqlpkDAPFIVFNCADyannpqlLLGQLFGIkkgaytGASDQKGLIEKAHE---G 183
Cdd:pfam00004   2 LLYGPPGTGKTTLAkAVAKEL---------GAPFIEISGSE-------LVSKYVGE------SEKRLRELFEAAKKlapC 59

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2529623216 184 ILFLDEVHRLPPEGQEMLFTFIDRGV---YRRLGETENeRKARVLIITATT--EEPNSFLLKTFTRRI 246
Cdd:pfam00004  60 VIFIDEIDALAGSRGSGGDSESRRVVnqlLTELDGFTS-SNSKVIVIAATNrpDKLDPALLGRFDRII 126
Sigma54_activ_2 pfam14532
Sigma-54 interaction domain;
108-255 2.45e-04

Sigma-54 interaction domain;


Pssm-ID: 434021 [Multi-domain]  Cd Length: 138  Bit Score: 41.94  E-value: 2.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 108 LLLGETGVGKSMFASLMHEYAIeveqlPKDAPFivfNCADYANNPQLLLgqlfgikkgaytgasdqkgliEKAHEGILFL 187
Cdd:pfam14532  25 FLTGEPGSGKEFCARYLHNPST-----PWVQPF---DIEYLAHAPLELL---------------------EQAKGGTLYL 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2529623216 188 DEVHRLPPEGQemlftfidRGVYRRLGETENERkARVLIITATT----EEPNSFLLKTFTRRIPMTVTLPPL 255
Cdd:pfam14532  76 KDIADLSKALQ--------KGLLLLLAKAEGYR-VRLVCTSSKDlpqlAAAGLFDEQLYFELSALRLHVPPL 138
BglG COG3711
Transcriptional antiterminator [Transcription];
782-879 5.98e-04

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 43.69  E-value: 5.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 782 EQQMQRNDGALLIKTIRYALNTIQELISLQLTPDS--LMGVILHMSCMVDRLQKGESLlPHP--DKEKRRQDEywMYMKV 857
Cdd:COG3711   276 DNELSEIITLEITKLIKEIINIIEEELGIDLDEDSllYERLITHLKPAINRLKYGIPI-RNPllEEIKEKYPE--AFELA 352

                          90       100
                  ....*....|....*....|..
gi 2529623216 858 KKALQPIENTFEIQIPDDEVFY 879
Cdd:COG3711   353 KKIAKYLEKELGIEIPEDEIGY 374
AAA_22 pfam13401
AAA domain;
106-196 1.17e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.02  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2529623216 106 HTLLLGETGVGKSMFASLMHeyaievEQLPKDAPFIVFNCADYANNPQLLLGQL---FGIKKGAYTGASD-----QKGLI 177
Cdd:pfam13401   7 ILVLTGESGTGKTTLLRRLL------EQLPEVRDSVVFVDLPSGTSPKDLLRALlraLGLPLSGRLSKEEllaalQQLLL 80

                          90
                  ....*....|....*....
gi 2529623216 178 EKAHEGILFLDEVHRLPPE 196
Cdd:pfam13401  81 ALAVAVVLIIDEAQHLSLE 99
 
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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