Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012675479.1 PERMA_RS06115 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000021565.1:WP_012675479.1 Length = 321 Score = 170 bits (431), Expect = 6e-47 Identities = 110/324 (33%), Positives = 185/324 (57%), Gaps = 18/324 (5%) Query: 4 MKVLIADSI---NEKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVI 60 MK++ D+ ++ +S E + + T E+ D + D D I++ ++ + REVI Sbjct: 1 MKIVFLDAKTVGDDIDLSVFEAFGDFIAYPTTKGSEVFDRVYDAD-IIITNKVIIDREVI 59 Query: 61 EAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIA 120 + A LK+I A G +NVD+ A ++GI V N ++ +V +H+ ++ + ++ Sbjct: 60 DYARDLKLICVAATGTNNVDILYAKEKGIAVTNVAGYSTESVVQHTFAMLFYILEQLRYY 119 Query: 121 DRSVKEGKW-EKNRFMGI-----ELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYI 174 D VK G++ E + F + E+NGK GIIG+G IG +V ++FG D++ + Sbjct: 120 DDYVKSGQYAESDIFTHLGRPFSEINGKRWGIIGLGTIGRRVGQVAESFGCDVIYHS--- 176 Query: 175 SKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGG 234 + E L+ LL+ SDIV+IH PL +TR+LI+ D+ LMK +A ++N RGG Sbjct: 177 TSGVKREERYREYPLDELLKTSDIVSIHAPLNEKTRNLITYDKISLMKPSAILLNLGRGG 236 Query: 235 IIDEDALYRALKDGEIAGAALDVFEEEPPEG-SPLLELEN---VVLTPHIGASTSEAQRD 290 I++E+ L RAL +G I+GA LDV E+EP + SPLL ++N +++TPHI ++ EA++ Sbjct: 237 IVNEEDLARALDEGLISGAGLDVLEKEPIDPYSPLLSIKNRDRLLITPHIAWTSIEARKR 296 Query: 291 AAIIVANEIKTVFQGGAPRNVLNM 314 +A I+ F G RN +++ Sbjct: 297 LIQEIAENIR-AFLNGKERNRVDL 319 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: 348 Number of extensions: 17 Number of successful extensions: 4 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: 525 Length of database: 321 Length adjustment: 31 Effective length of query: 494 Effective length of database: 290 Effective search space: 143260 Effective search space used: 143260 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