Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Dsui_0124 Dsui_0124 lactate dehydrogenase-like oxidoreductase
Query= curated2:O27051 (525 letters) >FitnessBrowser__PS:Dsui_0124 Length = 322 Score = 164 bits (416), Expect = 3e-45 Identities = 99/280 (35%), Positives = 158/280 (56%), Gaps = 16/280 (5%) Query: 46 AIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEH 105 +I + ++ ++ ++ P+LK++A A G +NVD++AA +GI+V N TV EH Sbjct: 44 SIAIVNKLPISGALMARLPQLKMVAVAATGTNNVDLEAARRQGIVVSNIQGYAVHTVPEH 103 Query: 106 SIGLMLALARKIAIADRSVKEGKWEKNRFMGI------ELNGKTLGIIGMGRIGSQVVVR 159 L+LAL+R + +SV EG+W++ +L+G TLG++G G +G VV Sbjct: 104 VFSLLLALSRNLLAYRQSVAEGRWQRAEQFCFFDHPIRDLHGATLGVVGGGSLGQGVVRL 163 Query: 160 TKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFK 219 +AFGM ++ + ++ A + T T+L E+D +++H PLT ETRHLI E + Sbjct: 164 AQAFGMKVLQAE----RKGAAVVRPGYTAFATVLAEADALSLHCPLTAETRHLIGAAELQ 219 Query: 220 LMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEG-----SP-LLELEN 273 MK +A ++N ARGG++DE AL RAL++G IAGA DV EPP SP LL N Sbjct: 220 AMKPSALLINTARGGLVDEAALARALREGWIAGAGFDVLTAEPPTDDHPLLSPDLLAAPN 279 Query: 274 VVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVLN 313 +LTPH+ +++ A + A + + ++ +G N Sbjct: 280 FLLTPHVAWASAPAMQALADQLIDNLEAFARGAMTPGAAN 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: 344 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: 322 Length adjustment: 31 Effective length of query: 494 Effective length of database: 291 Effective search space: 143754 Effective search space used: 143754 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 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