Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF892 PS417_04530 glycerate dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >FitnessBrowser__WCS417:GFF892 Length = 321 Score = 132 bits (332), Expect = 1e-35 Identities = 91/284 (32%), Positives = 145/284 (51%), Gaps = 13/284 (4%) Query: 49 ESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSN 108 E ++ AH + + ++ L + A +L I GTN VDL+AA GI V N Sbjct: 45 ERVQGAHVV-ISNKIALNTATLAACPELKLILVSATGTNNVDLEAARAHGITVSNCQGYG 103 Query: 109 TRSVAELVIGELLLLLRGVPEANAKAHRGVWNK------LAAGSFEARGKKLGIIGYGHI 162 T SVA+ I LL L + + G W + L E GK LG++G+G + Sbjct: 104 TPSVAQHTIMLLLNLATRLKDYQRDVSAGKWQEAKQFCLLDHPIVELEGKTLGLLGHGEL 163 Query: 163 GTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMG 222 G + LAE+ GM V I + + L +LL D ++LH P N T++ +G Sbjct: 164 GGAVARLAEAFGMRVLLGAIPGRPARADRVP---LDELLAQVDALTLHCPLNEHTRDFIG 220 Query: 223 AKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLC 282 A+E++L+KPG+ ++N +RG +++ AL DAL S HL GAA DV EP + +P + Sbjct: 221 ARELALLKPGAFVVNTARGGLINEQALADALRSGHLGGAATDVLSVEPPVHGNPLLAG-- 278 Query: 283 EFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN 326 + +++TPH ++EA++ I ++A + NG+ L V+ Sbjct: 279 DIPRLIVTPHNAWGSREARQRIVGQLAENARGFF-NGAPLRVVS 321 Lambda K H 0.318 0.135 0.383 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: 253 Number of extensions: 12 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: 410 Length of database: 321 Length adjustment: 29 Effective length of query: 381 Effective length of database: 292 Effective search space: 111252 Effective search space used: 111252 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 (21.7 bits) S2: 49 (23.5 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