Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Ac3H11_142 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= BRENDA::H9JRZ9 (432 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_142 Length = 313 Score = 183 bits (465), Expect = 6e-51 Identities = 113/306 (36%), Positives = 166/306 (54%), Gaps = 11/306 (3%) Query: 110 IKSVLIVDG--VGAKCAELLNAYGIATTTKAKISKEELLMEIPNHD--ALVVRSATQVTK 165 + +IV G + ELL Y I KA ++++L+ H+ A++VR +V Sbjct: 1 VSPTIIVTGADLAQHALELLAGYDIVYAGKAP-TEDDLVALCGAHNPVAIIVRYG-KVGA 58 Query: 166 EVLDAGVKLKVVGRAGAGVDNIDVDSAGKKGVGVINAPGANALSACELTCTLMLVLARHV 225 V+DA LKV+ + G+G D ID +A +G+ V+ A GANA + E TL+L A+ V Sbjct: 59 AVMDAAPALKVISKHGSGTDTIDKVAAKARGIEVVAAVGANAAAVAEQALTLLLACAKSV 118 Query: 226 VPASTALKAGRWDRALYTGSELAGKTLAILGLGRVGREVATRMYAFGMNIIGFDPFVSAD 285 V + AG WD+A + EL G+T+ ++GLG +G A A GM +IGFDPF Sbjct: 119 VQLDARMHAGHWDKATHKSLELGGRTVGLVGLGAIGLRFAKMADALGMRVIGFDPFA--- 175 Query: 286 QCAQFHCTKMELEDIWPLADYITLHTPLIESTRNFINADVLKQCKKGVKIINVGRGGLIQ 345 + + + LE IW AD ++LH PL + R +NA L QCK+GV ++N RGGLI Sbjct: 176 KNLPDYVQSVGLETIWREADAVSLHCPLTDENRGMLNATTLAQCKRGVIVVNTARGGLID 235 Query: 346 ETDFLQALKSGKVGGAALDVFEQEPPTDPVTLEIIQQPAVIATPHLGASTKEAQVRVGQE 405 E L A++SG+V A LD F EP T + + I +PH+G T +A V +G Sbjct: 236 EAALLAAVRSGQVMAAGLDSFAVEPMTTGHPFQ--GEKHFILSPHIGGVTSDAYVNMGVG 293 Query: 406 IAEQLV 411 A+ L+ Sbjct: 294 AAQNLL 299 Lambda K H 0.320 0.135 0.387 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: 299 Number of extensions: 11 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: 432 Length of database: 313 Length adjustment: 30 Effective length of query: 402 Effective length of database: 283 Effective search space: 113766 Effective search space used: 113766 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 (21.8 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