Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_027456447.1 K420_RS0101245 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000519045.1:WP_027456447.1 Length = 317 Score = 165 bits (417), Expect = 3e-45 Identities = 104/277 (37%), Positives = 154/277 (55%), Gaps = 17/277 (6%) Query: 46 AIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEH 105 A+ + ++ + I A P LK+IA + G +NVD+ A RGI+V N TV EH Sbjct: 43 AVAITNKVPLDAAAIAALPELKMIAVSATGTNNVDLDACRARGIVVSNIRGYAEHTVPEH 102 Query: 106 SIGLMLALARKIAIADRSVKEGKWEKNRFMGI------ELNGKTLGIIGMGRIGSQVVVR 159 I L+LAL+R + ++ G W+++ + +L+G TLG+IG G +G+ V Sbjct: 103 VIALLLALSRNLVAWRETLLAGCWQQSSQFCLFDHPIRDLHGATLGLIGSGTLGNGVARL 162 Query: 160 TKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFK 219 +AFGM ++ + ++AA + T +L ++D +++H PLTPET LI E E + Sbjct: 163 AEAFGMRVLRAE----RKAAATVRPGYTAFGDVLAQADAISLHCPLTPETTGLIGEAELQ 218 Query: 220 LMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVF-EEEPPEGSP-----LLELEN 273 MK +A ++N ARGGI+DE AL RAL +G IAGA DV E PP G P LL N Sbjct: 219 AMKPSALLINTARGGIVDEAALIRALTEGWIAGAGFDVITAEPPPAGHPMVDPALLARPN 278 Query: 274 VVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRN 310 +LTPH+ S+ A + A + + I+ F G PRN Sbjct: 279 FLLTPHVAWSSRPAMQALADQLIDNIE-AFAAGTPRN 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: 316 Number of extensions: 11 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: 317 Length adjustment: 31 Effective length of query: 494 Effective length of database: 286 Effective search space: 141284 Effective search space used: 141284 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