Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_068460615.1 APY04_RS05785 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_001541235.1:WP_068460615.1 Length = 322 Score = 168 bits (425), Expect = 3e-46 Identities = 101/314 (32%), Positives = 164/314 (52%), Gaps = 9/314 (2%) Query: 1 MSRMKVLIADSINEKGISELEEVAEVVVN---TTITPEELLDAIKDFDAIVVRSRTKVTR 57 MS+ K+LI + + +V+ + IT EE+L+ K DAI++ K + Sbjct: 1 MSKKKILITWPLPPAAMERARATYDVIAHGDDPKITIEEMLETAKSVDAILLTLNEKCPK 60 Query: 58 EVIEAAPR-LKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARK 116 VI+ P +K I+ +G D++D++A RGI V NAP ++ AE ++ L+L AR+ Sbjct: 61 AVIDQIPENIKCISTFSIGFDHIDLEACKARGIKVGNAPHGVTVATAEIAMLLLLGAARR 120 Query: 117 IAIADRSVKEGKW---EKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY 173 + +R ++ W + + +G L+ K LGI G G+IG + R + F M+I YD Y Sbjct: 121 ASEGERMIRTRSWPGWQPLQLVGQRLDNKKLGIYGFGKIGQALAQRARGFDMEIHYYDIY 180 Query: 174 ISKEAAEEM--GVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCA 231 +K E V L++LL S+ +I+ P TPETR+ ++D + + A +VN A Sbjct: 181 RAKPEVEAKYNAVYHDSLDSLLSVSEFFSINAPSTPETRYFFNKDVIEKLPQGAIVVNTA 240 Query: 232 RGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDA 291 RG +++++ + ALK G +A A LDVF EP +L N L PH+G++ EA+ Sbjct: 241 RGDLVNDEDMIAALKSGRLAYAGLDVFAGEPKINEGYYDLPNTFLFPHLGSAAIEARNQM 300 Query: 292 AIIVANEIKTVFQG 305 + I F G Sbjct: 301 GFEALDNIDAFFAG 314 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: 385 Number of extensions: 24 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: 322 Length adjustment: 31 Effective length of query: 494 Effective length of database: 291 Effective search space: 143754 Effective search space used: 143754 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