Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_018262605.1 M446_RS03980 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000019365.1:WP_018262605.1 Length = 314 Score = 136 bits (343), Expect = 6e-37 Identities = 92/274 (33%), Positives = 143/274 (52%), Gaps = 13/274 (4%) Query: 42 RFDGIIVSPTTKITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAV 101 R G+ VS ++ +L+ L++++ GYD ID +RG+ VT +L++ V Sbjct: 38 RVRGLAVSGV-RVDDALLDRLPALEIVANFGVGYDTIDAAACGRRGVVVTNTPDVLTDEV 96 Query: 102 AEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAI 161 A+ VGL++ +R+I D+++R G+W TG +L G+ VGILG+G IG+AI Sbjct: 97 ADLAVGLLLATLRQIPQVDRYLREGKWLEKPYPLTG-----TLRGRHVGILGLGRIGRAI 151 Query: 162 ARRLIPFGVKLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEE 221 A RL FGV L Y R + +V MD L E D++I+ P +T +I++ Sbjct: 152 AHRLEAFGVTLAYHGRRPQEDVPYAYHPTLMD---LAEAVDVLIVVAPGGPETRNIVDAA 208 Query: 222 RVKKL--EGKYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWET 279 + L EG L+N+ RG+LVDE+A+ A+K + DVF EP EL E Sbjct: 209 VLAALGPEG-ILINVARGSLVDEEALIAALKNRTILSAGLDVFADEPRVPAELIAQE-HA 266 Query: 280 VLTPHYAGLALEAQEDVGFRAVENLLKVLRGEVP 313 VL PH ++ + +G V+NL+ G+ P Sbjct: 267 VLLPHVGSASVHTRTAMGQLCVDNLVSWFSGKGP 300 Lambda K H 0.319 0.139 0.393 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: 244 Number of extensions: 11 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: 333 Length of database: 314 Length adjustment: 28 Effective length of query: 305 Effective length of database: 286 Effective search space: 87230 Effective search space used: 87230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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