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Conserved domains on  [gi|1258770608|gb|PEK90955|]
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transcriptional regulator YeiL [Bacillus mycoides]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10402 super family cl28241
DNA-binding transcriptional activator YeiL; Provisional
 1-229 5.26e-56

DNA-binding transcriptional activator YeiL; Provisional


The actual alignment was detected with superfamily member PRK10402:

Pssm-ID: 236682 [Multi-domain]  Cd Length: 226  Bit Score: 178.00  E-value: 5.26e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608   1 MKKVCNSNKLAEYMKQNNIDSFFSSDMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSL 80
Cdd:PRK10402    1 MKESKNSEEISHYMSESAFKDCFSFDVSADTELFHFLAREYIVQEGQQPSYLFYLTRGRAKLYATLANGKVSLIDFFAAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  81 QLLGDVELIHSQKTASNVQVMADSYCVGLPLGKVRNQLFHDAKFLRCICGSLAHKLNRLSKNSTINLLYPLENRLASYML 160
Cdd:PRK10402   81 CFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFIL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1258770608 161 AAgeravQHGNriVFSGNLTEIAELLGTSYRHLLRTLNVFCDKEIIKKSNGCFEVMNVDVLRELAADVY 229
Cdd:PRK10402  161 LT-----QEGD--LYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLALELK 222
 
Name Accession Description Interval E-value
PRK10402 PRK10402
DNA-binding transcriptional activator YeiL; Provisional
 1-229 5.26e-56

DNA-binding transcriptional activator YeiL; Provisional


Pssm-ID: 236682 [Multi-domain]  Cd Length: 226  Bit Score: 178.00  E-value: 5.26e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608   1 MKKVCNSNKLAEYMKQNNIDSFFSSDMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSL 80
Cdd:PRK10402    1 MKESKNSEEISHYMSESAFKDCFSFDVSADTELFHFLAREYIVQEGQQPSYLFYLTRGRAKLYATLANGKVSLIDFFAAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  81 QLLGDVELIHSQKTASNVQVMADSYCVGLPLGKVRNQLFHDAKFLRCICGSLAHKLNRLSKNSTINLLYPLENRLASYML 160
Cdd:PRK10402   81 CFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFIL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1258770608 161 AAgeravQHGNriVFSGNLTEIAELLGTSYRHLLRTLNVFCDKEIIKKSNGCFEVMNVDVLRELAADVY 229
Cdd:PRK10402  161 LT-----QEGD--LYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLALELK 222
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 26-225 1.32e-36

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 127.80  E-value: 1.32e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  26 DMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTASNVQVMADSY 105
Cdd:COG0664    11 ALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPATAEALEDSE 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608 106 CVGLPLGKVRNQLFHDAKFLRCICGSLAHKLNRLSKNSTINLLYPLENRLASYMLaagERAVQHGNRIVFSGNLTEIAEL 185
Cdd:COG0664    91 LLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLL---ELADRLDGRIDLPLTQEEIASY 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1258770608 186 LGTSYRHLLRTLNVFCDKEIIKKSNGCFEVMNVDVLRELA 225
Cdd:COG0664   168 LGLTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 33-121 7.97e-16

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 69.95  E-value: 7.97e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  33 LIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTASNVQVMADSYCVGLPLG 112
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ....*....
gi 1258770608 113 KVRNQLFHD 121
Cdd:pfam00027  81 DFLELLERD 89
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 17-128 1.88e-11

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 59.26  E-value: 1.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  17 NNIDSFFSSDMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTAS 96
Cdd:cd00038     3 SGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSA 82

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1258770608  97 NVQVMADSYCVGLPLGKVRNQLFHDAKFLRCI 128
Cdd:cd00038    83 TVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 30-118 4.61e-07

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 47.40  E-value: 4.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608   30 YMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTASN--VQVMADSYCV 107
Cdd:smart00100  16 ALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASaaAVALELATLL 95

                           90
                   ....*....|.
gi 1258770608  108 GLPLGKVRNQL 118
Cdd:smart00100  96 RIDFRDFLQLL 106
 
Name Accession Description Interval E-value
PRK10402 PRK10402
DNA-binding transcriptional activator YeiL; Provisional
 1-229 5.26e-56

DNA-binding transcriptional activator YeiL; Provisional


Pssm-ID: 236682 [Multi-domain]  Cd Length: 226  Bit Score: 178.00  E-value: 5.26e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608   1 MKKVCNSNKLAEYMKQNNIDSFFSSDMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSL 80
Cdd:PRK10402    1 MKESKNSEEISHYMSESAFKDCFSFDVSADTELFHFLAREYIVQEGQQPSYLFYLTRGRAKLYATLANGKVSLIDFFAAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  81 QLLGDVELIHSQKTASNVQVMADSYCVGLPLGKVRNQLFHDAKFLRCICGSLAHKLNRLSKNSTINLLYPLENRLASYML 160
Cdd:PRK10402   81 CFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFIL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1258770608 161 AAgeravQHGNriVFSGNLTEIAELLGTSYRHLLRTLNVFCDKEIIKKSNGCFEVMNVDVLRELAADVY 229
Cdd:PRK10402  161 LT-----QEGD--LYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLALELK 222
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 26-225 1.32e-36

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 127.80  E-value: 1.32e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  26 DMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTASNVQVMADSY 105
Cdd:COG0664    11 ALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPATAEALEDSE 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608 106 CVGLPLGKVRNQLFHDAKFLRCICGSLAHKLNRLSKNSTINLLYPLENRLASYMLaagERAVQHGNRIVFSGNLTEIAEL 185
Cdd:COG0664    91 LLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLL---ELADRLDGRIDLPLTQEEIASY 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1258770608 186 LGTSYRHLLRTLNVFCDKEIIKKSNGCFEVMNVDVLRELA 225
Cdd:COG0664   168 LGLTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 33-121 7.97e-16

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 69.95  E-value: 7.97e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  33 LIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTASNVQVMADSYCVGLPLG 112
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ....*....
gi 1258770608 113 KVRNQLFHD 121
Cdd:pfam00027  81 DFLELLERD 89
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 17-128 1.88e-11

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 59.26  E-value: 1.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608  17 NNIDSFFSSDMKPYMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTAS 96
Cdd:cd00038     3 SGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSA 82

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1258770608  97 NVQVMADSYCVGLPLGKVRNQLFHDAKFLRCI 128
Cdd:cd00038    83 TVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 154-224 3.99e-07

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 45.91  E-value: 3.99e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1258770608 154 RLASYMLAAGERavQHGNRIVFSGNLTEIAELLGTSYRHLLRTLNVFCDKEIIKKsnGCFEVMNVDVLREL 224
Cdd:pfam13545   2 RLARFLLELAAR--DGGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLIER--GRITILDPEALEAL 68
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 30-118 4.61e-07

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 47.40  E-value: 4.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1258770608   30 YMELIFFKKNEFICRENEEIDYLYFFVEGKAKAFNTLSNGKSVLLCFYDSLQLLGDVELIHSQKTASN--VQVMADSYCV 107
Cdd:smart00100  16 ALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASaaAVALELATLL 95

                           90
                   ....*....|.
gi 1258770608  108 GLPLGKVRNQL 118
Cdd:smart00100  96 RIDFRDFLQLL 106
 
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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