Align D-3-phosphoglycerate dehydrogenase 2; 3-PGDH 2; 2-oxoglutarate reductase; EC 1.1.1.95; EC 1.1.1.399 (characterized)
to candidate H281DRAFT_01746 H281DRAFT_01746 D-3-phosphoglycerate dehydrogenase
Query= SwissProt::P40510 (469 letters) >FitnessBrowser__Burk376:H281DRAFT_01746 Length = 335 Score = 129 bits (324), Expect = 1e-34 Identities = 101/315 (32%), Positives = 147/315 (46%), Gaps = 20/315 (6%) Query: 69 ATAIKIFKDQGYQVEFHKSSLPEDELIEKIKDVHAIGIRSKTRLTEKILQHARNLVCIGC 128 A A+ F D Y E + +L E L + ++ I +T + + L Sbjct: 22 AAALAKFADVTYNSEDRELTLTE--LADAAREADVIIAYRQTPAPRALFEALPKLAAFVR 79 Query: 129 FCIGTNQVDLKYAASKGIAVFNSPFSNSRSVAELVIGEIISLARQLGD--RSIELHTGTW 186 + VD+ A+ G+ V + +V+E VIG ++ LAR + H Sbjct: 80 CAVDIRTVDVDAASELGVLVTQASAGFIPAVSEWVIGAMLDLARGTTAYAEAYHRHEAPA 139 Query: 187 NKVAARCWEVRGKTLGIIGYGHIGSQLSVLAEAMGLHVLYYDIVTIMALGTARQVSTLDE 246 K+ E+RG T G+IGYG I L LA A G+ V+ D + +QV LD+ Sbjct: 140 PKMGR---ELRGSTFGVIGYGQISRYLCPLASAFGMRVIVSDPYATIDDTHVQQVG-LDD 195 Query: 247 LLNKSDFVTLHVPATPETEKMLSAPQFAAMKDGAYVINASRGTVVDIPSLIQAVKANKIA 306 LL +SDFV PATP+T +++A FA+MK GAY INA+RG +VD +L+ A++ +A Sbjct: 196 LLAESDFVVCLAPATPQTANLMNAQTFASMKAGAYFINAARGELVDDAALLAALERGHLA 255 Query: 307 GAALDVYPHEPAKNGEGSFNDELNSWTSELVSLPNIILTPHIGGSTEEAQSSIGIEVATA 366 G ALDV G D++ S EL + P +I TPHIGG T A +E Sbjct: 256 GCALDV----------GRAADQMPS--PELAAHPRVIATPHIGGLTPGAIEHQSMETVAQ 303 Query: 367 LSKYINEGNSVGSVN 381 G+VN Sbjct: 304 TQALFQGRMPAGAVN 318 Lambda K H 0.315 0.131 0.367 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: 283 Number of extensions: 9 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: 469 Length of database: 335 Length adjustment: 31 Effective length of query: 438 Effective length of database: 304 Effective search space: 133152 Effective search space used: 133152 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 09 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