Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028312068.1 H566_RS0114955 3-phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000482785.1:WP_028312068.1 Length = 345 Score = 154 bits (388), Expect = 6e-42 Identities = 102/274 (37%), Positives = 150/274 (54%), Gaps = 18/274 (6%) Query: 25 EVVVNTTITPEELLDAIKDFDAIV-VRSRTKVTREVIEAAPRLKIIARAG-VGVDN---V 79 ++ NT +L ++D +A+V +R RT++ V + P L++I++ G VG N + Sbjct: 28 KIFTNTVKGAGQLSVRLRDAEALVLIRERTRLNAAVFDKLPNLRVISQTGRVGRGNDSHL 87 Query: 80 DVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEK-------- 131 D+ A T RGI V + AE + L+LA R++ + G W++ Sbjct: 88 DLDACTARGIAVFEGT-GDPVAAAELTWALVLAAQRRLPQYVMKLIHGAWQQSGLKGATM 146 Query: 132 --NRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMG-VTVTD 188 N +G L G TLGI G GRIG V +AFGM +MV+ S+EAA G +T Sbjct: 147 PPNHGLGRVLRGSTLGIWGYGRIGRLVAGYGRAFGMKVMVWGSERSREAARADGYLTAES 206 Query: 189 LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDG 248 ESD++++H+ L+ TR LI+ D+ + MK TA VN +R +++ DAL R+L +G Sbjct: 207 RNQFFGESDVLSVHLRLSEATRGLITHDDLQRMKPTALFVNTSRAELVEPDALLRSLNNG 266 Query: 249 EIAGAALDVFEEEP-PEGSPLLELENVVLTPHIG 281 AALDVFE EP +G PLL LEN + TPHIG Sbjct: 267 RPGFAALDVFESEPILQGHPLLRLENTICTPHIG 300 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: 324 Number of extensions: 17 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: 345 Length adjustment: 32 Effective length of query: 493 Effective length of database: 313 Effective search space: 154309 Effective search space used: 154309 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: 51 (24.3 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