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Conserved domains on  [gi|1883388595|ref|WP_181238725|]
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transcriptional regulator SdiA [Enterobacter roggenkampii]

Protein Classification

transcriptional regulator SdiA( domain architecture ID 11484603)

transcriptional regulator SdiA is involved in quorum sensing and activates gene expression in response to an extracellular autoinducer

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10188 PRK10188
transcriptional regulator SdiA;
1-240 5.77e-174

transcriptional regulator SdiA;


:

Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 477.74  E-value: 5.77e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595   1 MKDLDFFTWRRDCSFRFQELTCAAEVYQELERQTQALEFDYYALCVRHPVPFTRPKISLQTTYPKLWMAQYQSANYFAID 80
Cdd:PRK10188    1 MQDTDFFSWRRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYFAID 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  81 PVLKPENFIQGHLPWTDALFAEAQELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQEGPLAHEEIELRLQMLVQM 160
Cdd:PRK10188   81 PVLKPENFSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRCSAREIPILSDELELRLQLLVRE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 161 ALTSLMRFDDEMVMPPEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:PRK10188  161 SLMALMRLEDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
 
Name Accession Description Interval E-value
PRK10188 PRK10188
transcriptional regulator SdiA;
1-240 5.77e-174

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 477.74  E-value: 5.77e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595   1 MKDLDFFTWRRDCSFRFQELTCAAEVYQELERQTQALEFDYYALCVRHPVPFTRPKISLQTTYPKLWMAQYQSANYFAID 80
Cdd:PRK10188    1 MQDTDFFSWRRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYFAID 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  81 PVLKPENFIQGHLPWTDALFAEAQELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQEGPLAHEEIELRLQMLVQM 160
Cdd:PRK10188   81 PVLKPENFSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRCSAREIPILSDELELRLQLLVRE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 161 ALTSLMRFDDEMVMPPEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:PRK10188  161 SLMALMRLEDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 23-165 1.47e-36

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 125.94  E-value: 1.47e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  23 AAEVYQELERQTQALEFDYYALCVRHPVPFTRPKISLQTTYPKLWMAQYQSANYFAIDPVLKPENFIQGHLPWTDALFAE 102
Cdd:pfam03472   2 EEELFDALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAE 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1883388595 103 AQ----ELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQEGPLAHEEIELRLQMLVQMALTSL 165
Cdd:pfam03472  82 ARgaerRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
63-240 6.68e-24

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 94.44  E-value: 6.68e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  63 YPKLWMAQYQSANYFAIDPVLKPENFIQGHLPWTDALFAEAQELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQE 142
Cdd:COG2771    11 LALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLAL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 143 GPLAHEEIELRLQMLVQMALTSLMRFDDEMVMPPEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKF 222
Cdd:COG2771    91 LALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170

                         170
                  ....*....|....*...
gi 1883388595 223 NAPNKTQIACYAAATGLI 240
Cdd:COG2771   171 GVSSRAELVALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 180-234 1.43e-20

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 81.80  E-value: 1.43e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1883388595  180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 180-234 2.28e-20

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 81.04  E-value: 2.28e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1883388595 180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYA 55
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 136-216 5.60e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.56  E-value: 5.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 136 SRTRVQEGPLAHEEIELRLQMLVQmALTSLmrfddemvmppemkfSKREREILKWTA-EGKTSAEIAIILSISENTVNFH 214
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREALRE-ALEKL---------------PEREREVLVLRYlEGLSYKEIAEILGISVGTVKRR 146


                  ..
gi 1883388595 215 QK 216
Cdd:TIGR02937 147 LK 148
 
Name Accession Description Interval E-value
PRK10188 PRK10188
transcriptional regulator SdiA;
1-240 5.77e-174

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 477.74  E-value: 5.77e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595   1 MKDLDFFTWRRDCSFRFQELTCAAEVYQELERQTQALEFDYYALCVRHPVPFTRPKISLQTTYPKLWMAQYQSANYFAID 80
Cdd:PRK10188    1 MQDTDFFSWRRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYFAID 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  81 PVLKPENFIQGHLPWTDALFAEAQELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQEGPLAHEEIELRLQMLVQM 160
Cdd:PRK10188   81 PVLKPENFSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRCSAREIPILSDELELRLQLLVRE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 161 ALTSLMRFDDEMVMPPEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:PRK10188  161 SLMALMRLEDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 23-165 1.47e-36

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 125.94  E-value: 1.47e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  23 AAEVYQELERQTQALEFDYYALCVRHPVPFTRPKISLQTTYPKLWMAQYQSANYFAIDPVLKPENFIQGHLPWTDALFAE 102
Cdd:pfam03472   2 EEELFDALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAE 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1883388595 103 AQ----ELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQEGPLAHEEIELRLQMLVQMALTSL 165
Cdd:pfam03472  82 ARgaerRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
63-240 6.68e-24

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 94.44  E-value: 6.68e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  63 YPKLWMAQYQSANYFAIDPVLKPENFIQGHLPWTDALFAEAQELWHSAQDHGLRSGITQCLMLPNHALGFLSVSRTRVQE 142
Cdd:COG2771    11 LALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLAL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 143 GPLAHEEIELRLQMLVQMALTSLMRFDDEMVMPPEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKF 222
Cdd:COG2771    91 LALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170

                         170
                  ....*....|....*...
gi 1883388595 223 NAPNKTQIACYAAATGLI 240
Cdd:COG2771   171 GVSSRAELVALALRLGLI 188
GerE pfam00196
Bacterial regulatory proteins, luxR family;
180-234 7.04e-22

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 85.33  E-value: 7.04e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1883388595 180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 180-234 1.43e-20

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 81.80  E-value: 1.43e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1883388595  180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 180-234 2.28e-20

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 81.04  E-value: 2.28e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1883388595 180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYA 55
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 180-240 7.56e-19

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 79.55  E-value: 7.56e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1883388595 180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:COG2197    70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 174-240 1.08e-17

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 74.61  E-value: 1.08e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1883388595 174 MPPEMKF------SKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:COG5905     1 MMPSSSTshpsllTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLL 73
PRK15369 PRK15369
two component system response regulator;
183-240 3.12e-09

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 55.08  E-value: 3.12e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1883388595 183 REREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:PRK15369  153 RERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGLI 210
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 181-226 2.33e-07

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


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 49.71  E-value: 2.33e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1883388595 181 SKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPN 226
Cdd:COG4566   139 TPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
192-240 2.00e-06

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 46.62  E-value: 2.00e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1883388595 192 AEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:COG2909   135 AEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 61-240 8.50e-06

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 45.37  E-value: 8.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595  61 TTYPKLWMAQYQSANYFAIDPVLKPENFIQGHLPWT-----DALFAEAQELWHSAQDHGLRSGITQCLMLPNhalGFLSV 135
Cdd:PRK13870   51 TNYHREWQSVYFDKKFDALDPVVKRARSRKHIFTWSgeqerPRLSKDERAFYAHAADFGIRSGITIPIKTAN---GSMSM 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 136 SrTRVQEGPLAHEEIEL----------RLQMLVQMALTSLMRFDDEMVMPPEMKFskrereiLKWTAEGKTSAEIAIILS 205
Cdd:PRK13870  128 F-TLASEKPVIDLDREIdavaaaatigQIHARISFLRTTPTAEDAAWLDPKEATY-------LRWIAVGKTMEEIADVEG 199

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1883388595 206 ISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:PRK13870  200 VKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
PRK10100 PRK10100
transcriptional regulator CsgD;
181-234 8.96e-06

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 45.25  E-value: 8.96e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1883388595 181 SKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
Cdd:PRK10100  157 THREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWA 210
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 155-234 9.63e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 45.02  E-value: 9.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 155 QMLVQMALTSLM----RFDDEMVMPPEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQI 230
Cdd:PRK10651  127 EMVLSEALTPVLaaslRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEA 206


                  ....
gi 1883388595 231 ACYA 234
Cdd:PRK10651  207 AVWV 210
PRK10360 PRK10360
transcriptional regulator UhpA;
180-231 2.89e-04

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 40.73  E-value: 2.89e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1883388595 180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIA 231
Cdd:PRK10360  138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELA 189
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
181-223 2.99e-04

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 40.61  E-value: 2.99e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1883388595 181 SKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFN 223
Cdd:PRK10403  155 TERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
177-240 4.11e-04

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 40.24  E-value: 4.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883388595 177 EMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Cdd:PRK09935  147 DTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHELL 210
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
180-233 2.10e-03

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 38.10  E-value: 2.10e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1883388595 180 FSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACY 233
Cdd:PRK15201  134 FSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLKY 187
rcsA PRK15411
transcriptional regulator RcsA;
176-230 2.35e-03

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 37.80  E-value: 2.35e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1883388595 176 PEMKFSKREREILKWTAEGKTSAEIAIILSISENTVNFHQKNMQKKFNAPNKTQI 230
Cdd:PRK15411  134 PTLSLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVI 188
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 136-216 5.60e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.56  E-value: 5.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883388595 136 SRTRVQEGPLAHEEIELRLQMLVQmALTSLmrfddemvmppemkfSKREREILKWTA-EGKTSAEIAIILSISENTVNFH 214
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREALRE-ALEKL---------------PEREREVLVLRYlEGLSYKEIAEILGISVGTVKRR 146


                  ..
gi 1883388595 215 QK 216
Cdd:TIGR02937 147 LK 148
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 181-214 7.75e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 33.58  E-value: 7.75e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1883388595 181 SKREREILKWTA-EGKTSAEIAIILSISENTVNFH 214
Cdd:pfam08281  12 PPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSR 46
 
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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