Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate YP_001328133.1 Smed_2466 NAD-binding D-isomer specific 2-hydroxyacid dehydrogenase
Query= BRENDA::Q972A9 (313 letters) >NCBI__GCF_000017145.1:YP_001328133.1 Length = 310 Score = 158 bits (400), Expect = 1e-43 Identities = 105/313 (33%), Positives = 169/313 (53%), Gaps = 16/313 (5%) Query: 3 IYTVKALITDPIDEILIKTLREKGIQVDY-----MPEISKEELLNIIGNYDIIVVRSRTK 57 + T ++L DP E+ + LR+ G ++ + MP S+ EL+ ++ I + Sbjct: 5 LVTPRSLSLDPPPEL--EPLRQAGFELVFPTPGRMP--SEAELIGLVPGC-IGWLAGVEP 59 Query: 58 VTKDVIEKGKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGASTDSAVELTIGLMIAAA 117 V+ VI L+ I+R G G+DN+ ++R I ++ A GA+ EL++GLM+AA Sbjct: 60 VSDKVIAAADSLRAISRNGTGIDNLPLPLLKERGIGILKAEGANAVGVAELSVGLMLAAL 119 Query: 118 RKMYTSMALAKSGIFKKIEGLELAGKTIGIVGFGRIGTKVGIIANAMGMKVLAYDILDIR 177 R + A ++G + + G E+A +T+GI+G G IG +V +AM V+A D R Sbjct: 120 RHIPAETAGIRAGGWPRSRGREIAERTVGIIGCGAIGKRVARAVSAMRASVIACD--PFR 177 Query: 178 EKAEKINA-KAVSLEELLKNSDVISLHVTVSKDAKPIIDYPQFELMKDNVIIVNTSRAVA 236 E K SL+E+ +D++SLH D KPI+D P+ + + I++NT+RA Sbjct: 178 PNVEVYGPFKWASLDEVFAGADIVSLHCPAPADGKPIVDAPRLATVPPHAILINTARATL 237 Query: 237 VNGKALLDYIKKGKVYAYATDVFWNEPPKEEWELELLKHERVIVTTHIGAQTKEAQKRVA 296 V+ A+ + +G++ AYATDVF EPP L H RVI T+HIG T E+ + Sbjct: 238 VDEDAVRAALDEGRLQAYATDVFTTEPPAPG---SLASHPRVIATSHIGGLTDESVGKAT 294 Query: 297 EMTTQNLLNAMKE 309 ++ NLL+A+ E Sbjct: 295 KIAVANLLSALVE 307 Lambda K H 0.317 0.134 0.361 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: 212 Number of extensions: 14 Number of successful extensions: 3 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: 313 Length of database: 310 Length adjustment: 27 Effective length of query: 286 Effective length of database: 283 Effective search space: 80938 Effective search space used: 80938 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: 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