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Conserved domains on  [gi|489514496|ref|WP_003419333|]
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YlxM family DNA-binding protein [Clostridioides difficile]

Protein Classification

YlxM family protein( domain architecture ID 10006579)

YlxM family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
3-118 4.09e-35

Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];


:

Pssm-ID: 442041  Cd Length: 112  Bit Score: 116.79  E-value: 4.09e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489514496   3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEKn 82
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQK- 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489514496  83 ikiIKDKIIDIKEDLLHNRDCANLIPKLENIEDVCR 118
Cdd:COG2739   80 ---LLEEIKELLEELEESEDDEELEKLIEELEELEE 112
 
Name Accession Description Interval E-value
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
3-118 4.09e-35

Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];


Pssm-ID: 442041  Cd Length: 112  Bit Score: 116.79  E-value: 4.09e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489514496   3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEKn 82
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQK- 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489514496  83 ikiIKDKIIDIKEDLLHNRDCANLIPKLENIEDVCR 118
Cdd:COG2739   80 ---LLEEIKELLEELEESEDDEELEKLIEELEELEE 112
PRK00118 PRK00118
putative DNA-binding protein; Validated
 3-81 2.11e-30

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 104.56  E-value: 2.11e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489514496   3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEK 81
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNE 79
UPF0122 pfam04297
Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to ...
 3-81 8.04e-20

Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.


Pssm-ID: 282193  Cd Length: 98  Bit Score: 77.42  E-value: 8.04e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489514496    3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEK 81
Cdd:pfam04297   1 LEKTLRMNYLFDFYQSLLTDKQRNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKILEDYEKKLHLYEKYKLRNE 79
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 8-66 1.29e-06

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: 44.65  E-value: 1.29e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489514496    8 EIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDY 66
Cdd:TIGR02937  99 EEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 20-64 6.04e-05

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: 37.85  E-value: 6.04e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489514496  20 LTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILR 64
Cdd:cd06171   11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
3-118 4.09e-35

Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];


Pssm-ID: 442041  Cd Length: 112  Bit Score: 116.79  E-value: 4.09e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489514496   3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEKn 82
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQK- 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489514496  83 ikiIKDKIIDIKEDLLHNRDCANLIPKLENIEDVCR 118
Cdd:COG2739   80 ---LLEEIKELLEELEESEDDEELEKLIEELEELEE 112
PRK00118 PRK00118
putative DNA-binding protein; Validated
 3-81 2.11e-30

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 104.56  E-value: 2.11e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489514496   3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEK 81
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNE 79
UPF0122 pfam04297
Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to ...
 3-81 8.04e-20

Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.


Pssm-ID: 282193  Cd Length: 98  Bit Score: 77.42  E-value: 8.04e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489514496    3 IEKMVEIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDYEEKLHLVSKIQEQEK 81
Cdd:pfam04297   1 LEKTLRMNYLFDFYQSLLTDKQRNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKILEDYEKKLHLYEKYKLRNE 79
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 8-66 1.29e-06

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: 44.65  E-value: 1.29e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489514496    8 EIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRDY 66
Cdd:TIGR02937  99 EEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-65 1.48e-05

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: 41.90  E-value: 1.48e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 489514496  18 ELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRD 65
Cdd:COG1595  126 ERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 20-64 6.04e-05

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: 37.85  E-value: 6.04e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489514496  20 LTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILR 64
Cdd:cd06171   11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 20-49 8.22e-05

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. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 37.41  E-value: 8.22e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 489514496   20 LTDKQKEIVALYYEEDYSLGEISENLNVSR 49
Cdd:pfam04545   5 LPPRERQVLVLRYGEGLTLEEIGERLGISR 34
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 18-63 7.18e-04

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: 35.12  E-value: 7.18e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 489514496   18 ELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKIL 63
Cdd:pfam08281   9 EELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 8-65 7.32e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 37.53  E-value: 7.32e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489514496   8 EIGLLFEQYKELLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSEKILRD 65
Cdd:PRK12538 160 ELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
20-77 4.39e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 35.12  E-value: 4.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489514496  20 LTDKQKEIVALYYEeDYSLGEISENLNVSRQGVYDTLKRsekILRdyeeKLHLVSKIQ 77
Cdd:COG2771  128 LTPREREVLRLLAE-GLTLKEIARILGISERTVRTHLKR---IYR----KLGVSSRAE 177
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 18-49 5.67e-03

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: 34.80  E-value: 5.67e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489514496  18 ELLTDKQKEIVALYYEEDYSLGEISENLNVSR 49
Cdd:COG1191  185 EQLPERERLVLSLYYFEELTLKEIAEVLGVSE 216
PRK06930 PRK06930
positive control sigma-like factor; Validated
 19-70 8.49e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 34.32  E-value: 8.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489514496  19 LLTDKQKEIVALYYEEDYSLGEISENLNVSRQGVYDTLKRSE-KILRDYEEKL 70
Cdd:PRK06930 114 VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEkKIARQINESL 166
 
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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