Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_013841723.1 DESRU_RS08625 2-hydroxyacid dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000215085.1:WP_013841723.1 Length = 313 Score = 279 bits (714), Expect = 9e-80 Identities = 151/307 (49%), Positives = 211/307 (68%), Gaps = 4/307 (1%) Query: 2 VKILVTDPLHEDAIKILEEVGEVEVATGLTKEE-LLEKIKDADVLVVRSGTKVTRDVIEK 60 +KI+VT+ + E+ ++IL E+GEV L K + L E IKDAD L+VR+ TKVT+ ++ + Sbjct: 1 MKIVVTELIWEEGLEILRELGEVVYDQTLWKSDNLAEIIKDADALIVRNQTKVTKALMGQ 60 Query: 61 AEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATA 120 A LKV+GR GVG+DNIDV AA E GI VV A +A++ISVAE M + +R + +A+ Sbjct: 61 APNLKVVGRLGVGLDNIDVAAAKEAGIKVVFARNANAISVAEYVFSAMFSFSRPLEKASQ 120 Query: 121 SLKRGEWDRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIP--KEVAE 178 +K+G W+RK F E+YGKTLG++G+G IG ++ RAKAFGM +IGYDP++P + Sbjct: 121 DVKQGNWNRKLFTREEIYGKTLGLVGVGEIGARLASRAKAFGMKVIGYDPFLPPYELACT 180 Query: 179 SMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEK 238 +GV + + + AD+I+LHVPL KTR++I +E++A MKK + I+N ARGG+I+E+ Sbjct: 181 DIGVSMT-SLETVLAEADYISLHVPLNDKTRNLINKERLATMKKTSYIINTARGGVINEE 239 Query: 239 ALYEALKEGKIRAAALDVFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQI 298 LYEA+K I AALDV E+EPP N LL LDN+I TPH TEEAQ +VA + Sbjct: 240 DLYEAVKAQIIAGAALDVLEKEPPTGNKLLELDNIIVTPHIAGLTEEAQVRTSELVAREC 299 Query: 299 KKVLRGE 305 KVL G+ Sbjct: 300 AKVLCGQ 306 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: 423 Number of extensions: 21 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