Clusters of Characterized Proteins

GapMind for Amino acid biosynthesis

Clusters of Characterized Proteins

Clustering the characterized proteins for lysA (diaminopimelate decarboxylase) in L-lysine biosynthesis

Or see other characterized proteins similar to lysA

Or see all steps for L-lysine biosynthesis

Or cluster curated proteins matching a keyword

Definition of lysA

Curated proteins or TIGRFams with EC 4.1.1.20
Ignore hits to A0A0H3H393 when looking for 'other' hits (lysine decarboxylase (EC 4.1.1.18))
Predicted: UniProt sequence U7D9L6: SubName: Full=Diaminopimelate decarboxylase {ECO:0000313|EMBL:ERP38717.1};
Ignore hits to MONOMER-21197 when looking for 'other' hits (dimethylsulfonio-2-hydroxybutanoate hydroxylase/decarboxylase)
Comment: A0A0H3H393 is reported to be a lysine decarboxylase but is 87% identical to E. coli's diaminopimelate decarboxylase, so it is ignored. CALK_RS03395 (U7D9L6) has conserved functional residues (see alignment to 1ko0A) and is in an operon with meso-diaminopimelate D-dehydrogenase (ddh), so it must be the missing lysA. MetaCyc annotates THAPSDRAFT_20613 (link), which is probably a diaminopimelate decarboxylase, as a dimethylsulfonio-2-hydroxybutanoate hydroxylase/decarboxylase, but there is no experimental evidence, so it is ignored.

Fetched 17 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 16 of these sequences

Found 1 clusters of similar sequences. Another 1 sequences are not clustered. Download as table or as draft rules or view by organism

Cluster 1 386-489 amino acids (not heteromeric)

The first sequence in each cluster is the seed.

DCDA_THEMA / Q9X1K5 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
PFams: Orn_Arg_deC_N, Orn_DAP_Arg_deC
386 amino acids: PaperBLAST, CDD, Compare to cluster

b2838 diaminopimelate decarboxylase (EC 4.1.1.20) from Escherichia coli K-12 substr. MG1655
P00861 diaminopimelate decarboxylase (EC 4.1.1.20) from Escherichia coli (strain K12)
DCDA_ECOLW / E0IWI3 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Escherichia coli (strain ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB 8666 / NRRL B-766 / W)
DCDA_ECOLI / P00861 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Escherichia coli (strain K12)
P00861 diaminopimelate decarboxylase (EC 4.1.1.20) from Escherichia coli
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
420 amino acids: PaperBLAST, CDD, Compare to cluster

DCDA_CORGL / P09890 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)
P09890 diaminopimelate decarboxylase (EC 4.1.1.20) from Corynebacterium glutamicum
PFams: Orn_Arg_deC_N, Orn_DAP_Arg_deC
445 amino acids: PaperBLAST, CDD, Compare to cluster

P56129 diaminopimelate decarboxylase (EC 4.1.1.20) from Helicobacter pylori
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
405 amino acids: PaperBLAST, CDD, Compare to cluster

DCDA_MYCTU / P9WIU7 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
P9WIU7 diaminopimelate decarboxylase (EC 4.1.1.20) from Mycobacterium tuberculosis
PFams: Orn_Arg_deC_N, Orn_DAP_Arg_deC
447 amino acids: PaperBLAST, CDD, Compare to cluster

Q949X7 diaminopimelate decarboxylase (EC 4.1.1.20) from Arabidopsis thaliana
DCDA1_ARATH / Q949X7 Diaminopimelate decarboxylase 1, chloroplastic; DAP decarboxylase 1; DAPDC 1; EC 4.1.1.20 from Arabidopsis thaliana (Mouse-ear cress)
Q949X7 diaminopimelate decarboxylase (EC 4.1.1.20) from Arabidopsis thaliana
PFams: Orn_DAP_Arg_deC, Ala_racemase_N, Orn_Arg_deC_N
484 amino acids: PaperBLAST, CDD, Compare to cluster

Q94A94 diaminopimelate decarboxylase (EC 4.1.1.20) from Arabidopsis thaliana
DCDA2_ARATH / Q94A94 Diaminopimelate decarboxylase 2, chloroplastic; DAP decarboxylase 2; DAPDC 2; EC 4.1.1.20 from Arabidopsis thaliana (Mouse-ear cress)
Q94A94 diaminopimelate decarboxylase (EC 4.1.1.20) from Arabidopsis thaliana
PFams: Orn_DAP_Arg_deC, Ala_racemase_N, Orn_Arg_deC_N
489 amino acids: PaperBLAST, CDD, Compare to cluster

Q9KVL7 diaminopimelate decarboxylase (EC 4.1.1.20) from Vibrio cholerae serotype O1
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N, Ala_racemase_N
417 amino acids: PaperBLAST, CDD, Compare to cluster

DCDA_HELPX / B4XMC6 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Helicobacter pylori (Campylobacter pylori)
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
405 amino acids: PaperBLAST, CDD, Compare to cluster

DCDA_METJA / Q58497 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
PFams: Orn_Arg_deC_N, Orn_DAP_Arg_deC
438 amino acids: PaperBLAST, CDD, Compare to cluster

DCDA_STAAC / Q5HG20 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Staphylococcus aureus (strain COL)
PFams: Orn_Arg_deC_N, Orn_DAP_Arg_deC
421 amino acids: PaperBLAST, CDD, Compare to cluster

U7D9L6 Diaminopimelate decarboxylase
442 amino acids: PaperBLAST, CDD, Compare to cluster

P23630 diaminopimelate decarboxylase subunit (EC 4.1.1.20) from Bacillus subtilis (strain 168)
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
439 amino acids: PaperBLAST, CDD, Compare to cluster

BT1374 diaminopimelate decarboxylase (EC 4.1.1.20) from Bacteroides thetaiotaomicron VPI-5482
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
386 amino acids: PaperBLAST, CDD, Compare to cluster

Echvi_1295 diaminopimelate decarboxylase (EC 4.1.1.20) from Echinicola vietnamensis KMM 6221, DSM 17526
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
410 amino acids: PaperBLAST, CDD, Compare to cluster

Ga0059261_2051 diaminopimelate decarboxylase (EC 4.1.1.20) from Sphingomonas koreensis DSMZ 15582
PFams: Orn_DAP_Arg_deC, Orn_Arg_deC_N
419 amino acids: PaperBLAST, CDD, Compare to cluster

Singletons (0/1 heteromeric)

N515DRAFT_4002 aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) from Dyella japonica UNC79MFTsu3.2
PFams: AA_kinase, Orn_Arg_deC_N, Orn_DAP_Arg_deC
853 amino acids: PaperBLAST, CDD