Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_068174208.1 HTA01S_RS18420 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_001592305.1:WP_068174208.1 Length = 331 Score = 172 bits (435), Expect = 2e-47 Identities = 106/322 (32%), Positives = 171/322 (53%), Gaps = 8/322 (2%) Query: 3 RMKVLIADSINEKGISELEEVAEVVVN---TTITPEELLDAIKDFDAIVVRSRTKVTREV 59 R +LIA ++ + ++ L E EV N TP +L++ ++ ++ ++ + Sbjct: 4 RPAILIARAVFPEVVARLREHFEVETNEQDAPFTPAQLIERLQGKVGVMTTGSERIDAAL 63 Query: 60 IEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAI 119 + A P+L++ A VG +N DV A T G++ N P+ + T A+ L++A AR+I Sbjct: 64 LAACPQLRVAANIAVGYNNFDVPAMTAAGVLATNTPDVLTETTADFGFALLMATARRICE 123 Query: 120 ADRSVKEGKWEK---NRFMGIELNGKTLGIIGMGRIGSQVVVR-TKAFGMDIMVYDPYIS 175 ++ ++ G+W + + F G E++G TLGI+GMGRIG + R FGM+++ ++ Sbjct: 124 SEHFLRAGQWNRWALDMFAGAEVHGSTLGILGMGRIGQAIARRGAHGFGMNVIYHNRSRL 183 Query: 176 KEAAEEM-GVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGG 234 +E LL+++D + + VP + E+ H I E MK TA +VN ARGG Sbjct: 184 DTGSEAACRARYVSKAELLQQADHLVLVVPYSAESHHTIGAAELAQMKPTATLVNIARGG 243 Query: 235 IIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAII 294 I+D+ AL AL++ IA A LDVFE EP LL + NVVLTPHI ++T + A + Sbjct: 244 IVDDAALAVALREKRIAAAGLDVFEGEPKVHPDLLTVPNVVLTPHIASATLPTRLAMANL 303 Query: 295 VANEIKTVFQGGAPRNVLNMPV 316 A+ + G LN V Sbjct: 304 AADNLIAYLGTGQALTPLNPSV 325 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: 372 Number of extensions: 14 Number of successful extensions: 3 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