Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_027722163.1 H589_RS0111585 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000425265.1:WP_027722163.1 Length = 320 Score = 182 bits (462), Expect = 2e-50 Identities = 118/322 (36%), Positives = 178/322 (55%), Gaps = 16/322 (4%) Query: 4 MKVLIADSIN----EKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREV 59 MK+ I D + +ELE++ E+ V ++++ + + I++ ++T +T + Sbjct: 1 MKITILDGYTVNPGDNPWTELEKLGELTVYDRTDQNQIVERSINAE-IIMTNKTVITENI 59 Query: 60 IEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAI 119 I + P LK I G + V++ AAT GI V N P + +VA+H ++L A ++++ Sbjct: 60 ISSLPNLKYIVVLATGYNAVNINAATACGITVSNIPSYSPPSVAQHVFAMLLGFANQVSL 119 Query: 120 ADRSVKEGKWE-KNRFMG-----IELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY 173 D +VK G+W +N F EL K +GI+G G IG +V + AFGM++M Y P Sbjct: 120 HDHAVKNGEWAAQNDFCFWKTALFELKDKKIGIVGFGDIGQKVGIIANAFGMEVMAYAPR 179 Query: 174 ISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARG 233 K + E L RESD+V++H PLT + + I + MK TA I+N ARG Sbjct: 180 -PKSTPDYSPFKFCSREELFRESDVVSLHCPLTDDNKGFIDKALISSMKSTAIIINTARG 238 Query: 234 GIIDEDALYRALKDGEIAGAALDVFEEEPP-EGSPLLELENVVLTPHIGASTSEAQ-RDA 291 +I+E L AL + IAGAALDV E EP G+PL N+++TPHI +T EA+ R + Sbjct: 239 PLINEKDLAEALTNRVIAGAALDVVENEPMLPGNPLAGAPNLIITPHIAWATLEARSRLS 298 Query: 292 AIIVANEIKTVFQGGAPRNVLN 313 AI V N T FQ G+P NV+N Sbjct: 299 AIAVQN--VTAFQNGSPINVVN 318 Lambda K H 0.316 0.135 0.366 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: 367 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 525 Length of database: 320 Length adjustment: 31 Effective length of query: 494 Effective length of database: 289 Effective search space: 142766 Effective search space used: 142766 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