Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Ga0059261_0219 Ga0059261_0219 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::Q972A9 (313 letters) >FitnessBrowser__Korea:Ga0059261_0219 Length = 336 Score = 106 bits (265), Expect = 7e-28 Identities = 75/255 (29%), Positives = 126/255 (49%), Gaps = 15/255 (5%) Query: 66 GKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGASTDSAVELTIGLMIAAARKMYTSMA 125 G ++++A G +N+D AE+ I VV P S + E TIGLM+A R + + A Sbjct: 66 GSGVRLVALRCAGFNNVDLAAAERLGIDVVRVPAYSPHAVAEFTIGLMLAVDRHIPRAWA 125 Query: 126 LAKSGIFKK--IEGLELAGKTIGIVGFGRIGTKVGIIANA-MGMKVLAYDILDIREKAEK 182 + F + G L G+ +G++G G+IG V A G VLA D++ E E+ Sbjct: 126 RVRDNNFALDGLIGRNLHGRMVGVIGTGKIGALVARSLRAGFGCDVLASDVVTDPE-LER 184 Query: 183 INAKAVSLEELLKNSDVISLHVTVSKDAKPIIDYPQFELMKDNVIIVNTSRAVAVNGKAL 242 + + V LL+ +++++LH ++ + +ID ++ ++IVNTSR ++ AL Sbjct: 185 VGVRYVPRATLLEQAEIVTLHCPLTPVTRHLIDAAAISRAREGLLIVNTSRGALIDTAAL 244 Query: 243 LDYIKKGKVYAYATDVF-----------WNEPPKEEWELELLKHERVIVTTHIGAQTKEA 291 +D +K K+ A DV+ NE ++ LL V+VT H T+EA Sbjct: 245 IDGLKSRKIGGVALDVYEQEADLFFEDLSNEIVGDDVFQRLLTFPNVLVTGHQAFLTEEA 304 Query: 292 QKRVAEMTTQNLLNA 306 +AE T ++ +A Sbjct: 305 LTAIAETTLASISDA 319 Lambda K H 0.317 0.134 0.361 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: 195 Number of extensions: 12 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: 313 Length of database: 336 Length adjustment: 28 Effective length of query: 285 Effective length of database: 308 Effective search space: 87780 Effective search space used: 87780 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: 48 (23.1 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