Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 8501168 DvMF_1902 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= curated2:O27051 (525 letters) >FitnessBrowser__Miya:8501168 Length = 301 Score = 179 bits (455), Expect = 9e-50 Identities = 110/293 (37%), Positives = 170/293 (58%), Gaps = 17/293 (5%) Query: 4 MKVLIADS----INEKGISELEEVA-EVVVNTT---ITPEELLDAIKDFDAIVVRSRTKV 55 MKV I S +++ + L E E V+N T IT +E ++ ++ + + + Sbjct: 1 MKVAITTSSFAKFSDEPLRLLREAGIEYVLNPTGRAITEDEAIELLQGCIGVAAGTEP-L 59 Query: 56 TREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALAR 115 TR V++A P LK+I+R G G+D+VD AA + GI V N P++ ++ VAE ++G L L R Sbjct: 60 TRRVMQALPELKVISRCGTGMDSVDRAAAAELGIAVRNTPDAPTLAVAELTLGYALDLMR 119 Query: 116 KIAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYIS 175 ++ DR ++ G W+K MG L GK +G+IG GRIG +AFG ++ DP+ Sbjct: 120 LVSRMDRELRAGTWKKR--MGNLLAGKKVGLIGFGRIGRATGKLFEAFGCEVAFADPFAE 177 Query: 176 KEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGI 235 + M +++ LL +DIV++H +++ E LM+ +++N ARGG+ Sbjct: 178 SDTNARM-----EVDALLAWADIVSLHCSKPEGGGYILDEHRLGLMRPGTWVINAARGGL 232 Query: 236 IDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQ 288 IDE AL+ L G +AGAALDVF +EP EG PL +L NV+LTPH+G+ EA+ Sbjct: 233 IDEAALHALLASGHLAGAALDVFAKEPYEG-PLRDLPNVILTPHVGSYAVEAR 284 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: 356 Number of extensions: 15 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: 301 Length adjustment: 31 Effective length of query: 494 Effective length of database: 270 Effective search space: 133380 Effective search space used: 133380 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