Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_034990692.1 DL88_RS00700 D-glycerate dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000745425.1:WP_034990692.1 Length = 331 Score = 178 bits (451), Expect = 3e-49 Identities = 109/292 (37%), Positives = 163/292 (55%), Gaps = 9/292 (3%) Query: 33 DRDKLLAAVPEADALLVRSATTVDAEVLAAA-PKLKIVARAGVGLDNVDVDAATARGVLV 91 DR+ L A+ A+ L+ +DAE++AAA P+L+++A G G+DN+DVD+A RG+ V Sbjct: 38 DREALSRALATAEVLVPTVTDRIDAELIAAAGPQLRLIANFGNGVDNIDVDSALKRGLTV 97 Query: 92 VNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSS---FSGTEIFGKTVGVVG 148 N P A+ +AL+LA +R++ + E W + G I GK +G++G Sbjct: 98 TNTPGVLTEDTADMTMALILAVARRLVEGARIIPESEWNGWAPTWMLGRRITGKRLGIIG 157 Query: 149 LGRIGQLVAQRIAAFGAYVVAYDPY-VSPARAAQLGIELL-SLDDLLARADFISVHLPKT 206 +GRIGQ +A+R AFG + ++ + V+P L SLD +LAR D +S++ P T Sbjct: 158 MGRIGQALARRAKAFGLQIHYHNRHKVAPQIEEALEATYWESLDQMLARMDIVSINCPHT 217 Query: 207 PETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDS 266 P T L+ L+ +P I+VN ARG L+DEAAL + G V AGLDVF EP S Sbjct: 218 PATYHLLSARRLSHLQPHAILVNTARGELIDEAALTRMLEAGQVAGAGLDVFEHEPAVSS 277 Query: 267 PLFELA---QVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVG 315 L LA +V + PH+G++T E + G V +++ + G PD V G Sbjct: 278 KLIRLAKAGKVTLLPHMGSATTEGRIDMGEKVLINIKTFMDGHRPPDRVLPG 329 Lambda K H 0.317 0.133 0.370 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: 344 Number of extensions: 18 Number of successful extensions: 5 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: 528 Length of database: 331 Length adjustment: 32 Effective length of query: 496 Effective length of database: 299 Effective search space: 148304 Effective search space used: 148304 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