Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_051181594.1 G579_RS0112525 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000423825.1:WP_051181594.1 Length = 330 Score = 178 bits (452), Expect = 2e-49 Identities = 113/290 (38%), Positives = 165/290 (56%), Gaps = 20/290 (6%) Query: 34 PEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVIN 93 PE L D ++ D IV+ ++T ++ E + APRLK+I A G +NVD+ AA GI V N Sbjct: 48 PEALNDHLQAAD-IVISNKTVISAEALRQAPRLKLICIAATGTNNVDLAAAGALGIPVCN 106 Query: 94 APESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEK--------NRFMGIELNGKTLG 145 + +V +H+ LMLAL ++ V G W + +RF EL GKTLG Sbjct: 107 VRNYATPSVVQHTFALMLALRNRLFDYHGDVMAGAWARAGQFCFLDHRFQ--ELAGKTLG 164 Query: 146 IIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPL 205 I+G G +G V +AFGM+++V ++ E + L LL + D++++H PL Sbjct: 165 IVGFGTLGQAVARVAEAFGMEVLVAQRPGAQPRTERL-----PLRELLPQVDVLSLHCPL 219 Query: 206 TPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPP-E 264 TPETR LI D M+ A +VN ARGGI+DE AL AL+ G + GA +DV EEPP Sbjct: 220 TPETRGLIDADALARMRPDALLVNTARGGIVDEAALAAALRAGRLGGAGVDVLAEEPPVH 279 Query: 265 GSPLL--ELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 GSPLL ++ +++TPHI ++ EA++ +A I+ F G PRN++ Sbjct: 280 GSPLLAPDVPRLIVTPHIAWASREARQRMVDELAANIR-AFLAGMPRNLV 328 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: 367 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 525 Length of database: 330 Length adjustment: 31 Effective length of query: 494 Effective length of database: 299 Effective search space: 147706 Effective search space used: 147706 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