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Conserved domains on  [gi|447062978|ref|WP_001140234|]
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MULTISPECIES: L-serine ammonia-lyase, iron-sulfur-dependent subunit beta [Staphylococcus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sda_beta super family cl31026
L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine ...
 7-163 1.34e-35

L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine deaminase. This model describes the beta chain of an iron-sulfur-dependent L-serine dehydratase, as in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of beta chains from the homologous region of single chain forms such as found in E. coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]


The actual alignment was detected with superfamily member TIGR00719:

Pssm-ID: 129802 [Multi-domain]  Cd Length: 208  Bit Score: 125.04  E-value: 1.34e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978    7 YQSAFDIIGPVMMGPSSSHTAGAVKIGNSARAILGDIPKNIEIHYYESFAQTHQGHGTDVAIVGGAMGYSTFDNRIKSSL 86
Cdd:TIGR00719   3 DRSAFDIIGPIMIGPSSSHTAGAAKIANVARSIFGNEPEQIEFQFHGSFAETFKGHGTDRAIIGGILDFDPDDDRIKTAF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 447062978   87 EIAADDGIKIDI-IEEEGDSIgqHPNCAYIKSSRNDGRyiEIIGISIGGGTIKIKGIHINGLEVDLNHGLPILVVDGN 163
Cdd:TIGR00719  83 EIAEAAGIDIEFrTEDAGDNV--HPNSAKITFSDEKGE--EEELIGISIGGGAIEITEINGFAIEFRGEHPAILLEHN 156
 
Name Accession Description Interval E-value
sda_beta TIGR00719
L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine ...
 7-163 1.34e-35

L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine deaminase. This model describes the beta chain of an iron-sulfur-dependent L-serine dehydratase, as in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of beta chains from the homologous region of single chain forms such as found in E. coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]


Pssm-ID: 129802 [Multi-domain]  Cd Length: 208  Bit Score: 125.04  E-value: 1.34e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978    7 YQSAFDIIGPVMMGPSSSHTAGAVKIGNSARAILGDIPKNIEIHYYESFAQTHQGHGTDVAIVGGAMGYSTFDNRIKSSL 86
Cdd:TIGR00719   3 DRSAFDIIGPIMIGPSSSHTAGAAKIANVARSIFGNEPEQIEFQFHGSFAETFKGHGTDRAIIGGILDFDPDDDRIKTAF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 447062978   87 EIAADDGIKIDI-IEEEGDSIgqHPNCAYIKSSRNDGRyiEIIGISIGGGTIKIKGIHINGLEVDLNHGLPILVVDGN 163
Cdd:TIGR00719  83 EIAEAAGIDIEFrTEDAGDNV--HPNSAKITFSDEKGE--EEELIGISIGGGAIEITEINGFAIEFRGEHPAILLEHN 156
SdaA COG1760
L-serine deaminase [Amino acid transport and metabolism];
11-96 1.38e-17

L-serine deaminase [Amino acid transport and metabolism];


Pssm-ID: 441366 [Multi-domain]  Cd Length: 275  Bit Score: 79.09  E-value: 1.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978  11 FDIIGPVMM-----GPS-SSHTAGAVKIGNSARAIL--------GDIPKNIEIHYYESFAQTHQGHGTDVAIVGGAMGYS 76
Cdd:COG1760   36 LDRIWDVMKecveiGPStSSHTAGALRIGRRARKLLrygekplpGDVLDWVNIYALASFEENAAGGGTVTAPTAGALGVI 115

                         90       100       110
                 ....*....|....*....|....*....|..
gi 447062978  77 T------------FDNRIKSSLEIAADDGIKI 96
Cdd:COG1760  116 PavllyyqeflgaDDERIRDALLTAAAIGILI 147
SDH_beta pfam03315
Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer ...
 20-111 1.77e-08

Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.


Pssm-ID: 427239 [Multi-domain]  Cd Length: 146  Bit Score: 51.63  E-value: 1.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978   20 GPSSSHTAGAVKIGNSARAIL---GDIPK--NIEIHYYESFAQTHQGHGTDVAIVGGAMGYS--TFD--------NRIKS 84
Cdd:pfam03315   2 GPSSSHTVGPMRAAARFLDELrekGLLDRvaRVRVELYGSLAATGKGHGTDRAVLLGLEGEDpeTVDpdaidarlAAIRA 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 447062978   85 SLEIAADDGIKI------DIIEEEGDSIGQHPN 111
Cdd:pfam03315  82 TGRLPLGGEHEIpfdpdrDIVFHRRESLPFHPN 114
PRK15040 PRK15040
L-serine ammonia-lyase;
9-84 7.43e-08

L-serine ammonia-lyase;


Pssm-ID: 185000 [Multi-domain]  Cd Length: 454  Bit Score: 51.97  E-value: 7.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978   9 SAFDIIgPVMMGPSSSHTAGAVKIGNSARAIL---GDIPK--NIEIHYYESFAQTHQGHGTDVAIVGGAMGYSTFDNRIK 83
Cdd:PRK15040   3 SAFDIF-KIGIGPSSSHTVGPMNAGKSFIDRLessGLLTAtsHIVVDLYGSLSLTGKGHATDVAIIMGLAGNSPQDVVID 81


                 .
gi 447062978  84 S 84
Cdd:PRK15040  82 E 82
 
Name Accession Description Interval E-value
sda_beta TIGR00719
L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine ...
 7-163 1.34e-35

L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine deaminase. This model describes the beta chain of an iron-sulfur-dependent L-serine dehydratase, as in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of beta chains from the homologous region of single chain forms such as found in E. coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]


Pssm-ID: 129802 [Multi-domain]  Cd Length: 208  Bit Score: 125.04  E-value: 1.34e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978    7 YQSAFDIIGPVMMGPSSSHTAGAVKIGNSARAILGDIPKNIEIHYYESFAQTHQGHGTDVAIVGGAMGYSTFDNRIKSSL 86
Cdd:TIGR00719   3 DRSAFDIIGPIMIGPSSSHTAGAAKIANVARSIFGNEPEQIEFQFHGSFAETFKGHGTDRAIIGGILDFDPDDDRIKTAF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 447062978   87 EIAADDGIKIDI-IEEEGDSIgqHPNCAYIKSSRNDGRyiEIIGISIGGGTIKIKGIHINGLEVDLNHGLPILVVDGN 163
Cdd:TIGR00719  83 EIAEAAGIDIEFrTEDAGDNV--HPNSAKITFSDEKGE--EEELIGISIGGGAIEITEINGFAIEFRGEHPAILLEHN 156
SdaA COG1760
L-serine deaminase [Amino acid transport and metabolism];
11-96 1.38e-17

L-serine deaminase [Amino acid transport and metabolism];


Pssm-ID: 441366 [Multi-domain]  Cd Length: 275  Bit Score: 79.09  E-value: 1.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978  11 FDIIGPVMM-----GPS-SSHTAGAVKIGNSARAIL--------GDIPKNIEIHYYESFAQTHQGHGTDVAIVGGAMGYS 76
Cdd:COG1760   36 LDRIWDVMKecveiGPStSSHTAGALRIGRRARKLLrygekplpGDVLDWVNIYALASFEENAAGGGTVTAPTAGALGVI 115

                         90       100       110
                 ....*....|....*....|....*....|..
gi 447062978  77 T------------FDNRIKSSLEIAADDGIKI 96
Cdd:COG1760  116 PavllyyqeflgaDDERIRDALLTAAAIGILI 147
sda_mono TIGR00720
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called ...
 9-76 4.30e-09

L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]


Pssm-ID: 273233 [Multi-domain]  Cd Length: 450  Bit Score: 55.81  E-value: 4.30e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447062978    9 SAFDI--IGpvmMGPSSSHTAGAVKIGNS------ARAILGDIpKNIEIHYYESFAQTHQGHGTDVAIVGGAMGYS 76
Cdd:TIGR00720   2 SVFDLfkIG---IGPSSSHTVGPMRAAKQfaddlrDKGLLEQT-TRVQVDLYGSLALTGKGHGTDKAVLLGLMGFL 73
SDH_beta pfam03315
Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer ...
 20-111 1.77e-08

Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.


Pssm-ID: 427239 [Multi-domain]  Cd Length: 146  Bit Score: 51.63  E-value: 1.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978   20 GPSSSHTAGAVKIGNSARAIL---GDIPK--NIEIHYYESFAQTHQGHGTDVAIVGGAMGYS--TFD--------NRIKS 84
Cdd:pfam03315   2 GPSSSHTVGPMRAAARFLDELrekGLLDRvaRVRVELYGSLAATGKGHGTDRAVLLGLEGEDpeTVDpdaidarlAAIRA 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 447062978   85 SLEIAADDGIKI------DIIEEEGDSIGQHPN 111
Cdd:pfam03315  82 TGRLPLGGEHEIpfdpdrDIVFHRRESLPFHPN 114
PRK15040 PRK15040
L-serine ammonia-lyase;
9-84 7.43e-08

L-serine ammonia-lyase;


Pssm-ID: 185000 [Multi-domain]  Cd Length: 454  Bit Score: 51.97  E-value: 7.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447062978   9 SAFDIIgPVMMGPSSSHTAGAVKIGNSARAIL---GDIPK--NIEIHYYESFAQTHQGHGTDVAIVGGAMGYSTFDNRIK 83
Cdd:PRK15040   3 SAFDIF-KIGIGPSSSHTVGPMNAGKSFIDRLessGLLTAtsHIVVDLYGSLSLTGKGHATDVAIIMGLAGNSPQDVVID 81


                 .
gi 447062978  84 S 84
Cdd:PRK15040  82 E 82
PRK15023 PRK15023
L-serine deaminase; Provisional
 9-74 3.40e-04

L-serine deaminase; Provisional


Pssm-ID: 184984 [Multi-domain]  Cd Length: 454  Bit Score: 41.21  E-value: 3.40e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 447062978   9 SAFDIIgPVMMGPSSSHTAGAVKIGNS------ARAILGDIPKnIEIHYYESFAQTHQGHGTDVAIVGGAMG 74
Cdd:PRK15023   3 SLFDMF-KVGIGPSSSHTVGPMKAGKQfvddlvEKGLLDSVTR-VAVDVYGSLSLTGKGHHTDIAIIMGLAG 72
 
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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