Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012385749.1 BIND_RS14265 3-phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000019845.1:WP_012385749.1 Length = 331 Score = 206 bits (525), Expect = 8e-58 Identities = 121/326 (37%), Positives = 188/326 (57%), Gaps = 8/326 (2%) Query: 6 VLIADSINEKGISELEEVAEVVVNTT--ITPEELLDAIKDFDAIVVRSRTKVTREVIEAA 63 +L+A I+E G+ L + + ++ ++ E + DAI++R++ + VI+ A Sbjct: 4 ILVAGRIHEAGLDILRNASGITLDLVDEVSTESYAPLVDRADAILIRTQP-LPESVIDRA 62 Query: 64 PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRS 123 +LK ++R GVG D VDV+A T R I + + S +VAEH++ LMLA+A+++ + D + Sbjct: 63 QKLKFVSRHGVGYDVVDVEALTRRNIPLAIVGDVNSRSVAEHAMMLMLAVAKRVCVYDAA 122 Query: 124 VKEGKWE-KNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEM 182 + GKW +N +++GKTL +IG GRIG V + F M I+ YDP++ + A + Sbjct: 123 TRAGKWGIRNDLYATDISGKTLLLIGFGRIGRLVASMARGFDMTILAYDPFLDEAAIKAA 182 Query: 183 GVTVT-DLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDAL 241 G T DLE LR +D V++H+P P L+ E E MK A ++N ARGG++DE AL Sbjct: 183 GAIPTRDLEGALRSADFVSLHMP-PPRNGALLGESELASMKPGAILINTARGGVVDEKAL 241 Query: 242 YRALKDGEIAGAALDVFEEEPPEGS-PLLELENVVLTPHIGASTSEAQRDAAIIVANEIK 300 +AL DG +AGA LDVF +EPP PLL+++ V+LTPH T E A+ + I Sbjct: 242 AKALTDGRLAGAGLDVFTQEPPPADHPLLQMDRVILTPHSAVMTRECAARMAVSASRNIL 301 Query: 301 TVFQGGA-PRNVLNMPVMDSETYKSL 325 F G P V+N V+ + +S+ Sbjct: 302 DYFAGRLDPSLVVNGEVLSAPARESV 327 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: 370 Number of extensions: 14 Number of successful extensions: 5 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: 331 Length adjustment: 31 Effective length of query: 494 Effective length of database: 300 Effective search space: 148200 Effective search space used: 148200 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