Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012466797.1 CLIM_RS09495 2-hydroxyacid dehydrogenase
Query= curated2:O29445 (527 letters) >NCBI__GCF_000020465.1:WP_012466797.1 Length = 269 Score = 97.4 bits (241), Expect = 6e-25 Identities = 88/280 (31%), Positives = 137/280 (48%), Gaps = 36/280 (12%) Query: 34 ELIREVP-KYEAIVVRSQTKVDAEVIQAAKNLKIIGRAGVGVDNIDINAATQRGIVVVNA 92 EL+ VP +Y I V +D +++ LK I + GVG DN+ A QRG VV+ Sbjct: 16 ELLETVPSEYAEIAVIGSKPIDLKLMPC---LKGIFKCGVGTDNVPFKEAEQRG-VVIGL 71 Query: 93 PGGNTI-----STAEHAIALMLAAARKIPQADRSVKEGKWERKKFMGIELRGKTAGVIGL 147 P T TA A+ L+ R + ++ K + F+G K VIG Sbjct: 72 PSDQTRRYIFEETANFAVYLIF---RMLYNDLGTLDPWKKSSRLFLG----NKKVLVIGQ 124 Query: 148 GRVGFEVAKRCKALEMNVLAYDPFVSKERAEQIGVKLVDFDTLLASSDVITVHVPRTKET 207 G +G V + + + VL +D V+KE + +L++ +DV+T+H+P +ET Sbjct: 125 GNIGKLVTAKLEPF-VEVLTFDIAVNKED---------ELRSLISLADVVTLHIPLNEET 174 Query: 208 IGLIGKGQFEKMKDGVIVVNAARGGIVDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPL 267 I + MKDG +VN ARG IV+E AL+E I +G++ AA DV+ KEP L Sbjct: 175 HNFIDVEKMAWMKDGAAIVNTARGPIVNEDALHEEILSGRL-HAAFDVFWKEP--YQGKL 231 Query: 268 LKLD--NVVTTPHIAASTREAQLNVGMIIAEDIVNMAKGL 305 +K D + TPH++++ + + +A+D K L Sbjct: 232 MKYDPESFFMTPHVSSNCEDFLIG----LAQDCREFVKSL 267 Lambda K H 0.317 0.136 0.376 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: 295 Number of extensions: 16 Number of successful extensions: 2 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: 527 Length of database: 269 Length adjustment: 30 Effective length of query: 497 Effective length of database: 239 Effective search space: 118783 Effective search space used: 118783 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 (21.6 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