Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate BWI76_RS26540 BWI76_RS26540 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= curated2:O27051 (525 letters) >FitnessBrowser__Koxy:BWI76_RS26540 Length = 317 Score = 210 bits (534), Expect = 7e-59 Identities = 121/309 (39%), Positives = 191/309 (61%), Gaps = 7/309 (2%) Query: 5 KVLIADSINEKGISELEEVAEVVVNTT-ITPEELLDAIKDFDAIVVRSRTKVTREVIEAA 63 K+L+ I +G LE ++N + + E+++ I D D I+VR +K++ V EAA Sbjct: 4 KILLPQEIMAEGREYLESRGYQLINGSGMEEEDIIRDIGDCDGIIVRL-SKMSDRVFEAA 62 Query: 64 PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIA-DR 122 +LK++AR G G D VD+++A G++V+NAP + S++VAE +I ML +R + ++ Sbjct: 63 KKLKVVARHGAGYDTVDLESAKRHGVVVLNAPIANSMSVAELAIFYMLHCSRNFKLVQEK 122 Query: 123 SVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRT-KAFGMDIMVYDPYISKEAAEE 181 +++ W K R +EL+GKTLG+IG+G IGS+V ++ F M ++ YDPY +++ E Sbjct: 123 MLEDYYWAKLRTPKVELDGKTLGLIGVGNIGSRVAIKALHGFNMKVIAYDPYKTQQQIPE 182 Query: 182 MGVTVT-DLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDA 240 GV +T D + + ESD V++H P T ET + E +F +MK +A+ +N ARG ++DE A Sbjct: 183 -GVELTDDFDRIFTESDFVSLHCPTTAETTDFVGEKQFSMMKPSAYFINTARGKLVDEKA 241 Query: 241 LYRALKDGEIAGAALDVFEEEPPEGS-PLLELENVVLTPHIGASTSEAQRDAAIIVANEI 299 LY AL IAGA +DV ++EP + + P+ L N+V+ PHIGA+T EA A++ A I Sbjct: 242 LYHALSTHAIAGAGVDVLKKEPFDANDPIFSLSNIVIAPHIGAATIEATDRASLHSAIGI 301 Query: 300 KTVFQGGAP 308 V G P Sbjct: 302 DEVLSGKKP 310 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: 395 Number of extensions: 22 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: 317 Length adjustment: 31 Effective length of query: 494 Effective length of database: 286 Effective search space: 141284 Effective search space used: 141284 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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