Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_019895926.1 A377_RS0108710 2-hydroxyacid dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000384235.1:WP_019895926.1 Length = 334 Score = 141 bits (355), Expect = 4e-38 Identities = 93/306 (30%), Positives = 150/306 (49%), Gaps = 23/306 (7%) Query: 24 VEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKI--VARAGVGLDNVDV 81 +E+ + D K + DA+ + DAEV+ I + G +NVD Sbjct: 26 IEMDYFDVHLSPKTVPLAKGFDAVCLFVNDHADAEVIEQLVGYGIDTIVLRCAGFNNVDA 85 Query: 82 DAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFG 141 AA V ++ P + + AEHALAL++ +R+ A +R+ + G ++F Sbjct: 86 KAAQQHKVTILRVPAYSPQAVAEHALALIMTLNRKTHKAFNRVRDSNFTLEGLLGFDLFE 145 Query: 142 KTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISV 201 KT GV+G GRIGQ + + G V+AYDPY S R QLG + +SLD+L A++D IS+ Sbjct: 146 KTAGVIGTGRIGQETVRILRGLGLKVLAYDPYPSE-RVTQLGGKYVSLDELYAQSDIISL 204 Query: 202 HLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATE 261 H+P P+T +I+ +++AK KPGV+++N +RGGL+ L + G + G+DV+ E Sbjct: 205 HVPLIPQTEHMINADSIAKMKPGVMLINTSRGGLMQAKDLIHGLKKGQIGYLGIDVYEQE 264 Query: 262 PCTDSPLFE-----------------LAQVVVTPHLGASTAEAQDRAGTDVAESVRLALA 304 D+ FE V++T H T EA D ++++ Sbjct: 265 ---DNLFFEDHSEEIIHDDVFERLITFPNVLITAHQAFFTQEALDNITATTLDNLQDVQR 321 Query: 305 GEFVPD 310 + P+ Sbjct: 322 NQLKPE 327 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: 313 Number of extensions: 15 Number of successful extensions: 2 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: 334 Length adjustment: 32 Effective length of query: 496 Effective length of database: 302 Effective search space: 149792 Effective search space used: 149792 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 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