Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 3609586 Dshi_2970 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= curated2:O27051 (525 letters) >FitnessBrowser__Dino:3609586 Length = 328 Score = 179 bits (454), Expect = 1e-49 Identities = 116/319 (36%), Positives = 177/319 (55%), Gaps = 9/319 (2%) Query: 3 RMKVLIADSINEKGISELEEVAEVVVNTTITP---EELLDAIKDFDAIVVRSRTKVTREV 59 R+ V++ + E + L+E+ +V +N + TP + L A++ D +V + + Sbjct: 5 RLSVVVTRRLPEAVETRLKELFDVELNESDTPMSRDALQAAMRRADVLVPTVSDHIDGAM 64 Query: 60 IEAA-PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 + RLK+IA G GVD++DV A RGI V N P + A+ ++ L+LA+ R+I Sbjct: 65 LAGVGDRLKLIANYGAGVDHIDVATARQRGIHVSNTPGVLTDDTADMTLALILAVTRRIP 124 Query: 119 IADRSVKEGKW---EKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY-I 174 ++ G W MG + G+ LGI+GMGRIG V R KAFGM I ++ + Sbjct: 125 EGLALMQTGAWTGWSPTALMGGRIAGRRLGILGMGRIGQAVARRAKAFGMQIHYHNRRRL 184 Query: 175 SKEAAEEMGVTVTD-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARG 233 K EE+ T + L+ ++ D+++++ P TP T HL++ KLMK +A IVN +RG Sbjct: 185 HKGIEEELEATWWESLDQMVSRMDVISVNCPHTPSTFHLMNARRLKLMKPSAVIVNTSRG 244 Query: 234 GIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAI 293 +IDE+AL R L+ G+IAGA LDVFE L EL NVVL PH+G++T E + + Sbjct: 245 EVIDENALTRMLRAGDIAGAGLDVFEHGHEVNPRLRELPNVVLLPHMGSATEEGRAEMGE 304 Query: 294 IVANEIKTVFQGGAPRNVL 312 V IKT G P +++ Sbjct: 305 KVIINIKTFDDGHRPPDLV 323 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: 396 Number of extensions: 22 Number of successful extensions: 3 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: 328 Length adjustment: 31 Effective length of query: 494 Effective length of database: 297 Effective search space: 146718 Effective search space used: 146718 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