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Conserved domains on  [gi|515553254|ref|WP_016986179|]
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autoinducer binding domain-containing protein [Pseudomonas crudilactis]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK10188 super family cl32472
transcriptional regulator SdiA;
3-236 1.83e-33

transcriptional regulator SdiA;


The actual alignment was detected with superfamily member PRK10188:

Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 120.66  E-value: 1.83e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254   3 TWKESQLKQLTFAKGIDTAYPILLRFAENLGFNFFAISVTSPRQVTKTNALQINNYPTQWNEQYEQLHYSEVDPVIAHCN 82
Cdd:PRK10188   8 SWRRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYFAIDPVLKPEN 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254  83 HSMMPVIWNETLFSNAPRLWQGLQEQGLQHGWSQSFH--HEASGFCSILSLARKHCPISPLELYEHFGYIfyAASHLSEL 160
Cdd:PRK10188  88 FSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMlpNRALGFLSFSRCSAREIPILSDELELRLQLL--VRESLMAL 165
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515553254 161 FARTLPMAAkTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:PRK10188 166 MRLEDEMVM-TPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
 
Name Accession Description Interval E-value
PRK10188 PRK10188
transcriptional regulator SdiA;
3-236 1.83e-33

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 120.66  E-value: 1.83e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254   3 TWKESQLKQLTFAKGIDTAYPILLRFAENLGFNFFAISVTSPRQVTKTNALQINNYPTQWNEQYEQLHYSEVDPVIAHCN 82
Cdd:PRK10188   8 SWRRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYFAIDPVLKPEN 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254  83 HSMMPVIWNETLFSNAPRLWQGLQEQGLQHGWSQSFH--HEASGFCSILSLARKHCPISPLELYEHFGYIfyAASHLSEL 160
Cdd:PRK10188  88 FSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMlpNRALGFLSFSRCSAREIPILSDELELRLQLL--VRESLMAL 165
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515553254 161 FARTLPMAAkTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:PRK10188 166 MRLEDEMVM-TPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
24-146 5.40e-24

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: 93.58  E-value: 5.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254   24 ILLRFAENLGFNFFAISVTSPRQVTKTNALQINNYPTQWNEQYEQLHYSEVDPVIAHCNHSMMPVIWNETLFSNAP---- 99
Cdd:pfam03472   8 ALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARgaer 87
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 515553254  100 RLWQGLQEQGLQHGWSQSFhHEASGFCSILSLARKHCPISPLELYEH 146
Cdd:pfam03472  88 RFLDEARDFGLRDGYTVPV-HGPGGRLGALSFAGPGEDLDPAEAIEA 133
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
176-236 8.11e-20

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: 81.86  E-value: 8.11e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
174-230 1.13e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 74.10  E-value: 1.13e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 515553254   174 PHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAA 230
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
176-232 5.84e-16

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: 69.49  E-value: 5.84e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAAR 232
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
175-218 2.57e-04

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: 40.41  E-value: 2.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 515553254  175 HLSPRELEILQLSAG-GKTAYEISKILSLSERTVNYHVQNVIEKL 218
Cdd:TIGR02937 110 KLPEREREVLVLRYLeGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10188 PRK10188
transcriptional regulator SdiA;
3-236 1.83e-33

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 120.66  E-value: 1.83e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254   3 TWKESQLKQLTFAKGIDTAYPILLRFAENLGFNFFAISVTSPRQVTKTNALQINNYPTQWNEQYEQLHYSEVDPVIAHCN 82
Cdd:PRK10188   8 SWRRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYFAIDPVLKPEN 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254  83 HSMMPVIWNETLFSNAPRLWQGLQEQGLQHGWSQSFH--HEASGFCSILSLARKHCPISPLELYEHFGYIfyAASHLSEL 160
Cdd:PRK10188  88 FSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMlpNRALGFLSFSRCSAREIPILSDELELRLQLL--VRESLMAL 165
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515553254 161 FARTLPMAAkTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:PRK10188 166 MRLEDEMVM-TPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
24-146 5.40e-24

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: 93.58  E-value: 5.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254   24 ILLRFAENLGFNFFAISVTSPRQVTKTNALQINNYPTQWNEQYEQLHYSEVDPVIAHCNHSMMPVIWNETLFSNAP---- 99
Cdd:pfam03472   8 ALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARgaer 87
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 515553254  100 RLWQGLQEQGLQHGWSQSFhHEASGFCSILSLARKHCPISPLELYEH 146
Cdd:pfam03472  88 RFLDEARDFGLRDGYTVPV-HGPGGRLGALSFAGPGEDLDPAEAIEA 133
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
176-236 8.11e-20

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: 81.86  E-value: 8.11e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
165-236 8.46e-20

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: 80.39  E-value: 8.46e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515553254 165 LPMAAKTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:COG5905    2 MPSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLL 73
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
174-230 1.13e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 74.10  E-value: 1.13e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 515553254   174 PHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAA 230
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
58-236 2.55e-17

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 77.10  E-value: 2.55e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254  58 YPTQWNEQYEQLHYSEVDPVIAHCNHSMMPVIWN---ETLFSNAPRLWQGLQEQGLQHGWSQSFHHEASGFCSILSLARK 134
Cdd:COG2771    7 ALLLLALLLLLLALLALLLLLLLAALLLLLALLLlaaLLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLL 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254 135 HCPISPLELYEHFGYIFYAASHLSELFARTLPMAAKTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNV 214
Cdd:COG2771   87 LLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRI 166
                        170       180
                 ....*....|....*....|..
gi 515553254 215 IEKLNVCNKISAVIAAARAGII 236
Cdd:COG2771  167 YRKLGVSSRAELVALALRLGLI 188
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
176-232 5.84e-16

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: 69.49  E-value: 5.84e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAAR 232
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
176-230 1.45e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 66.07  E-value: 1.45e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 515553254  176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAA 230
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
153-236 3.00e-09

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 54.71  E-value: 3.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254 153 AASHLSELFARTLPMAAKTRQPHLSPRELEIL--QLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAA 230
Cdd:COG2909   98 RLLALAEAAGRLLLRALALRALGDREEALAALrrRLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARA 177

                 ....*.
gi 515553254 231 ARAGII 236
Cdd:COG2909  178 RELGLL 183
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
168-222 6.65e-08

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: 50.87  E-value: 6.65e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 515553254 168 AAKTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCN 222
Cdd:COG4566  130 ELRARLASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
176-228 2.03e-07

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 49.85  E-value: 2.03e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVI 228
Cdd:PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATI 206
PRK10360 PRK10360
transcriptional regulator UhpA;
105-224 3.12e-07

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 49.21  E-value: 3.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254 105 LQEQGLQHGwsqsfhheASGFCSilslarKHCpiSPLELYEHFGYIFYAASHLSELFARTLpmaAKTRQPHLSPRELEIL 184
Cdd:PRK10360  86 LVEQALNAG--------ARGFLS------KRC--SPDELIAAVHTVATGGCYLTPDIAIKL---ASGRQDPLTKRERQVA 146
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 515553254 185 QLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKI 224
Cdd:PRK10360 147 EKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDV 186
PRK15369 PRK15369
two component system response regulator;
168-236 1.02e-06

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 47.77  E-value: 1.02e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515553254 168 AAKTRQPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:PRK15369 142 ADDTNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGLI 210
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
167-228 8.52e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 45.40  E-value: 8.52e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515553254 167 MAAKTRQP---------HLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVI 228
Cdd:PRK10651 138 LAASLRANratterdvnQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAV 208
PRK09483 PRK09483
response regulator; Provisional
176-236 1.47e-04

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 41.63  E-value: 1.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAVIAAARAGII 236
Cdd:PRK09483 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLL 209
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
1-236 2.45e-04

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 41.13  E-value: 2.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254   1 METWkesqLKQLTFAKGIDTAYPILLR----FAENLGFNFFAISVTSPRQVTKtnalqINNYPTQWNEQYEQLHYSEVDP 76
Cdd:PRK13870   1 MQHW----LDKLTDLAAIEGDECILKTgladIADHFGFTGYAYLHIQHRHITA-----VTNYHREWQSVYFDKKFDALDP 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254  77 VIAHCNHsmmpviwNETLFSnaprlWQGLQEQGLQHGWSQSFHHEAS----------------GFCSILSLARKHcPISP 140
Cdd:PRK13870  72 VVKRARS-------RKHIFT-----WSGEQERPRLSKDERAFYAHAAdfgirsgitipiktanGSMSMFTLASEK-PVID 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254 141 LElyEHFGYIFYAAS----HLSELFARTLPMAAKTrqPHLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIE 216
Cdd:PRK13870 139 LD--REIDAVAAAATigqiHARISFLRTTPTAEDA--AWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMK 214
                        250       260
                 ....*....|....*....|
gi 515553254 217 KLNVCNKISAVIAAARAGII 236
Cdd:PRK13870 215 RFDVRSKAHLTALAIRRKLI 234
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
175-218 2.57e-04

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: 40.41  E-value: 2.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 515553254  175 HLSPRELEILQLSAG-GKTAYEISKILSLSERTVNYHVQNVIEKL 218
Cdd:TIGR02937 110 KLPEREREVLVLRYLeGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
148-233 5.07e-04

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 39.86  E-value: 5.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515553254 148 GYIFYAASHLSELFARTLPMAAKTRQPhLSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNkISAV 227
Cdd:PRK09935 123 GYTFFPSETLNYIKSNKCSTNSSTDTV-LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS-IVEL 200

                 ....*.
gi 515553254 228 IAAARA 233
Cdd:PRK09935 201 IDYAKL 206
PRK10100 PRK10100
transcriptional regulator CsgD;
176-227 5.36e-04

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 39.85  E-value: 5.36e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 515553254 176 LSPRELEILQLSAGGKTAYEISKILSLSERTVNYHVQNVIEKLNVCNKISAV 227
Cdd:PRK10100 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
175-218 1.35e-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: 35.89  E-value: 1.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 515553254  175 HLSPRELEILQLSA-GGKTAYEISKILSLSERTVNYHVQNVIEKL 218
Cdd:pfam08281  10 ELPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
COG1777 COG1777
Predicted transcriptional regulator, ArsR family [Transcription];
177-212 1.92e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441383  Cd Length: 113  Bit Score: 36.94  E-value: 1.92e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 515553254 177 SPRELEILQ-LSAGGKTAYEISKILSLSERTVNYHVQ 212
Cdd:COG1777   16 NPTRRRILAlLSEEPAYVSELARELGVSRQAVYKHLR 52
 
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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