NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|90111724|ref|NP_418715|]
View 

putative DNA-binding transcriptional regulator YjhU [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

sugar-binding transcriptional regulator( domain architecture ID 11457260)

sugar-binding transcriptional regulator similar to Priestia megaterium central glycolytic genes regulator, in the absence of glucose, which represses the transcription of the gapA operon that encodes five key glycolytic enzymes

CATH:  1.10.10.60|3.40.50.1360
Gene Ontology:  GO:0030246|GO:0003677|GO:0006355
PubMed:  19232357
SCOP:  4002188

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
21-323 2.23e-110

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


:

Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 322.85  E-value: 2.23e-110
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  21 WLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGLVHINLDVNVFGSIDAALQIRDKFNLQRVIIVPDGEhagkrDDTK 100
Cdd:COG2390   4 WLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDS-----DDDE 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724 101 LMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIHQMSKTMTPKSCKNVTVIQMLGSMPSQPDLTIIESSSQIAYKLSGRVA 180
Cdd:COG2390  79 EVLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGEDVEAQANEIARRLAEKLGGEYY 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724 181 SLHVPAVVSSARLAMELQAEPIIRSNFDVLTRCTKAFFVVGNALDENPLIRVGVLNKKEMQTYRDLGAVGVICGRFYDKE 260
Cdd:COG2390 159 LLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDAD 238

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90111724 261 GMPVVADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGALLGGYVTDLIVDEGTAEFLLA 323
Cdd:COG2390 239 GRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
21-323 2.23e-110

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 322.85  E-value: 2.23e-110
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  21 WLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGLVHINLDVNVFGSIDAALQIRDKFNLQRVIIVPDGEhagkrDDTK 100
Cdd:COG2390   4 WLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDS-----DDDE 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724 101 LMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIHQMSKTMTPKSCKNVTVIQMLGSMPSQPDLTIIESSSQIAYKLSGRVA 180
Cdd:COG2390  79 EVLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGEDVEAQANEIARRLAEKLGGEYY 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724 181 SLHVPAVVSSARLAMELQAEPIIRSNFDVLTRCTKAFFVVGNALDENPLIRVGVLNKKEMQTYRDLGAVGVICGRFYDKE 260
Cdd:COG2390 159 LLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDAD 238

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90111724 261 GMPVVADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGALLGGYVTDLIVDEGTAEFLLA 323
Cdd:COG2390 239 GRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 63-323 2.45e-100

Putative sugar-binding domain; This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.


Pssm-ID: 427778  Cd Length: 256  Bit Score: 295.68  E-value: 2.45e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724    63 VNVFGSIDAALQIRDKFNLQRVIIVPDGEhagkrDDTKLMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIHQMSKTMTPK 142
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKEAIVVPGDS-----DENDLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724   143 SCKNVTVIQMLGSMPSQPDLTIIESSSQIAYKLSGRVASLHVPAVVSSARLAMELQAEPIIRSNFDVLTRCTKAFFVVGN 222
Cdd:pfam04198  76 SLRNLKFVPLIGGLGRDGSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGS 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724   223 ALDENPLIRVGVLNKKEMQTYRDLGAVGVICGRFYDKEGMPVVADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGA 302
Cdd:pfam04198 156 ASEMAPLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAA 235

                         250       260
                  ....*....|....*....|.
gi 90111724   303 LLGGYVTDLIVDEGTAEFLLA 323
Cdd:pfam04198 236 LRGGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 21-323 4.43e-26

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 105.57  E-value: 4.43e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724   21 WLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGLVHINLDVNVFGSIDAALQIRDKFNLQRVIIVPDGEHAGkrddtk 100
Cdd:PRK15418  23 WFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPALADAD------ 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  101 lMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIhqmsktmtpkscknVTVIQMLGSMPSQPDLTIIESSSQIAYKLSG--- 177
Cdd:PRK15418  97 -IGGRLGIGAAHMLMSLLQPQQLLAVGFGEAT--------------MNTLQHLSGFISSQQIRLVTLSGGVGPYMTGigq 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  178 -----RVASLHVPAVVSSARLAMELQAEPIIRsnfDV-LTRCTKAFFVVG----NALDENPLIRVGVLNKKEMQTYRDLG 247
Cdd:PRK15418 162 ldaacSVSIIPAPLRASSAEIARTLRNENSVR---DVmLAAQAADVAIVGigavNQKDDATILRSGYISQGEQLMIGRKG 238

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 90111724  248 AVGVICGRFYDKEGMPVV-ADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGALLGGYVTDLIVDEGTAEFLLA 323
Cdd:PRK15418 239 AVGDILGYFFDADGELVPdIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAILA 315
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-53 4.16e-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: 4.16e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 90111724    18 HATWLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARE 53
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 22-53 6.89e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 37.08  E-value: 6.89e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 90111724  22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTARE 53
Cdd:cd06171  21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
transpos_IS630 NF033545
IS630 family transposase;
22-56 2.08e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 39.16  E-value: 2.08e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 90111724   22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGL 56
Cdd:NF033545   7 LLAAEGLSITEIAERLGVSRSTVYRWLKRFNEGGL 41
transpos_IS21 NF033546
IS21 family transposase;
22-51 3.37e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 38.73  E-value: 3.37e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 90111724   22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTA 51
Cdd:NF033546   3 LLFRQGLSIREIARELGISRNTVRKYLRRA 32
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
21-323 2.23e-110

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 322.85  E-value: 2.23e-110
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  21 WLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGLVHINLDVNVFGSIDAALQIRDKFNLQRVIIVPDGEhagkrDDTK 100
Cdd:COG2390   4 WLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDS-----DDDE 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724 101 LMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIHQMSKTMTPKSCKNVTVIQMLGSMPSQPDLTIIESSSQIAYKLSGRVA 180
Cdd:COG2390  79 EVLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGEDVEAQANEIARRLAEKLGGEYY 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724 181 SLHVPAVVSSARLAMELQAEPIIRSNFDVLTRCTKAFFVVGNALDENPLIRVGVLNKKEMQTYRDLGAVGVICGRFYDKE 260
Cdd:COG2390 159 LLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDAD 238

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90111724 261 GMPVVADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGALLGGYVTDLIVDEGTAEFLLA 323
Cdd:COG2390 239 GRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 63-323 2.45e-100

Putative sugar-binding domain; This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.


Pssm-ID: 427778  Cd Length: 256  Bit Score: 295.68  E-value: 2.45e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724    63 VNVFGSIDAALQIRDKFNLQRVIIVPDGEhagkrDDTKLMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIHQMSKTMTPK 142
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKEAIVVPGDS-----DENDLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724   143 SCKNVTVIQMLGSMPSQPDLTIIESSSQIAYKLSGRVASLHVPAVVSSARLAMELQAEPIIRSNFDVLTRCTKAFFVVGN 222
Cdd:pfam04198  76 SLRNLKFVPLIGGLGRDGSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGS 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724   223 ALDENPLIRVGVLNKKEMQTYRDLGAVGVICGRFYDKEGMPVVADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGA 302
Cdd:pfam04198 156 ASEMAPLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAA 235

                         250       260
                  ....*....|....*....|.
gi 90111724   303 LLGGYVTDLIVDEGTAEFLLA 323
Cdd:pfam04198 236 LRGGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 21-323 4.43e-26

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 105.57  E-value: 4.43e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724   21 WLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGLVHINLDVNVFGSIDAALQIRDKFNLQRVIIVPDGEHAGkrddtk 100
Cdd:PRK15418  23 WFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPALADAD------ 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  101 lMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIhqmsktmtpkscknVTVIQMLGSMPSQPDLTIIESSSQIAYKLSG--- 177
Cdd:PRK15418  97 -IGGRLGIGAAHMLMSLLQPQQLLAVGFGEAT--------------MNTLQHLSGFISSQQIRLVTLSGGVGPYMTGigq 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111724  178 -----RVASLHVPAVVSSARLAMELQAEPIIRsnfDV-LTRCTKAFFVVG----NALDENPLIRVGVLNKKEMQTYRDLG 247
Cdd:PRK15418 162 ldaacSVSIIPAPLRASSAEIARTLRNENSVR---DVmLAAQAADVAIVGigavNQKDDATILRSGYISQGEQLMIGRKG 238

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 90111724  248 AVGVICGRFYDKEGMPVV-ADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGALLGGYVTDLIVDEGTAEFLLA 323
Cdd:PRK15418 239 AVGDILGYFFDADGELVPdIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAILA 315
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 22-56 3.25e-05

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 45.23  E-value: 3.25e-05
                        10        20        30
                ....*....|....*....|....*....|....*
gi 90111724  22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGL 56
Cdd:COG3415  33 LLLAEGLSVREIAERLGVSRSTVYRWLKRYREGGL 67
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-53 4.16e-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: 4.16e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 90111724    18 HATWLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARE 53
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 22-53 6.89e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 37.08  E-value: 6.89e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 90111724  22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTARE 53
Cdd:cd06171  21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 22-44 7.57e-04

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 40.19  E-value: 7.57e-04
                        10        20
                ....*....|....*....|...
gi 90111724  22 LYYQEGKSQTEVAAIMGVSRVTV 44
Cdd:COG1191 197 LYYFEELTLKEIAEVLGVSESRV 219
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 21-53 1.31e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 39.21  E-value: 1.31e-03
                        10        20        30
                ....*....|....*....|....*....|...
gi 90111724  21 WLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARE 53
Cdd:COG1595 137 VLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 22-58 1.55e-03

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 39.71  E-value: 1.55e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 90111724    22 LYYQEGKSQTEVAAIMGVSRVTVVKYlqtARENGLVH 58
Cdd:pfam15978 194 LVEDEGLSLREIAKELGVDIKTVKRY---ARKLGLLH 227
transpos_IS630 NF033545
IS630 family transposase;
22-56 2.08e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 39.16  E-value: 2.08e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 90111724   22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGL 56
Cdd:NF033545   7 LLAAEGLSITEIAERLGVSRSTVYRWLKRFNEGGL 41
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
24-53 2.32e-03

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 39.43  E-value: 2.32e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 90111724  24 YQEGKSQTEVAAIMGVSRVTVVKYLQTARE 53
Cdd:COG4584  14 LREGLSIREIARELGISRNTVRKYLRRAEE 43
HTH_23 pfam13384
Homeodomain-like domain;
24-56 2.89e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.32  E-value: 2.89e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 90111724    24 YQEGKSQTEVAAIMGVSRVTVVKYLQTARENGL 56
Cdd:pfam13384  14 LAEGLSVKEIAELLGVSRRTVYRWLKRYNEEGL 46
transpos_IS21 NF033546
IS21 family transposase;
22-51 3.37e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 38.73  E-value: 3.37e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 90111724   22 LYYQEGKSQTEVAAIMGVSRVTVVKYLQTA 51
Cdd:NF033546   3 LLFRQGLSIREIARELGISRNTVRKYLRRA 32
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH