Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_038210988.1 Q392_RS18915 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000745855.1:WP_038210988.1 Length = 320 Score = 131 bits (329), Expect = 3e-35 Identities = 92/284 (32%), Positives = 147/284 (51%), Gaps = 18/284 (6%) Query: 23 ADVEIILYPSGEELKGVIGRFDGIIVSPTTKITREVLENAERLKVISCHSAGYDNIDLEE 82 AD + L + G+I G+ TR ++ RL+++ +G +++D+ Sbjct: 44 ADPQAYLATHAAGVSGIITHTHGL------DTTRALIGLLPRLEIVVNLGSGSESVDIAA 97 Query: 83 ATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTGFKRIE 142 +RGI +G + VAE + L++ R + D+ +R G W T +R+ Sbjct: 98 VRERGIRFLNGAGANAPDVAELAISLMLAAGRNLVAGDRHVRAGRWPIERAPIT--RRVS 155 Query: 143 SLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSRHRKVNVEKELKARYM-DIDELLEKS 201 GK++GILG G IG+AIARR F +++ Y++R V RYM D+ EL + Sbjct: 156 ---GKRLGILGFGEIGRAIARRAAAFDMEIAYFARRPAEGVAW----RYMPDLLELARWA 208 Query: 202 DIVILALPLTRDTYHIINEERVKKLEGK-YLVNIGRGALVDEKAVTEAIKQGKLKGYATD 260 D ++ ALP +T+HI++E + L + LVN+GRG +VDE A+ A++QG++ G D Sbjct: 209 DFLVAALPGGAETHHIVDEHVLDALGPQGMLVNVGRGTVVDEAALVRALQQGRIAGAGLD 268 Query: 261 VFEKEPVREHELFKYEWETVLTPHYAGLALEAQEDVGFRAVENL 304 VFE EP L + + + VL H+ G EA + V RA NL Sbjct: 269 VFEHEPHVPQALIESD-KVVLQAHHGGSTFEAYQAVANRAAANL 311 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: 222 Number of extensions: 13 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: 320 Length adjustment: 28 Effective length of query: 305 Effective length of database: 292 Effective search space: 89060 Effective search space used: 89060 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