Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_019867321.1 METMI_RS0116070 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000384075.1:WP_019867321.1 Length = 323 Score = 169 bits (428), Expect = 1e-46 Identities = 105/320 (32%), Positives = 175/320 (54%), Gaps = 10/320 (3%) Query: 1 MSRMKVLIADSINEKGISELEEVAEVVVNTT---ITPEELLDAIKDFDAIVVRSRTKVTR 57 M++ K+++ + ++L+ + +V +N + +T +EL A++ DA++ +T Sbjct: 1 MNKPKIIVTRRWPAEVENQLKALYDVQLNESDIPMTADELKLAMQTADALLPTVTDPITS 60 Query: 58 EVIEAAPR-LKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARK 116 ++I R +K+I GVG +N+D+ +A G++V N P + A+ ++ L+L AR+ Sbjct: 61 DIIGVENRRVKVIGNFGVGYNNIDINSAKGHGMVVTNTPHVLTDCTADIAMLLLLMSARR 120 Query: 117 IAIADRSVKEGKWE---KNRFMGIELNGKTLGIIGMGRIGSQVVVRTK-AFGMDIMVYDP 172 A +R + +W+ + +G ++ GKTLG+IG GRI + + FGM I+ Y P Sbjct: 121 AAEGERLILNKQWKGWGPTQLVGQKVTGKTLGLIGFGRIAQAMARKAHHGFGMKILFYVP 180 Query: 173 YISKEAAEE--MGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNC 230 A E V LE LL E+ V++H P T+HL++ KLM+ +A ++N Sbjct: 181 SAPDPAIVEELQAVRCGSLEELLTEAHFVSLHCPGGAATKHLLNGQRLKLMRPSAHLINT 240 Query: 231 ARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRD 290 ARG ++D DAL +ALK+ IAGA LDV+E EP LEL+NV L PH+G+++ E + Sbjct: 241 ARGDVVDSDALIKALKERWIAGAGLDVYENEPHLNPGFLELDNVTLLPHLGSASEETRVA 300 Query: 291 AAIIVANEIKTVFQGGAPRN 310 V I F G P + Sbjct: 301 MGNRVLANIAAFFAGSEPED 320 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: 386 Number of extensions: 16 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: 323 Length adjustment: 31 Effective length of query: 494 Effective length of database: 292 Effective search space: 144248 Effective search space used: 144248 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