Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012406157.1 BPHY_RS34745 2-hydroxyacid dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_000020045.1:WP_012406157.1 Length = 335 Score = 126 bits (316), Expect = 1e-33 Identities = 101/286 (35%), Positives = 133/286 (46%), Gaps = 8/286 (2%) Query: 42 LDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPV 101 L +L ++ DA I +T + + A KL A + +D+DAA++ G+ + Sbjct: 40 LTPAELADAACDADVIIAYRQTPGSRALFEALPKLAAFVRCAVDIRTIDVDAASELGVLI 99 Query: 102 FNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGH 161 A SV+E VIG +L L RG A AKA+ E RG G+IGYG Sbjct: 100 TQASAGFVPSVSEWVIGAMLDLARGTT-AYAKAYHRREAPAPKMGRELRGSTFGVIGYGQ 158 Query: 162 IGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMM 221 I L LA + GM V D + QV L DLL SD V P P T N+M Sbjct: 159 ISRYLCDLALAFGMRVIVSDPYATIDDARVHQVG-LDDLLAESDFVVCLAPATPQTANLM 217 Query: 222 GAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSP- 280 A+ + MKPG+ INA+RG +VD AL AL HLAG A+DV +D SP Sbjct: 218 NARAFAAMKPGAYFINAARGELVDDAALLAALERGHLAGCALDV-----GRAADQMPSPS 272 Query: 281 LCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN 326 L V+ TPHIGG T A E+ +E + + AVN Sbjct: 273 LAAHSRVIATPHIGGLTPGAIEHQSMETIAQTEALLQGRIPVGAVN 318 Lambda K H 0.318 0.135 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 274 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 410 Length of database: 335 Length adjustment: 30 Effective length of query: 380 Effective length of database: 305 Effective search space: 115900 Effective search space used: 115900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory