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Conserved domains on  [gi|490209081|ref|WP_004107487|]
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MULTISPECIES: HTH-type transcriptional activator RhaS [Klebsiella]

Protein Classification

HTH-type transcriptional activator RhaS( domain architecture ID 11486659)

HTH-type transcriptional activator RhaS is an AraC family transcriptional regulator that controls the expression of one or many genes with potentially diverse biological functions including metabolism, stress response, and virulence

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
1-278 0e+00

HTH-type transcriptional activator RhaS;


:

Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 557.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   1 MTMLHSVDFFKSGVSAVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLC 80
Cdd:PRK13503   1 MTVLHSVDFFPSGNAPVAIEPRLPQAAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCFVRDHDRHLYEHTDNLC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  81 LTNVLYRAPDAFRFLSGLNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKS 160
Cdd:PRK13503  81 LTNVLYRSPDAFRFLAGLNQLLPQEQDGQYPSHWRVNQSVLQQVRQLVAQMEQQEESNDLEAIASREILFMQLLVLLRKS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 161 SLAEGAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVT 240
Cdd:PRK13503 161 SLQENGENSDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVT 240

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 490209081 241 DIAYRCGFGDSNHFSTLFRREFDWSPRDIRQGRDAILQ 278
Cdd:PRK13503 241 DIAYRCGFGDSNHFSTLFRREFSWSPRDIRQGRDGFLQ 278
 
Name Accession Description Interval E-value
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
1-278 0e+00

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 557.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   1 MTMLHSVDFFKSGVSAVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLC 80
Cdd:PRK13503   1 MTVLHSVDFFPSGNAPVAIEPRLPQAAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCFVRDHDRHLYEHTDNLC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  81 LTNVLYRAPDAFRFLSGLNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKS 160
Cdd:PRK13503  81 LTNVLYRSPDAFRFLAGLNQLLPQEQDGQYPSHWRVNQSVLQQVRQLVAQMEQQEESNDLEAIASREILFMQLLVLLRKS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 161 SLAEGAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVT 240
Cdd:PRK13503 161 SLQENGENSDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVT 240

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 490209081 241 DIAYRCGFGDSNHFSTLFRREFDWSPRDIRQGRDAILQ 278
Cdd:PRK13503 241 DIAYRCGFGDSNHFSTLFRREFSWSPRDIRQGRDGFLQ 278
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 16-160 4.15e-57

HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, including the HTH-type transcription activators RhaS and RhaR. RhaS and RhaR respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. The E. coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic operon rhaBAD as well as the transport operon rhaT. These proteins bind DNA as dimers, via their HTH motifs. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380382 [Multi-domain]  Cd Length: 147  Bit Score: 179.77  E-value: 4.15e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  16 AVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLCLTNVLYRAPDAFRFL 95
Cdd:cd06977    3 PVAVEPRAPQEPFPEHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDDLCLTNILFRPERLFLFL 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490209081  96 SGLNELLPQEQeGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKS 160
Cdd:cd06977   83 DWLDTLPGYLA-HQFQSHWRLNSSTLREIRQLIDQLESELEERDAGSELMAEALFLQLLVLLSRH 146
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 160-271 2.96e-36

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 131.43  E-value: 2.96e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 160 SSLAEGAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSV 239
Cdd:COG4977  199 SPLLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSI 278

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490209081 240 TDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:COG4977  279 EEIAAACGFGSASHFRRAFRRRFGVSPSAYRR 310
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
187-270 2.76e-30

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 108.79  E-value: 2.76e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   187 DICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSP 266
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 490209081   267 RDIR 270
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
193-271 7.45e-26

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 97.28  E-value: 7.45e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  193 VAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLL-RHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
 
Name Accession Description Interval E-value
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
1-278 0e+00

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 557.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   1 MTMLHSVDFFKSGVSAVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLC 80
Cdd:PRK13503   1 MTVLHSVDFFPSGNAPVAIEPRLPQAAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCFVRDHDRHLYEHTDNLC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  81 LTNVLYRAPDAFRFLSGLNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKS 160
Cdd:PRK13503  81 LTNVLYRSPDAFRFLAGLNQLLPQEQDGQYPSHWRVNQSVLQQVRQLVAQMEQQEESNDLEAIASREILFMQLLVLLRKS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 161 SLAEGAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVT 240
Cdd:PRK13503 161 SLQENGENSDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVT 240

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 490209081 241 DIAYRCGFGDSNHFSTLFRREFDWSPRDIRQGRDAILQ 278
Cdd:PRK13503 241 DIAYRCGFGDSNHFSTLFRREFSWSPRDIRQGRDGFLQ 278
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
3-271 2.40e-59

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 190.50  E-value: 2.40e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   3 MLHSVDFFKSGVSAVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLCLT 82
Cdd:PRK13501   6 LLESRDYLLSEQMPVAVTNRYPQETFVEHTHQFCEIVIVWRGNGLHVLNDHPYRITCGDVFYIQAADHHSYESVHDLVLD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  83 NVLYrAPDAFRFLSGLNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKSSL 162
Cdd:PRK13501  86 NIIY-CPERLHLNAQWHKLLPPLGPEQNQGYWRLTTQGMAQARPIIQQLAQESRKTDSWSIQLTEVLLLQLAIVLKRHRY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 163 AEGAAN---NDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSV 239
Cdd:PRK13501 165 RAEQAHllpDGEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRI 244

                        250       260       270
                 ....*....|....*....|....*....|..
gi 490209081 240 TDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:PRK13501 245 SDIAARCGFEDSNYFSAVFTREAGMTPRDYRQ 276
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 16-160 4.15e-57

HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, including the HTH-type transcription activators RhaS and RhaR. RhaS and RhaR respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. The E. coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic operon rhaBAD as well as the transport operon rhaT. These proteins bind DNA as dimers, via their HTH motifs. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380382 [Multi-domain]  Cd Length: 147  Bit Score: 179.77  E-value: 4.15e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  16 AVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLCLTNVLYRAPDAFRFL 95
Cdd:cd06977    3 PVAVEPRAPQEPFPEHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDDLCLTNILFRPERLFLFL 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490209081  96 SGLNELLPQEQeGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKS 160
Cdd:cd06977   83 DWLDTLPGYLA-HQFQSHWRLNSSTLREIRQLIDQLESELEERDAGSELMAEALFLQLLVLLSRH 146
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
8-271 1.41e-52

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 172.93  E-value: 1.41e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   8 DFFKSGVSAVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLCLTNVLYr 87
Cdd:PRK13502  11 DFFTDEQQAVTVADRYPQDVFAEHTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSYTSVNDLVLQNIIY- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  88 APDAFRFLSGLNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKSSLAEG-- 165
Cdd:PRK13502  90 CPERLKLNVNWQAMIPGFQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKRHRYATDdl 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 166 -AANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAY 244
Cdd:PRK13502 170 pATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISM 249

                        250       260
                 ....*....|....*....|....*..
gi 490209081 245 RCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:PRK13502 250 QCGFEDSNYFSVVFTRETGMTPSQWRH 276
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
8-271 5.10e-46

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 156.80  E-value: 5.10e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   8 DFFKSGVSAVAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLCLTNVLYr 87
Cdd:PRK13500  41 DFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIY- 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  88 APDAFRFLSGLNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHL---RKSSLAE 164
Cdd:PRK13500 120 CPERLKLNLDWQGAIPGFSASAGQPHWRLGSVGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLnrhRYTSDSL 199

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 165 GAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAY 244
Cdd:PRK13500 200 PPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDIST 279

                        250       260
                 ....*....|....*....|....*..
gi 490209081 245 RCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:PRK13500 280 ECGFEDSNYFSVVFTRETGMTPSQWRH 306
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 160-271 2.96e-36

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 131.43  E-value: 2.96e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 160 SSLAEGAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSV 239
Cdd:COG4977  199 SPLLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSI 278

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490209081 240 TDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:COG4977  279 EEIAAACGFGSASHFRRAFRRRFGVSPSAYRR 310
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
187-270 2.76e-30

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 108.79  E-value: 2.76e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   187 DICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSP 266
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 490209081   267 RDIR 270
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
193-271 7.45e-26

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 97.28  E-value: 7.45e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  193 VAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLL-RHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
18-273 1.13e-24

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 99.47  E-value: 1.13e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  18 AIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDNLCLTNVLYRAPDAFRFLSG 97
Cdd:COG2207    5 ILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081  98 LNELLPQEQEGNYLSHWRVNQNALQQVRQIVEQMENVGADADMHAIASREILFMQLLVHLRKSSLAEGAANNDARLNHLM 177
Cdd:COG2207   85 LLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 178 AwledhfAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTL 257
Cdd:COG2207  165 L------LLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRA 238

                        250
                 ....*....|....*.
gi 490209081 258 FRREFDWSPRDIRQGR 273
Cdd:COG2207  239 FKKRFGVTPSEYRKRL 254
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 162-273 1.99e-24

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 100.51  E-value: 1.99e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 162 LAEGAANNDARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLrHSDDSVTD 241
Cdd:COG2169   75 LAPGSPPRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLL-QTGLSVTD 153

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490209081 242 IAYRCGFGDSNHFSTLFRREFDWSPRDIRQGR 273
Cdd:COG2169  154 AAYAAGFGSLSRFYEAFKKLLGMTPSAYRRGG 185
ftrA PRK09393
transcriptional activator FtrA; Provisional
 170-270 6.22e-18

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 81.93  E-value: 6.22e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 170 DARLNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFG 249
Cdd:PRK09393 217 SDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFG 296

                         90       100
                 ....*....|....*....|.
gi 490209081 250 DSNHFSTLFRREFDWSPRDIR 270
Cdd:PRK09393 297 SEESLRHHFRRRAATSPAAYR 317
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 17-154 7.10e-18

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 77.86  E-value: 7.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   17 VAIEPRLPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLY--EHTDNLCLTNVLYRAPDAFRF 94
Cdd:pfam02311   5 EGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYepESEDGWRYRWLYFEPELLERI 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081   95 LSGLNELLPQEQegnylsHWRVNQNALQQVRQIVEQMENVGADADMHAiasrEILFMQLL 154
Cdd:pfam02311  85 LADISILAGGPL------PLLRDPELAALLRALFRLLEEAGRSDDLLA----EALLYQLL 134
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 191-272 4.32e-13

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 67.75  E-value: 4.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 191 EEVAARFSLSLRTLHRQLKQQtGLTPQRYLNRVRLMK-ARHLLRHSDD-SVTDIAYRCGFGDSNHFSTLFRREFDWSPRD 268
Cdd:PRK09685 218 EWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLDRcADDLRPAADDeKITSIAYKWGFSDSSHFSTAFKQRFGVSPGE 296


                 ....
gi 490209081 269 IRQG 272
Cdd:PRK09685 297 YRRK 300
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
173-271 5.20e-11

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 58.40  E-value: 5.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 173 LNHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSN 252
Cdd:PRK10219   7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQ 86

                         90
                 ....*....|....*....
gi 490209081 253 HFSTLFRREFDWSPRDIRQ 271
Cdd:PRK10219  87 TFSRVFRRQFDRTPSDYRH 105
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
121-273 4.17e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 59.22  E-value: 4.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 121 LQQVRQIVEQMENVGADADMHAiasrEILFMQLLVHLRKSSLAEGAANN----DARLNHLMAWLEDHFAEDICWEEVAAR 196
Cdd:PRK10572 133 QPEFSDLFGQIEQAGQSEGRYS----ELLAMNLLERLLLRCMEAIPESLhppmDPRVREACQYISDHLASEFDIESVAQH 208

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490209081 197 FSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQGR 273
Cdd:PRK10572 209 VCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARC 285
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 191-268 9.74e-10

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 58.15  E-value: 9.74e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490209081 191 EEVAARFSLSLRTLHRQLKQQTGLTPQRYLNrVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSPRD 268
Cdd:PRK15186 201 KDISDSLYMSCSTLKRKLKQENTSFSEVYLN-ARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTPSE 277
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
168-270 7.69e-09

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 52.80  E-value: 7.69e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 168 NNDARLNH-LMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRC 246
Cdd:PRK11511   5 NTDAITIHsILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERY 84

                         90       100
                 ....*....|....*....|....
gi 490209081 247 GFGDSNHFSTLFRREFDWSPRDIR 270
Cdd:PRK11511  85 GFESQQTLTRTFKNYFDVPPHKYR 108
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
24-74 8.71e-07

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 46.38  E-value: 8.71e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490209081  24 PQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYE 74
Cdd:COG1917   32 PGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFR 82
PRK10371 PRK10371
transcriptional regulator MelR;
109-271 1.57e-06

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 48.66  E-value: 1.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 109 NYLSHWRVNQNALQQVRQIVE----QMENVGADADMHAIASREILFM---------QLLVHLRKSSLAEGAANNDAR--L 173
Cdd:PRK10371 114 NHVTHGMVIKSLATQQLSPFEvrrwQQELNSPNEQIRQLAIDEIGLMlkrfslsgwEPILVNKTSRTHKNSVSRHAQfyV 193

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 174 NHLMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSNH 253
Cdd:PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSR 273

                        170
                 ....*....|....*...
gi 490209081 254 FSTLFRREFDWSPRDIRQ 271
Cdd:PRK10371 274 FYSTFGKYVGMSPQQYRK 291
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 180-221 1.83e-06

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 43.68  E-value: 1.83e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 490209081  180 LEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLN 221
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 234-271 5.17e-06

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 42.53  E-value: 5.17e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 490209081  234 HSDDSVTDIAYRCGFgDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:pfam00165   6 STNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 25-77 1.08e-05

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 42.76  E-value: 1.08e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 490209081  25 QSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTD 77
Cdd:cd07001   12 QKSFPNHFHDFYVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVHSCIQIS 64
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
191-276 1.29e-05

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 45.94  E-value: 1.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 191 EEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSdDSVTDIAYRCGFGDSnhfSTLFR---REFDWSPR 267
Cdd:PRK15435 103 EALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKG-ESVTTSILNAGFPDS---SSYYRkadETLGMTAK 178


                 ....*....
gi 490209081 268 DIRQGRDAI 276
Cdd:PRK15435 179 QFRHGGENL 187
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 191-266 6.00e-05

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 43.83  E-value: 6.00e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490209081 191 EEVAARFSLSLRTLHRQLKQQTGLTPQRYLNrVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSP 266
Cdd:PRK15185 226 TDVADHIFMSTSTLKRKLAEEGTSFSDIYLS-ARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 192-266 3.32e-04

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 41.56  E-value: 3.32e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490209081 192 EVAARFSLSLRTLHRQLKQQTGLTPQRYLNrVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSP 266
Cdd:PRK15044 213 EVAGKLFMSVSSLKRKLAAEEVSFSKIYLD-ARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITP 286
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
176-266 9.54e-04

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 39.99  E-value: 9.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490209081 176 LMAWLEDHFAEDICWEEVAARFSLSLRTLHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIA--YRcgFGDSNH 253
Cdd:PRK15121  10 LLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIAlqYR--FDSQQT 87

                         90
                 ....*....|...
gi 490209081 254 FSTLFRREFDWSP 266
Cdd:PRK15121  88 FTRAFKKQFAQTP 100
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 199-271 1.35e-03

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 39.30  E-value: 1.35e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490209081 199 LSLRTLHRQLKQQTGLTPQRYLNrVRLMKARHLLRhSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:PRK09940 162 ISESLLKKKLKQEQTTFSQILLD-ARMQHAKNLIR-VEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSK 232
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 29-81 2.56e-03

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 36.27  E-value: 2.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 490209081  29 PEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRHLYEHTDN-----LCL 81
Cdd:cd02222   31 PLHTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDeplgfLCI 88
cupin_Lmo2851-like_N cd06996
AraC/XylS family transcriptional regulators similar to Listeria monocytogenes Lmo2851 protein, ...
 26-87 3.05e-03

AraC/XylS family transcriptional regulators similar to Listeria monocytogenes Lmo2851 protein, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is Listeria monocytogenes Lmo2851 protein, whose function is unknown. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380400 [Multi-domain]  Cd Length: 87  Bit Score: 36.01  E-value: 3.05e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490209081  26 SAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRH-LYEHTDNLCLTNVLYR 87
Cdd:cd06996   24 ADYPLHTHNFLEINYMYSGSCTQIVNGQEITLKEGDLLLLDQGSTHsIKALGEDDILINIIFR 86
cupin_TM1287-like cd02221
Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial ...
 30-71 4.05e-03

Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold and forms a homodimer.


Pssm-ID: 380350 [Multi-domain]  Cd Length: 93  Bit Score: 35.91  E-value: 4.05e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 490209081  30 EHHHDFhEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRH 71
Cdd:cd02221   36 QHEGEF-EIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESH 76
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 10-71 4.37e-03

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380393 [Multi-domain]  Cd Length: 76  Bit Score: 35.29  E-value: 4.37e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490209081  10 FKSGVSAVAieprlPQSAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRH 71
Cdd:cd06988    2 FGGAWCVVR-----PGTTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEH 58
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
24-71 5.89e-03

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 35.89  E-value: 5.89e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 490209081  24 PQSAFPEH-HHDFHEIVIVEHGTGIHVFNGQPYTISGGSVCFIRDHDRH 71
Cdd:COG0662   36 PGAELSLHvHPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPH 84
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 204-271 8.92e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 37.04  E-value: 8.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490209081 204 LHRQLKQQTGLTPQRYLNRVRLMKARHLLRHSDDSVTDIAYRCGFGDSNHFSTLFRREFDWSPRDIRQ 271
Cdd:PRK10296 205 LTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRK 272
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 24-78 9.22e-03

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 34.38  E-value: 9.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490209081  24 PQSAFPEHHHDFH-EIVIVEHGTG-IHVFNGQPYTISGGSVCFIRDHDRHLYEHTDN 78
Cdd:cd02208    8 PGTSSPPHWHPEQdEIFYVLSGEGeLTLDDGETVELKAGDIVLIPPGVPHSFVNTSD 64
 
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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