Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_020563164.1 A3OW_RS0109280 D-glycerate dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000372865.1:WP_020563164.1 Length = 324 Score = 188 bits (477), Expect = 3e-52 Identities = 118/312 (37%), Positives = 176/312 (56%), Gaps = 10/312 (3%) Query: 3 KILVTD--PLHEDA-IKILEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIE 59 K++VT P+ +A +K L +V E +T +EL ++ AD L+ +T DV+ Sbjct: 5 KVVVTRKWPVEVEARLKELYDVTLNESDVPMTADELKRALQTADALLPTVTDPITADVLR 64 Query: 60 KAEKLK-VIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQA 118 K +IG GVG +NID+ AA E+G+ V N PD + A++ M L+L +AR Q Sbjct: 65 VENKRAGIIGNFGVGYNNIDIAAAREQGLTVTNTPDVLTDCTADIAMLLLLMSARRASQG 124 Query: 119 TASLKRGEWDR---KRFKGIELYGKTLGVIGLGRIGQQVVKRAK-AFGMNIIGYDPYIP- 173 ++ W + G ++ GKTLG+IGLGRI Q + K+A FGMNI+ Y P P Sbjct: 125 ERLVRSRRWTGWCPTQMLGQKVTGKTLGLIGLGRIAQAMAKKAHHGFGMNILFYTPRNPP 184 Query: 174 -KEVAESMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARG 232 ++V + +G + I +L +ADF++LH P +P+ H+I +++ M+ + ++N ARG Sbjct: 185 PRQVVDDLGAVRCETIEDLLAQADFVSLHCPGSPENHHLINEQRLKRMRPSTHLINTARG 244 Query: 233 GLIDEKALYEALKEGKIRAAALDVFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGT 292 ++D AL +ALKEG I A LDVFE EP LL LDN+ PH G++TEE + A G Sbjct: 245 DVVDNIALCKALKEGWIAGAGLDVFEGEPNVYPGLLELDNIALLPHLGSATEETRIAMGN 304 Query: 293 IVAEQIKKVLRG 304 V E I G Sbjct: 305 RVIENISAFFAG 316 Lambda K H 0.316 0.137 0.372 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: 383 Number of extensions: 24 Number of successful extensions: 5 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: 524 Length of database: 324 Length adjustment: 31 Effective length of query: 493 Effective length of database: 293 Effective search space: 144449 Effective search space used: 144449 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 (21.5 bits) S2: 50 (23.9 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