Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95; 2-oxoglutarate reductase; EC 1.1.1.399 (uncharacterized)
to candidate WP_024851661.1 N745_RS0108310 2-hydroxyacid dehydrogenase
Query= curated2:P73821 (554 letters) >NCBI__GCF_000526715.1:WP_024851661.1 Length = 330 Score = 159 bits (401), Expect = 2e-43 Identities = 99/277 (35%), Positives = 157/277 (56%), Gaps = 25/277 (9%) Query: 61 AEIIDIVPEYDAIML----RSATKVTEKIIQAGSQLKIIGRAGVGVDNIDVPAATRQGIV 116 A+ + + +Y+A+ + + V EK+ G +L ++ AG + +D+PAA + G+ Sbjct: 36 AKTVALAEDYNAVCVFVNDDISASVIEKLHDFGIRLILLRCAGF--NQVDLPAANQYGMT 93 Query: 117 VVNSPEGNTIAAAEHALAMMMALARHIPDANKSVKESKWERKQFIGTEVYKKTLGVVGLG 176 V+ P + +A AEHALAMMM+L R A V++ + + F+G +++ KT VVG G Sbjct: 94 VLRVPNYSPMAVAEHALAMMMSLNRKTYKAYNRVRDGNFSLEGFLGFDMFGKTAAVVGTG 153 Query: 177 KIGSHVAGVAKAMGMKLLAYDPFISQERAD--QIGCTLVDLDLLFSEADFITLHIPKTPE 234 IG +A + K +G+ +LAYD ++ D +G +LD L+ ++D I+LH+P E Sbjct: 154 HIGYEMARILKGLGLHVLAYDV---KQNPDVLALGIEYANLDTLYEQSDIISLHVPLFNE 210 Query: 235 TANLINAETLAKMKPTARIINCSRGGIIDEEALVTAIETAQIGGAALDVFAQ------EP 288 T +LIN ++AKMKP IIN SRGGI+D A++ A++T QIG +DV+ Q E Sbjct: 211 THHLINKTSIAKMKPGVMIINTSRGGILDASAVIDALKTGQIGYLGIDVYEQEADLFFED 270 Query: 289 LGE--------SRLREFSNVILTPHLGASTEEAQVNV 317 E RL F NV++T H G T+EA ++ Sbjct: 271 RSEQIIQDDIFERLLSFPNVLVTAHQGFYTKEALCHI 307 Lambda K H 0.318 0.135 0.375 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: 307 Number of extensions: 16 Number of successful extensions: 3 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: 554 Length of database: 330 Length adjustment: 32 Effective length of query: 522 Effective length of database: 298 Effective search space: 155556 Effective search space used: 155556 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: 51 (24.3 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