Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028313366.1 G491_RS0101815 2-hydroxyacid dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000429905.1:WP_028313366.1 Length = 326 Score = 152 bits (384), Expect = 2e-41 Identities = 97/272 (35%), Positives = 145/272 (53%), Gaps = 20/272 (7%) Query: 33 EELLEKIKD-ADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGIIVVN 91 EEL + D A+VL+ G + +++++ KL+ IG G +IDV+ A EKG+ VV Sbjct: 39 EELKPVVMDRAEVLLAPLGYYLGKEIMDACPKLRAIGSNTTGHPHIDVDYAREKGVKVVT 98 Query: 92 APDASSI-----SVAELTMGLMLAAARNIPQATASLKRGEWDRKRFKGIELYGK-TLGVI 145 D AELT GL++A RNI S+ G+W R F G + + +LGV Sbjct: 99 LKDHQDFLDTITPTAELTWGLIIALTRNIVPGFKSVLDGQWARWPFGGKAMLSRMSLGVA 158 Query: 146 GLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDDINELCKRADFITLHVPLT 205 GLGR+G+ AFGM++ YDP++ K + G+ + + EL + +D +T+H+P Sbjct: 159 GLGRLGKLTASYGVAFGMDVKYYDPFVEKSPVD--GITKLSSLEELVESSDIVTIHIPHE 216 Query: 206 PKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEE----- 260 P+T ++ E K A VN +RG L+D AL +AL+ GK+ AA+DV + E Sbjct: 217 PETENLFSAEMFEKFKDGAFFVNTSRGELVDHDALLKALESGKLAGAAVDVLDGEFDPDF 276 Query: 261 --PPKDNPLLTL----DNVIGTPHQGASTEEA 286 D PL+ DN+I TPH G ST +A Sbjct: 277 GSKVLDQPLVKYAQEHDNLIITPHIGGSTLDA 308 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: 401 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: 326 Length adjustment: 31 Effective length of query: 493 Effective length of database: 295 Effective search space: 145435 Effective search space used: 145435 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