Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_041936837.1 RL_RS29355 2-hydroxyacid dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000009265.1:WP_041936837.1 Length = 313 Score = 167 bits (424), Expect = 4e-46 Identities = 97/269 (36%), Positives = 153/269 (56%), Gaps = 6/269 (2%) Query: 32 KEELLEKI-KDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGIIVV 90 ++EL+ ++ KD + R + +++ + KL+++ GVG D ID+ A GI V Sbjct: 35 RQELISRVGKDIRAIATRGELGASAELMAQLPKLEIVSCYGVGTDAIDLSYARANGIRVT 94 Query: 91 NAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKRFKGI-ELYGKTLGVIGLGR 149 N PD + VA++ +GL+LA AR IPQA ++ G+W + + GK +G+ G+GR Sbjct: 95 NTPDVLTEDVADIALGLLLATARQIPQADVLVRSGQWGSVAMPLVTRVSGKKVGIAGMGR 154 Query: 150 IGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDDINELCKRADFITLHVPLTPKTR 209 IG+ + +RA AFG +I + + K+VA + +L+ L ADF+ + VP T Sbjct: 155 IGKAIARRAAAFGCDISYFARHNHKDVAYAYEPDLI----ALADWADFLIVIVPGGEATM 210 Query: 210 HIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEEPPKDNPLLT 269 II E + + N I++N +RG +DE+AL AL++ I+AA LDVF EP D LT Sbjct: 211 KIINAEVLKALGPNGILINVSRGTTVDEEALIAALQDRTIQAAGLDVFLNEPKIDARFLT 270 Query: 270 LDNVIGTPHQGASTEEAQKAAGTIVAEQI 298 L NV+ PH G+ T E +KA G +V + + Sbjct: 271 LGNVVLQPHHGSGTVETRKAMGQLVRDNL 299 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: 344 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: 524 Length of database: 313 Length adjustment: 31 Effective length of query: 493 Effective length of database: 282 Effective search space: 139026 Effective search space used: 139026 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