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Conserved domains on  [gi|115534439|ref|NP_502334|]
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Protein-lysine methyltransferase C42C1.13 [Caenorhabditis elegans]

Protein Classification

class I SAM-dependent methyltransferase( domain architecture ID 106779)

class I SAM-dependent methyltransferase catalyzes the methylation of one or more specific substrates using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AdoMet_MTases super family cl17173
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 1-138 3.28e-36

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


The actual alignment was detected with superfamily member pfam10294:

Pssm-ID: 473071  Cd Length: 172  Bit Score: 123.21  E-value: 3.28e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439    1 MTIHYFFKYPKP------FEGKKVLELGSGTGVGGIALAAL--GADVIITDLPERLALIEKNVEANrkLTGNRIKVQVLD 72
Cdd:pfam10294  27 VLSKYLEMKIFKelgannLSGLNVLELGSGTGLVGIAVALLlpGASVTITDLEEALELLKKNIELN--ALSSKVVVKVLD 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115534439   73 WTKDRIP-----EGLDMVLAIDCVYYNSTIDPLITLLNDCDAKE--IMVVSEERdigeaHLAQKSFFKDIQKF 138
Cdd:pfam10294 105 WGENLPPdlfdgHPVDLILAADCVYNEDSFPLLEKTLKDLLGKEsvILVAYKKR-----REAEKKFFKLLERF 172
 
Name Accession Description Interval E-value
Methyltransf_16 pfam10294
Lysine methyltransferase; Methyltrans_16 is a lysine methyltransferase. characterized members ...
 1-138 3.28e-36

Lysine methyltransferase; Methyltrans_16 is a lysine methyltransferase. characterized members of this family are protein methyltransferases targetting Lys residues in specific proteins, including calmodulin, VCP, Kin17 and Hsp70 proteins.


Pssm-ID: 313513  Cd Length: 172  Bit Score: 123.21  E-value: 3.28e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439    1 MTIHYFFKYPKP------FEGKKVLELGSGTGVGGIALAAL--GADVIITDLPERLALIEKNVEANrkLTGNRIKVQVLD 72
Cdd:pfam10294  27 VLSKYLEMKIFKelgannLSGLNVLELGSGTGLVGIAVALLlpGASVTITDLEEALELLKKNIELN--ALSSKVVVKVLD 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115534439   73 WTKDRIP-----EGLDMVLAIDCVYYNSTIDPLITLLNDCDAKE--IMVVSEERdigeaHLAQKSFFKDIQKF 138
Cdd:pfam10294 105 WGENLPPdlfdgHPVDLILAADCVYNEDSFPLLEKTLKDLLGKEsvILVAYKKR-----REAEKKFFKLLERF 172
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 15-87 2.46e-08

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 51.30  E-value: 2.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115534439  15 GKKVLELGSGTGVGGIALAALGADVIIT--DLPERLA-LIEKNVEANRKltGNRIKVQ---VLDWTKDRIPEGLDMVLA 87
Cdd:COG4123   38 GGRVLDLGTGTGVIALMLAQRSPGARITgvEIQPEAAeLARRNVALNGL--EDRITVIhgdLKEFAAELPPGSFDLVVS 114
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 8-87 1.37e-04

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 40.92  E-value: 1.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439   8 KYPKPFEGKKVLELGSGTGVGGIALAAL--GADVIITDL-PERLALIEKNVEANrklTGNRIKVQVLDWTKDRIPEGLDM 84
Cdd:PRK09328 102 EALLLKEPLRVLDLGTGSGAIALALAKErpDAEVTAVDIsPEALAVARRNAKHG---LGARVEFLQGDWFEPLPGGRFDL 178


                 ...
gi 115534439  85 VLA 87
Cdd:PRK09328 179 IVS 181
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 17-93 2.11e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 38.57  E-value: 2.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  17 KVLELGSGTGVGGIALA-ALGADVIITDLPERlaLIEKNVEANRKLTGNRIKVQVLDWTK--DRIPEGLDMVLAIDCVYY 93
Cdd:cd02440    1 RVLDLGCGTGALALALAsGPGARVTGVDISPV--ALELARKAAAALLADNVEVLKGDAEElpPEADESFDVIISDPPLHH 78
 
Name Accession Description Interval E-value
Methyltransf_16 pfam10294
Lysine methyltransferase; Methyltrans_16 is a lysine methyltransferase. characterized members ...
 1-138 3.28e-36

Lysine methyltransferase; Methyltrans_16 is a lysine methyltransferase. characterized members of this family are protein methyltransferases targetting Lys residues in specific proteins, including calmodulin, VCP, Kin17 and Hsp70 proteins.


Pssm-ID: 313513  Cd Length: 172  Bit Score: 123.21  E-value: 3.28e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439    1 MTIHYFFKYPKP------FEGKKVLELGSGTGVGGIALAAL--GADVIITDLPERLALIEKNVEANrkLTGNRIKVQVLD 72
Cdd:pfam10294  27 VLSKYLEMKIFKelgannLSGLNVLELGSGTGLVGIAVALLlpGASVTITDLEEALELLKKNIELN--ALSSKVVVKVLD 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115534439   73 WTKDRIP-----EGLDMVLAIDCVYYNSTIDPLITLLNDCDAKE--IMVVSEERdigeaHLAQKSFFKDIQKF 138
Cdd:pfam10294 105 WGENLPPdlfdgHPVDLILAADCVYNEDSFPLLEKTLKDLLGKEsvILVAYKKR-----REAEKKFFKLLERF 172
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 15-87 2.46e-08

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 51.30  E-value: 2.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115534439  15 GKKVLELGSGTGVGGIALAALGADVIIT--DLPERLA-LIEKNVEANRKltGNRIKVQ---VLDWTKDRIPEGLDMVLA 87
Cdd:COG4123   38 GGRVLDLGTGTGVIALMLAQRSPGARITgvEIQPEAAeLARRNVALNGL--EDRITVIhgdLKEFAAELPPGSFDLVVS 114
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 14-93 1.57e-07

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 47.70  E-value: 1.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  14 EGKKVLELGSGTGVGGIALAALGADVIITDL-PERLALieknveANRKLTGNRIKVQVLDWTK-DRIPEGLDMVLAIDCV 91
Cdd:COG2227   24 AGGRVLDVGCGTGRLALALARRGADVTGVDIsPEALEI------ARERAAELNVDFVQGDLEDlPLEDGSFDLVICSEVL 97


                 ..
gi 115534439  92 YY 93
Cdd:COG2227   98 EH 99
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 14-93 1.32e-06

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 45.37  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  14 EGKKVLELGSGTGVGGIALAALGADVIITDL-PERLALIEKNVEANrkltGNRIKVQVLDWTKDRIPEG-LDMVLAIDCV 91
Cdd:COG2226   22 PGARVLDLGCGTGRLALALAERGARVTGVDIsPEMLELARERAAEA----GLNVEFVVGDAEDLPFPDGsFDLVISSFVL 97


                 ..
gi 115534439  92 YY 93
Cdd:COG2226   98 HH 99
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 18-93 4.03e-06

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 43.32  E-value: 4.03e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115534439   18 VLELGSGTGVGGIALA-ALGADVIITDL-PERLALIEKNVEANrkltGNRIKVQVLDWTKDRIPEG-LDMVLAIDCVYY 93
Cdd:pfam13649   1 VLDLGCGTGRLTLALArRGGARVTGVDLsPEMLERARERAAEA----GLNVEFVQGDAEDLPFPDGsFDLVVSSGVLHH 75
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
13-56 2.32e-05

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 42.58  E-value: 2.32e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 115534439  13 FEGKKVLELGSGTGVGGIALAALGA-DVIITDL-PERLALIEKNVE 56
Cdd:COG2263   44 IEGKTVLDLGCGTGMLAIGAALLGAkKVVGVDIdPEALEIARENAE 89
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 15-93 2.80e-05

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 41.84  E-value: 2.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  15 GKKVLELGSGTGVGGIALAA-LGADVIITDL-PERLALIEKNVEAnRKLTgNRIKVQVLDWTKDRIPEGLDMVLAIDCVY 92
Cdd:COG2230   52 GMRVLDIGCGWGGLALYLARrYGVRVTGVTLsPEQLEYARERAAE-AGLA-DRVEVRLADYRDLPADGQFDAIVSIGMFE 129


                 .
gi 115534439  93 Y 93
Cdd:COG2230  130 H 130
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 10-86 7.96e-05

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 41.04  E-value: 7.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439   10 PKPFEGKkVLELGSGTGVGGIALAALGADVIIT--DLPER-LALIEKNVEANRkltGNRIKVQVLDWTKDRIPEGLDMVL 86
Cdd:pfam05175  28 PKDLSGK-VLDLGCGAGVLGAALAKESPDAELTmvDINARaLESARENLAANG---LENGEVVASDVYSGVEDGKFDLII 103
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 8-87 1.37e-04

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 40.92  E-value: 1.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439   8 KYPKPFEGKKVLELGSGTGVGGIALAAL--GADVIITDL-PERLALIEKNVEANrklTGNRIKVQVLDWTKDRIPEGLDM 84
Cdd:PRK09328 102 EALLLKEPLRVLDLGTGSGAIALALAKErpDAEVTAVDIsPEALAVARRNAKHG---LGARVEFLQGDWFEPLPGGRFDL 178


                 ...
gi 115534439  85 VLA 87
Cdd:PRK09328 179 IVS 181
PRK14968 PRK14968
putative methyltransferase; Provisional
 14-68 2.09e-04

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 39.88  E-value: 2.09e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 115534439  14 EGKKVLELGSGTGVGGIALAALGADVIITDL-PERLALIEKNVEANrKLTGNRIKV 68
Cdd:PRK14968  23 KGDRVLEVGTGSGIVAIVAAKNGKKVVGVDInPYAVECAKCNAKLN-NIRNNGVEV 77
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 17-93 2.11e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 38.57  E-value: 2.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  17 KVLELGSGTGVGGIALA-ALGADVIITDLPERlaLIEKNVEANRKLTGNRIKVQVLDWTK--DRIPEGLDMVLAIDCVYY 93
Cdd:cd02440    1 RVLDLGCGTGALALALAsGPGARVTGVDISPV--ALELARKAAAALLADNVEVLKGDAEElpPEADESFDVIISDPPLHH 78
TER_DECR_SDR_a cd05369
Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; TTER ...
 13-66 4.74e-04

Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; TTER is a peroxisomal protein with a proposed role in fatty acid elongation. Fatty acid synthesis is known to occur in the both endoplasmic reticulum and mitochondria; peroxisomal TER has been proposed as an additional fatty acid elongation system, it reduces the double bond at C-2 as the last step of elongation. This system resembles the mitochondrial system in that acetyl-CoA is used as a carbon donor. TER may also function in phytol metabolism, reducting phytenoyl-CoA to phytanoyl-CoA in peroxisomes. DECR processes double bonds in fatty acids to increase their utility in fatty acid metabolism; it reduces 2,4-dienoyl-CoA to an enoyl-CoA. DECR is active in mitochondria and peroxisomes. This subgroup has the Gly-rich NAD-binding motif of the classical SDR family, but does not display strong identity to the canonical active site tetrad, and lacks the characteristic Tyr at the usual position. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs.


Pssm-ID: 187627 [Multi-domain]  Cd Length: 249  Bit Score: 39.11  E-value: 4.74e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 115534439  13 FEGKKVLELGSGTGVG-GIA--LAALGADVIITDL-PERLaliEKNVEANRKLTGNRI 66
Cdd:cd05369    1 LKGKVAFITGGGTGIGkAIAkaFAELGASVAIAGRkPEVL---EAAAEEISSATGGRA 55
MDR cd05188
Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; ...
 3-104 4.80e-04

Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc.


Pssm-ID: 176178 [Multi-domain]  Cd Length: 271  Bit Score: 39.23  E-value: 4.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439   3 IHYFFKYPKPFEGKKVLELGSGT-GVGGIALA-ALGADVIITDL-PERLALIeknveanRKLTGNR-IKVQVLDWTKD-R 77
Cdd:cd05188  123 YHALRRAGVLKPGDTVLVLGAGGvGLLAAQLAkAAGARVIVTDRsDEKLELA-------KELGADHvIDYKEEDLEEElR 195

                         90       100
                 ....*....|....*....|....*..
gi 115534439  78 IPEGLDMVLAIDCVYYNSTIDPLITLL 104
Cdd:cd05188  196 LTGGGGADVVIDAVGGPETLAQALRLL 222
PRK08324 PRK08324
bifunctional aldolase/short-chain dehydrogenase;
10-49 5.47e-04

bifunctional aldolase/short-chain dehydrogenase;


Pssm-ID: 236241 [Multi-domain]  Cd Length: 681  Bit Score: 39.44  E-value: 5.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 115534439  10 PKPFEGKKVLELGSGTGVG-GIA--LAALGADVIITDL-PERLA 49
Cdd:PRK08324 417 PKPLAGKVALVTGAAGGIGkATAkrLAAEGACVVLADLdEEAAE 460
TrmR COG4122
tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; ...
 16-89 6.06e-04

tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; tRNA 5-hydroxyU34 O-methylase TrmR/YrrM is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443298  Cd Length: 173  Bit Score: 38.24  E-value: 6.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  16 KKVLELGSGTGVGGIALA-ALGADVIIT--DL-PERLALIEKNVEANRKltGNRIKVQV---LDWTKDRIPEGLDMVLaI 88
Cdd:COG4122   18 KRILEIGTGTGYSTLWLArALPDDGRLTtiEIdPERAAIARENFARAGL--ADRIRLILgdaLEVLPRLADGPFDLVF-I 94


                 .
gi 115534439  89 D 89
Cdd:COG4122   95 D 95
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
14-93 8.47e-04

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 36.73  E-value: 8.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  14 EGKKVLELGSGTGVGGIALAAL--GADVIITDLPErlALIEKnveANRKLTgnRIKVQVLDWTKDRIPEGLDMVLAIDCV 91
Cdd:COG4106    1 PPRRVLDLGCGTGRLTALLAERfpGARVTGVDLSP--EMLAR---ARARLP--NVRFVVADLRDLDPPEPFDLVVSNAAL 73


                 ..
gi 115534439  92 YY 93
Cdd:COG4106   74 HW 75
PRK05855 PRK05855
SDR family oxidoreductase;
8-46 9.28e-04

SDR family oxidoreductase;


Pssm-ID: 235628 [Multi-domain]  Cd Length: 582  Bit Score: 38.81  E-value: 9.28e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 115534439   8 KYPKPFEGKKVLELGSGTGVG---GIALAALGADVIITDLPE 46
Cdd:PRK05855 308 RPRGPFSGKLVVVTGAGSGIGretALAFAREGAEVVASDIDE 349
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 7-87 1.03e-03

Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 38.21  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439   7 FKYPKPFEGKKVLELGSGTGVGGIALAAL--GADVIITDL-PERLALIEKNVEANRklTGNRIKVQVLDWTKDRIPEG-L 82
Cdd:COG2890  105 LALLPAGAPPRVLDLGTGSGAIALALAKErpDARVTAVDIsPDALAVARRNAERLG--LEDRVRFLQGDLFEPLPGDGrF 182


                 ....*
gi 115534439  83 DMVLA 87
Cdd:COG2890  183 DLIVS 187
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 14-93 1.03e-03

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 37.97  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  14 EGKKVLELGSGTGVGGIALAAL-GADVIITDL-PERLALIEKNVEanrKLTGNRIKVQVLDWT--KDRIPEGLDMVLAID 89
Cdd:COG0500   26 KGGRVLDLGCGTGRNLLALAARfGGRVIGIDLsPEAIALARARAA---KAGLGNVEFLVADLAelDPLPAESFDLVVAFG 102


                 ....
gi 115534439  90 CVYY 93
Cdd:COG0500  103 VLHH 106
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 10-58 1.25e-03

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 37.48  E-value: 1.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 115534439  10 PKPFEGKkVLELGSGTGVGGIALAAL--GADVIITDLPER-LALIEKNVEAN 58
Cdd:COG2813   46 PEPLGGR-VLDLGCGYGVIGLALAKRnpEARVTLVDVNARaVELARANAAAN 96
DHRS6_like_SDR_c cd05368
human DHRS6-like, classical (c) SDRs; Human DHRS6, and similar proteins. These proteins are ...
 14-76 1.35e-03

human DHRS6-like, classical (c) SDRs; Human DHRS6, and similar proteins. These proteins are classical SDRs, with a canonical active site tetrad and a close match to the typical Gly-rich NAD-binding motif. Human DHRS6 is a cytosolic type 2 (R)-hydroxybutyrate dehydrogenase, which catalyses the conversion of (R)-hydroxybutyrate to acetoacetate. Also included in this subgroup is Escherichia coli UcpA (upstream cys P). Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. Note: removed : needed to make this chiodl smaller when drew final trees: rmeoved text form description: Other proteins in this subgroup include Thermoplasma acidophilum aldohexose dehydrogenase, which has high dehydrogenase activity against D-mannose, Bacillus subtilis BacC involved in the biosynthesis of the dipeptide bacilysin and its antibiotic moiety anticapsin, Sphingomonas paucimobilis strain B90 LinC, involved in the degradation of hexachlorocyclohexane isomers...... P).


Pssm-ID: 187626 [Multi-domain]  Cd Length: 241  Bit Score: 37.83  E-value: 1.35e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 115534439  14 EGKKVLELGSGTGVG---GIALAALGADVIITDL-PERLALIEKnveanrkltGNRIKVQVLDWTKD 76
Cdd:cd05368    1 DGKVALITAAAQGIGraiALAFAREGANVIATDInEEKLKELER---------GPGITTRVLDVTDK 58
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
12-104 1.80e-03

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 37.29  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  12 PFEGKKVLELGSGTGVGGIALAALGADVIITDL-PERLALieknveANRKLTGNRIKVQ-VLDWtkDRIPEGLDMVLAID 89
Cdd:COG4976   44 PGPFGRVLDLGCGTGLLGEALRPRGYRLTGVDLsEEMLAK------AREKGVYDRLLVAdLADL--AEPDGRFDLIVAAD 115

                         90
                 ....*....|....*
gi 115534439  90 CVYYNSTIDPLITLL 104
Cdd:COG4976  116 VLTYLGDLAAVFAGV 130
FabG COG1028
NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family [Lipid transport and ...
 11-72 3.75e-03

NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family [Lipid transport and metabolism]; NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family is part of the Pathway/BioSystem: Fatty acid biosynthesis


Pssm-ID: 440651 [Multi-domain]  Cd Length: 249  Bit Score: 36.69  E-value: 3.75e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115534439  11 KPFEGKKVLELGSGTGVG-GIA--LAALGADVIITDL-PERLALIEKNVEANrkltGNRIKVQVLD 72
Cdd:COG1028    2 TRLKGKVALVTGGSSGIGrAIAraLAAEGARVVITDRdAEALEAAAAELRAA----GGRALAVAAD 63
PRK06935 PRK06935
2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD;
14-81 4.02e-03

2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD;


Pssm-ID: 180761 [Multi-domain]  Cd Length: 258  Bit Score: 36.64  E-value: 4.02e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 115534439  14 EGKKVLELGSGTGVG---GIALAALGADVIIT----DLPERLALIEKnveanrklTGNRIKVQVLDWTKDRIPEG 81
Cdd:PRK06935  14 DGKVAIVTGGNTGLGqgyAVALAKAGADIIITthgtNWDETRRLIEK--------EGRKVTFVQVDLTKPESAEK 80
PrmA COG2264
Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];
12-106 4.27e-03

Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441865 [Multi-domain]  Cd Length: 284  Bit Score: 36.30  E-value: 4.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115534439  12 PFEGKKVLELGSGTGVGGIALAALGA-DVIITDL-PERLALIEKNVEANRklTGNRIKVQVLDWTKDripEGLDMVLAid 89
Cdd:COG2264  146 LKPGKTVLDVGCGSGILAIAAAKLGAkRVLAVDIdPVAVEAARENAELNG--VEDRIEVVLGDLLED---GPYDLVVA-- 218

                         90
                 ....*....|....*..
gi 115534439  90 cvyyNSTIDPLITLLND 106
Cdd:COG2264  219 ----NILANPLIELAPD 231
PRK12826 PRK12826
SDR family oxidoreductase;
11-72 5.02e-03

SDR family oxidoreductase;


Pssm-ID: 183775 [Multi-domain]  Cd Length: 251  Bit Score: 36.05  E-value: 5.02e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115534439  11 KPFEGKKVLELGSGTGVG-GIA--LAALGADVIITDL-PERLALIEKNVEAnrklTGNRIKVQVLD 72
Cdd:PRK12826   2 RDLEGRVALVTGAARGIGrAIAvrLAADGAEVIVVDIcGDDAAATAELVEA----AGGKARARQVD 63
 
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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