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 GFF377 Psest_0378 Lactate dehydrogenase and related dehydrogenases
Query= SwissProt::P40510 (469 letters) >FitnessBrowser__psRCH2:GFF377 Length = 309 Score = 115 bits (289), Expect = 2e-30 Identities = 86/292 (29%), Positives = 143/292 (48%), Gaps = 22/292 (7%) Query: 92 DELIEKIKDVHAIGIRSKTRLTEKILQHARNLVCIGCFCIGTNQVDLKYAASKGIAVFNS 151 DEL + I+ + S+ + +++ L I F +G + +D+ A ++GIA+ N+ Sbjct: 37 DELADAIE---VVVTGSRFGCSAELMARLPALKAIVSFGVGYDPIDVPAAQARGIAISNT 93 Query: 152 PFSNSRSVAELVIGEIISLARQLGDRSIELHTGTW---NKVAARCWEVRGKTLGIIGYGH 208 P + VA+L +G II RQL + G W N AR V G LGI+G G Sbjct: 94 PEVLNDCVADLAMGLIIDGRRQLSRADRFVRAGGWPSGNLPLAR--RVTGSRLGILGLGR 151 Query: 209 IGSQLSVLAEAMGLHVLYYDIVTIMALGTARQVSTLDELLNKSDFVTLHVPATPETEKML 268 IG ++ AE + V Y++ + A +L EL +D + L P+T ++ Sbjct: 152 IGHAVAKRAEGFSMPVRYHNRRPL-ADCPYEYAGSLVELARWADVLLLTCVGGPQTRGLV 210 Query: 269 SAPQFAAMKDGAYVINASRGTVVDIPSLIQAVKANKIAGAALDVYPHEPAKNGEGSFNDE 328 S A+ ++N +RG+VVD P+L++A++A ++ GAALDV+ EP Sbjct: 211 SREVLDALGPDGLLVNVARGSVVDEPALVEALQAGRLGGAALDVFAEEPQA--------- 261 Query: 329 LNSWTSELVSLPNIILTPHIGGSTEEAQSSIGIEVATALSKYINEGNSVGSV 380 L+ + N++L PHIG +T E + ++ V L +++ EG V V Sbjct: 262 ----PEALLGMDNVVLLPHIGSATRETRGAMEDLVLANLQRFLAEGQLVTPV 309 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: 279 Number of extensions: 13 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: 309 Length adjustment: 30 Effective length of query: 439 Effective length of database: 279 Effective search space: 122481 Effective search space used: 122481 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