Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 7026059 Shewana3_3201 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= curated2:Q58424 (524 letters) >FitnessBrowser__ANA3:7026059 Length = 317 Score = 158 bits (399), Expect = 3e-43 Identities = 99/292 (33%), Positives = 155/292 (53%), Gaps = 12/292 (4%) Query: 21 VGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVE 80 +GE E++ + + A++ V+ + T + + + + KLK IG G + +D+ Sbjct: 24 LGEFSCFARTPSAEIIPRAQHAEI-VLTNKTPLDANTLAQLPKLKYIGVLATGTNVVDLA 82 Query: 81 AATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDR------KRFKG 134 AA E GI+V N P +VA++ +L + + ++ G+W Sbjct: 83 AAKELGIVVTNVPAYGPDAVAQMVFAHILHHTQAVAAHHQAVAAGQWSNCSDFCFTLMPL 142 Query: 135 IELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDDINELCKR 194 L GKTLG+IG G IGQQV K A AFGM ++ P+++ + + D + K Sbjct: 143 QSLKGKTLGLIGYGDIGQQVAKLALAFGMKVLVNTRTQPRDLPQGVSWTSRDTV---FKE 199 Query: 195 ADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAAL 254 +D ++LH PLTP+T +I + + LMK A+++N ARGGLIDE AL AL++GK+ A + Sbjct: 200 SDILSLHCPLTPETTELINAQTLELMKPQALLINTARGGLIDEAALATALRQGKV-FAGV 258 Query: 255 DVFEEEPPK-DNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGE 305 DV EPP DNPLLT N+ +PH +T+EA++ I + L GE Sbjct: 259 DVLSTEPPSADNPLLTAPNISISPHNAWATKEARQNLLNIATANLSAYLAGE 310 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: 359 Number of extensions: 14 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: 317 Length adjustment: 31 Effective length of query: 493 Effective length of database: 286 Effective search space: 140998 Effective search space used: 140998 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 09 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