Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_013819322.1 METME_RS13620 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000214665.1:WP_013819322.1 Length = 322 Score = 162 bits (410), Expect = 2e-44 Identities = 103/298 (34%), Positives = 162/298 (54%), Gaps = 10/298 (3%) Query: 18 SELEEVAEVVVNTT---ITPEELLDAIKDFDAIVVRSRTKVTREVIEAAP-RLKIIARAG 73 ++L+E +V +N ++P E A++ +DA+ + EV+ R KI+ G Sbjct: 17 AKLQERYDVSLNRDDRPLSPAEFKRALQQYDAVCPTVCDSLPAEVLNVPDKRCKILGNFG 76 Query: 74 VGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWE--- 130 VG +++D+ AA +G++V N P + + A+ ++ L+L AR+ A DR V+ G W+ Sbjct: 77 VGYNHIDIAAAKQQGLIVTNTPGVLTESTADIAMTLLLMSARRGAEGDRLVRAGLWKGWC 136 Query: 131 KNRFMGIELNGKTLGIIGMGRIGSQVVVRTK-AFGMDIMVYDPY-ISKEAAEEMGVTVTD 188 M ++ G TLG+IG GRI + + FGM IM P +E +E+ D Sbjct: 137 PTHMMSSDVTGATLGLIGFGRIAQAMARKAHHGFGMKIMYVKPSPAQQEVVDELRAIRCD 196 Query: 189 -LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKD 247 +ETLL D V++H P ETRHL++++ LMK +A ++N ARG ++D AL AL+D Sbjct: 197 TVETLLPLCDFVSLHCPGGNETRHLMNDERLSLMKPSAHLINTARGDVVDSQALISALRD 256 Query: 248 GEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQG 305 IAGA LDV+E EP L L+NV L PH+G++T + V + + F G Sbjct: 257 KRIAGAGLDVYEGEPNIDPGFLALDNVSLLPHLGSATIATRTAMGQKVLDNLAAYFAG 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: 319 Number of extensions: 10 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: 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