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Conserved domains on  [gi|489079808|ref|WP_002989745|]
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putative DNA-binding protein [Streptococcus pyogenes]

Protein Classification

YlxM family DNA-binding protein( domain architecture ID 10011255)

YlxM family DNA-binding protein similar to Bacillus subtilis UPF0122 family protein YlxM

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00118 PRK00118
putative DNA-binding protein; Validated
 3-103 4.14e-51

putative DNA-binding protein; Validated


:

Pssm-ID: 234647  Cd Length: 104  Bit Score: 156.56  E-value: 4.14e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808   3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNEL 80

                         90       100
                 ....*....|....*....|....
gi 489079808  83 FDDMIA---HYPHDEYLQEKISIL 103
Cdd:PRK00118  81 FDKIAYlkeKYPDDEELKKLIEIL 104
 
Name Accession Description Interval E-value
PRK00118 PRK00118
putative DNA-binding protein; Validated
 3-103 4.14e-51

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 156.56  E-value: 4.14e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808   3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNEL 80

                         90       100
                 ....*....|....*....|....
gi 489079808  83 FDDMIA---HYPHDEYLQEKISIL 103
Cdd:PRK00118  81 FDKIAYlkeKYPDDEELKKLIEIL 104
UPF0122 pfam04297
Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to ...
 3-100 4.36e-45

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: 140.98  E-value: 4.36e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808    3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:pfam04297   1 LEKTLRMNYLFDFYQSLLTDKQRNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKILEDYEKKLHLYEKYKLRNEL 80

                          90
                  ....*....|....*...
gi 489079808   83 FDDMIAHYPHDEYLQEKI 100
Cdd:pfam04297  81 YDKIKDHQLRDKQLIEKI 98
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
3-106 7.93e-42

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


Pssm-ID: 442041  Cd Length: 112  Bit Score: 133.36  E-value: 7.93e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808   3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQKL 80

                         90       100
                 ....*....|....*....|....
gi 489079808  83 FDDmIAHYPHDEYLQEKISILTSI 106
Cdd:COG2739   81 LEE-IKELLEELEESEDDEELEKL 103
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 20-53 7.98e-05

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 36.92  E-value: 7.98e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 489079808  20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVY 53
Cdd:cd00569    6 LTPEQIAEARRLLAAGESVAEIARELGVSRSTLY 39
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-66 1.55e-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: 38.48  E-value: 1.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 489079808   20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETY 66
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
transpos_IS630 NF033545
IS630 family transposase;
28-58 1.39e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 36.46  E-value: 1.39e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489079808  28 IELYYADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:NF033545   5 ILLLAAEGLSITEIAERLGVSRSTVYRWLKR 35
 
Name Accession Description Interval E-value
PRK00118 PRK00118
putative DNA-binding protein; Validated
 3-103 4.14e-51

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 156.56  E-value: 4.14e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808   3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNEL 80

                         90       100
                 ....*....|....*....|....
gi 489079808  83 FDDMIA---HYPHDEYLQEKISIL 103
Cdd:PRK00118  81 FDKIAYlkeKYPDDEELKKLIEIL 104
UPF0122 pfam04297
Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to ...
 3-100 4.36e-45

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: 140.98  E-value: 4.36e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808    3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:pfam04297   1 LEKTLRMNYLFDFYQSLLTDKQRNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKILEDYEKKLHLYEKYKLRNEL 80

                          90
                  ....*....|....*...
gi 489079808   83 FDDMIAHYPHDEYLQEKI 100
Cdd:pfam04297  81 YDKIKDHQLRDKQLIEKI 98
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
3-106 7.93e-42

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


Pssm-ID: 442041  Cd Length: 112  Bit Score: 133.36  E-value: 7.93e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808   3 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEI 82
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQKL 80

                         90       100
                 ....*....|....*....|....
gi 489079808  83 FDDmIAHYPHDEYLQEKISILTSI 106
Cdd:COG2739   81 LEE-IKELLEELEESEDDEELEKL 103
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 20-52 4.31e-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: 37.79  E-value: 4.31e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 489079808   20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAV 52
Cdd:pfam04545   5 LPPRERQVLVLRYGEGLTLEEIGERLGISRERV 37
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 20-53 7.98e-05

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 36.92  E-value: 7.98e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 489079808  20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVY 53
Cdd:cd00569    6 LTPEQIAEARRLLAAGESVAEIARELGVSRSTLY 39
HTH_10 pfam04967
HTH DNA binding domain;
20-61 1.41e-04

HTH DNA binding domain;


Pssm-ID: 282780 [Multi-domain]  Cd Length: 53  Bit Score: 36.82  E-value: 1.41e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 489079808   20 LTDKQMNYIELYYADDY-------SLAEIADEFGVSRQAVYDNIKRTEK 61
Cdd:pfam04967   1 LTDRQLEVLRLAYEMGYfdyprrvTLKELAKELGISKSTLSEHLRRAES 49
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-66 1.55e-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: 38.48  E-value: 1.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 489079808   20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETY 66
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 30-58 4.76e-04

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 35.26  E-value: 4.76e-04
                          10        20
                  ....*....|....*....|....*....
gi 489079808   30 LYYADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:pfam13518   7 LLALEGESIKEAARLFGISRSTVYRWIRR 35
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 12-63 6.97e-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: 6.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 489079808   12 LFEFYAAL--LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKIL 63
Cdd:pfam08281   1 LEALLRALeeLPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 20-52 9.06e-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: 34.77  E-value: 9.06e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 489079808  20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAV 52
Cdd:cd06171   11 LPEREREVILLRFGEGLSYEEIAEILGISRSTV 43
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
20-58 1.00e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 36.78  E-value: 1.00e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 489079808  20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:COG2826    7 LTLEEREEIEALLKAGLSVREIARRLGRSPSTISRELKR 45
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-58 1.10e-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: 36.51  E-value: 1.10e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 489079808  14 EFYAAL--LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:COG1595  120 ALLAALerLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSR 166
HTH_23 pfam13384
Homeodomain-like domain;
32-58 1.13e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 34.17  E-value: 1.13e-03
                          10        20
                  ....*....|....*....|....*..
gi 489079808   32 YADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:pfam13384  14 LAEGLSVKEIAELLGVSRRTVYRWLKR 40
COG1356 COG1356
Transcriptional regulator [Transcription];
19-68 1.38e-03

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 35.60  E-value: 1.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489079808  19 LLTDKQMNYIElYYADDYSLAEIADEFGVSRQAV-------YDNIKRTEKILETYEM 68
Cdd:COG1356    8 LLTRRQAEVLA-LRERGLTQQEIADILGTSRANVssieksaRENIEKARETLAFYET 63
transpos_IS630 NF033545
IS630 family transposase;
28-58 1.39e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 36.46  E-value: 1.39e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489079808  28 IELYYADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:NF033545   5 ILLLAAEGLSITEIAERLGVSRSTVYRWLKR 35
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
20-53 1.62e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 33.87  E-value: 1.62e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 489079808   20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVY 53
Cdd:pfam02796   6 LNEEDINEVITLLEEGISIKQIAKIFGISRSTVY 39
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 20-58 4.07e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 32.87  E-value: 4.07e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 489079808   20 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKR 58
Cdd:pfam13936   5 LSLEEREEIARLLAEGLSLREIARRLGRSPSTISRELRR 43
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 32-73 4.95e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 34.53  E-value: 4.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489079808  32 YADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMY 73
Cdd:PRK06811 144 YLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNISLG 185
COG1777 COG1777
Predicted transcriptional regulator, ArsR family [Transcription];
40-89 8.75e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441383  Cd Length: 113  Bit Score: 33.08  E-value: 8.75e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489079808  40 EIADEFGVSRQAVYDNIKRTEK--ILETY--------EMKLHMYSDYVVRSEIFDDMIAH 89
Cdd:COG1777   35 ELARELGVSRQAVYKHLRKLEEagLVESYregredgrARKYYRLSAFRLEVTLTPDLFAR 94
 
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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