Clusters of Characterized Proteins

GapMind for Amino acid biosynthesis

Clusters of Characterized Proteins

Clustering the characterized proteins for serB (phosphoserine phosphatase) in L-serine biosynthesis

Or see other characterized proteins similar to serB

Or see all steps for L-serine biosynthesis

Or cluster curated proteins matching a keyword

Definition of serB

Curated proteins or TIGRFams with EC 3.1.3.3
Ignore hits to items matching EC 1.1.1.95 when looking for 'other' hits
Ignore hits to P60487 when looking for 'other' hits (pyridoxal phosphatase (EC 3.1.3.74). Chronophin; Pyridoxal 5'-phosphate phosphatase; Pyridoxal phosphate phosphatase; PLP phosphatase; EC 3.1.3.16; EC 3.1.3.74)
Ignore hits to Q96GD0 when looking for 'other' hits (pyridoxal phosphatase (EC 3.1.3.74). Chronophin; Pyridoxal phosphate phosphatase; PLP phosphatase; EC 3.1.3.16; EC 3.1.3.74)
Ignore hits to Q9P376 when looking for 'other' hits (CTD phosphatase Fcp1; EC 3.1.3.3. RNA polymerase II subunit A C-terminal domain phosphatase; CTD phosphatase fcp1; EC 3.1.3.16)
Ignore hits to O07014 when looking for 'other' hits (phosphoserine phosphatase (EC 3.1.3.3))
Ignore hits to Q3ZBF9 when looking for 'other' hits (Chronophin; Protein serine phosphatase; Pyridoxal phosphate phosphatase; PLP phosphatase; EC 3.1.3.16; EC 3.1.3.74)
Ignore hits to P00634 when looking for 'other' hits (alkaline phosphatase (EC 3.1.3.1). alkaline phosphatase (EC 3.1.3.1; EC 3.1.3.75; EC 3.1.3.41; EC 3.1.3.74; EC 3.1.3.99; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.91; EC 3.1.3.60; EC 3.1.3.15; EC 3.1.3.102; EC 3.1.3.108; EC 3.1.3.11; EC 3.1.3.20; EC 3.1.3.19; EC 3.1.3.3; EC 3.6.1.25; EC 3.6.1.1; EC 3.1.3.23; EC 3.1.3.38; EC 3.1.3.18; EC 3.1.3.68; EC 3.9.1.1). alkaline phosphatase (EC 3.1.3.1; EC 3.1.3.75; EC 3.1.3.41; EC 3.1.3.74; EC 3.1.3.99; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.91; EC 3.1.3.60; EC 3.1.3.15; EC 3.1.3.102; EC 3.1.3.108; EC 3.1.3.11; EC 3.1.3.20; EC 3.1.3.19; EC 3.1.3.3; EC 3.6.1.25; EC 3.6.1.1; EC 3.1.3.23; EC 3.1.3.38; EC 3.1.3.18; EC 3.1.3.68; EC 3.9.1.1))
Ignore hits to P0AE22 when looking for 'other' hits (acid phosphatase (EC 3.1.3.2). class B acid phosphatase; EC 3.1.3.2. Class B acid phosphatase; CBAP; EC 3.1.3.2. acid phosphatase / phosphotransferase (EC 3.1.3.2; EC 3.1.3.31; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.34; EC 3.1.3.3). acid phosphatase / phosphotransferase (EC 3.1.3.2; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.34; EC 3.1.3.3))
Ignore hits to P17906 when looking for 'other' hits (phosphoserine phosphatase (EC 3.1.3.3). Phosphoserine phosphatase RsbX; Sigma-B negative effector; EC 3.1.3.3)
Ignore hits to P40399 when looking for 'other' hits (phosphoserine phosphatase (EC 3.1.3.3). Phosphoserine phosphatase RsbU; Sigma factor SigB regulation protein RsbU; EC 3.1.3.3)
Ignore hits to P94526 when looking for 'other' hits (Sugar-phosphatase AraL; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.23; EC 3.1.3.3)
Ignore hits to D3DFP8 when looking for 'other' hits (Putative phosphoserine phosphatase 2; PSP 2; PSPase 2; Metal-independent phosphoserine phosphatase 2; iPSP2; O-phosphoserine phosphohydrolase 2; EC 3.1.3.3. phosphoserine phosphatase (EC 3.1.3.3))
UniProt sequence Q9K8N3: SubName: Full=BH2972 protein {ECO:0000313|EMBL:BAB06691.1};
UniProt sequence A0A1R2PVY2: RecName: Full=Phosphoserine phosphatase {ECO:0000256|ARBA:ARBA00015196}; EC=3.1.3.3 {ECO:0000256|ARBA:ARBA00012640}; AltName: Full=O-phosphoserine phosphohydrolase {ECO:0000256|ARBA:ARBA00031693};
UniProt sequence N9V397: SubName: Full=Phosphoglycerate mutase family protein, putative {ECO:0000313|EMBL:ENY63406.1};
Predicted: UniProt sequence A0A6B4WGC7: SubName: Full=DUF1015 domain-containing protein {ECO:0000313|EMBL:MBD5586605.1};
UniProt sequence P72649: SubName: Full=Phosphoglycerate mutase {ECO:0000313|EMBL:BAA16651.1};
UniProt sequence A0A3D8VK77: SubName: Full=Histidine phosphatase family protein {ECO:0000313|EMBL:RDY69752.1};
UniProt sequence A0A0H2XA29: SubName: Full=Phosphoglycerate mutase {ECO:0000313|EMBL:AAY50331.1};
UniProt sequence F9VNX9: SubName: Full=Phosphoserine aminotransferase {ECO:0000313|EMBL:BAK54487.1}; EC=2.6.1.52 {ECO:0000313|EMBL:BAK54487.1};
Comment: CA265_RS22635 (see Fitness Browser) is diverged serB and is auxotrophic. It also appears to be fused to diverged serA, but there is another serA in the genome (CA265_RS09010), so CA265_RS22635 may not be a functional dehydrogenase. Echvi_2777 (see Fitness Browser) from Echinicola vietnamensis KMM 6221 is a diverged serB and is auxotrophic, rescued by serine. It is fused to serA and probably provides that activity as well. Hits to serA are ignored because of serAB fusions. Some curated resources link this EC number to protein phosphatases, or to non-specific periplasmic phosphatases, that are unlikely to play a role in serine biosynthesis. These are all marked ignore (P60487, Q96GD0, Q3ZBF9, P00634, P0AE22, Q9P376, O07014). Similarly, Swiss-Prot annotates RsbX (P17906) and RsbU (P40399) with this EC number, but they probably act on proteins. And, AraL (P94526) is ignored because although it does have activity on phosphoserine, it is a promiscuous phosphatase (supplementary material of PMC4413258). Hydrogenobacter thermophilus (D3DFP8) has an unusual enzyme with both a homodimeric form (PspA) and a heterodimeric form (PspA-PspB) (PMID:22337887). PspB could not be purified on its own and the heteromeric form has lower activity than PspA, so it is not clear if PspB is active; thus PspB (D3DFP8) is ignored. PMID:25848029 shows that BH2972 (Q9K8N3) and X3MFA4 (now A0A1R2PVY2) have this activity. 5zr2C (N9V397) is serB in Entamoeba histolytica (see PMID:30935984) In Clostridiodes difficile, the serine synthesis operon includes CDIF630erm_01132 (A0A6B4WGC7), a DUF1015 protein which is speculated to replace serB (PMC6110889). This subfamily is usually colocated with serA or serC3 (see neighbors of ADT23_RS05570 or A0A6B4WGC7), and is structurally related to the N-terminal domain of serine kinases (using foldseek). Furthermore, genomes that encode this subfamily usually lack any known form of serB. The phosphoserine phosphatase from Synechocystis PCC 6803 (Slr1124, P72649) was confirmed by biochemical experiments (PMID:25701735). Similar proteins from Lysobacter OAE881 or Xanthomonas campestris 8004 (45% or 39% identity; GGC55_RS00335 = A0A3D8VK77 and Xcc-8004.4079.1 = A0A0H2XA29) are essential, and close homologs thereof are encoded adjacent to serA, so these must also be serB. ST1217 (F9VNX9) was shown to be a phosphoserine phosphatase (PMID:18054776).

Fetched 38 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 31 of these sequences

Found 6 clusters of similar sequences. Another 10 sequences are not clustered. Download as table or as draft rules or view by organism

Cluster 1 206-295 amino acids (not heteromeric)

SERB_ALBFT / Q21YU0 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118) (Rhodoferax ferrireducens)
PFams: Hydrolase, Put_Phosphatase, HAD, Hydrolase_3
237 amino acids: PaperBLAST, CDD, Compare to cluster

P78330 L-3-phosphoserine phosphatase (EC 3.1.3.3) from Homo sapiens
SERB_HUMAN / P78330 Phosphoserine phosphatase; PSP; PSPase; L-3-phosphoserine phosphatase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Homo sapiens (Human)
P78330 phosphoserine phosphatase (EC 3.1.3.3) from Homo sapiens
PFams: Hydrolase, HAD, UMPH-1
225 amino acids: PaperBLAST, CDD, Compare to cluster

Q5M819 phosphoserine phosphatase (EC 3.1.3.3) from Rattus norvegicus
PFams: Hydrolase, HAD
225 amino acids: PaperBLAST, CDD, Compare to cluster

Q99LS3 phosphoserine phosphatase (EC 3.1.3.3) from Mus musculus
PFams: Hydrolase, HAD
225 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_CAMJD / A7H590 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Campylobacter jejuni subsp. doylei (strain ATCC BAA-1458 / RM4099 / 269.97)
PFams: Hydrolase, HAD_2, HAD, Hydrolase_3
207 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_HALS3 / B0R7U7 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)
PFams: Hydrolase, HAD, Hydrolase_3
211 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_POLSJ / Q12A06 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Polaromonas sp. (strain JS666 / ATCC BAA-500)
PFams: Hydrolase, Put_Phosphatase, HAD, Hydrolase_3
236 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_METJA / Q58989 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Q58989 phosphoserine phosphatase (EC 3.1.3.3) from Methanocaldococcus jannaschii
PFams: Hydrolase, Put_Phosphatase, HAD_2, HAD, Hydrolase_3
211 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_STRT2 / Q5M3B3 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)
PFams: Hydrolase, HAD, HAD_2, Hydrolase_3
215 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_IDILO / Q5QXU4 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Idiomarina loihiensis (strain ATCC BAA-735 / DSM 15497 / L2-TR)
PFams: Hydrolase, HAD, Hydrolase_3
220 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_WOLSU / Q7M7U5 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (Vibrio succinogenes)
PFams: Hydrolase, HAD, HAD_2, Hydrolase_3
206 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_LACLA / Q9CHW3 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)
PFams: Hydrolase, HAD, HAD_2, Hydrolase_3
216 amino acids: PaperBLAST, CDD, Compare to cluster

A0A1R2PVY2 Phosphoserine phosphatase; EC=3.1.3.3; O-phosphoserine phosphohydrolase
295 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 2 205-238 amino acids (not heteromeric)

PSPA_HYDTT / D3DFG8 Phosphoserine phosphatase 1; PSP 1; PSPase 1; Metal-independent phosphoserine phosphatase 1; iPSP1; O-phosphoserine phosphohydrolase 1; EC 3.1.3.3 from Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)
D3DFG8 phosphoserine phosphatase (EC 3.1.3.3) from Hydrogenobacter thermophilus
PFams: His_Phos_1
211 amino acids: PaperBLAST, CDD, Compare to cluster

SERCL_ARATH / F4KI56 Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 from Arabidopsis thaliana (Mouse-ear cress)
PFams: His_Phos_1
238 amino acids: PaperBLAST, CDD, Compare to cluster

A0A0H2XA29 Phosphoglycerate mutase
214 amino acids: PaperBLAST, CDD, Compare to cluster

A0A3D8VK77 Histidine phosphatase family protein
213 amino acids: PaperBLAST, CDD, Compare to cluster

N9V397 Phosphoglycerate mutase family protein, putative
205 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 3 409-411 amino acids (not heteromeric)

SERB2_MYCTU / O53289 Phosphoserine phosphatase SerB2; PSP; PSPase; O-phosphoserine phosphohydrolase; Protein-serine/threonine phosphatase; EC 3.1.3.3; EC 3.1.3.16 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
O53289 phosphoserine phosphatase (EC 3.1.3.3) from Mycobacterium tuberculosis
PFams: ACT_6, ACT_PSP_2, Hydrolase, HAD, Hydrolase_3
409 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_MYCA1 / A0QJI1 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Mycobacterium avium (strain 104)
PFams: ACT_6, ACT_PSP_2, Hydrolase, HAD, Hydrolase_3
411 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_STRCO / Q9S281 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
PFams: ACT_6, ACT_PSP_2, Hydrolase, HAD, Hydrolase_3
410 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 4 309-328 amino acids (not heteromeric)

b4388 phosphoserine phosphatase (EC 3.1.3.3) from Escherichia coli K-12 substr. MG1655
P0AGB0 phosphoserine phosphatase (EC 3.1.3.3) from Escherichia coli (strain K12)
SERB_ECOLI / P0AGB0 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Escherichia coli (strain K12)
CH_024035 phosphoserine phosphatase; EC 3.1.3.3 from Escherichia coli K12
PFams: DUF5609, Hydrolase, HAD, Hydrolase_3
322 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_YEAST / P42941 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
PFams: Hydrolase, HAD, Hydrolase_3
309 amino acids: PaperBLAST, CDD, Compare to cluster

SERB_VIBCH / Q9KPM2 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
PFams: DUF5609, Hydrolase, HAD, Hydrolase_3
328 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 5 205-237 amino acids (not heteromeric)

THRH_PSESM / Q883R9 Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 from Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)
PFams: Hydrolase, HAD
237 amino acids: PaperBLAST, CDD, Compare to cluster

THRH_PSEAE / Q9I2Y2 Phosphoserine phosphatase ThrH; PSP; PSPase; EC 3.1.3.3 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PFams: Hydrolase, HAD
205 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 6 249-260 amino acids (not heteromeric)

PSP_BACSU / P94512 Phosphoserine phosphatase; PSP; EC 3.1.3.3 from Bacillus subtilis (strain 168)
PFams: Hydrolase, HAD_2, Hydrolase_like
260 amino acids: PaperBLAST, CDD, Compare to cluster

PSP_THET2 / Q72H00 Phosphoserine phosphatase; PSP; EC 3.1.3.3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
PFams: Hydrolase, HAD_2, Hydrolase_like
249 amino acids: PaperBLAST, CDD, Compare to cluster

Singletons (0/10 heteromeric)

B6YX36 phosphoserine phosphatase (EC 3.1.3.3) from Thermococcus onnurineus
PFams: Hydrolase, HAD
194 amino acids: PaperBLAST, CDD
(similar to SwissProt::Q58989 from Cluster 1, but similarity to seed sequence is below thresholds)

SERC_ARATH / O82796 Phosphoserine phosphatase, chloroplastic; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Arabidopsis thaliana (Mouse-ear cress)
PFams: Hydrolase, HAD
295 amino acids: PaperBLAST, CDD
(similar to BRENDA::P78330 from Cluster 1, but similarity to seed sequence is below thresholds)

SERB1_MYCTU / P9WGJ3 Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
PFams: Hydrolase, HAD, Hydrolase_3
308 amino acids: PaperBLAST, CDD

SERB_DROME / Q9VSY6 Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 from Drosophila melanogaster (Fruit fly)
PFams: Hydrolase, HAD
270 amino acids: PaperBLAST, CDD
(similar to BRENDA::P78330 from Cluster 1, but similarity to seed sequence is below thresholds)

A0A6B4WGC7 DUF1015 domain-containing protein
440 amino acids: PaperBLAST, CDD

F9VNX9 Phosphoserine aminotransferase; EC=2.6.1.52
372 amino acids: PaperBLAST, CDD

P72649 Phosphoglycerate mutase
349 amino acids: PaperBLAST, CDD

Q9K8N3 BH2972 protein
276 amino acids: PaperBLAST, CDD

Echvi_2777 fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) from Echinicola vietnamensis KMM 6221, DSM 17526
PFams: HAD, 2-Hacid_dh, 2-Hacid_dh_C, NAD_binding_2
630 amino acids: PaperBLAST, CDD

CA265_RS22635 phosphoserine phosphatase (EC 3.1.3.3) from Pedobacter sp. GW460-11-11-14-LB5
PFams: HAD, 2-Hacid_dh
433 amino acids: PaperBLAST, CDD