Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate HSERO_RS22255 HSERO_RS22255 3-phosphoglycerate dehydrogenase
Query= curated2:A1RYE4 (339 letters) >FitnessBrowser__HerbieS:HSERO_RS22255 Length = 308 Score = 190 bits (482), Expect = 5e-53 Identities = 110/255 (43%), Positives = 149/255 (58%), Gaps = 8/255 (3%) Query: 59 IDAEVMDAAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVT 118 + A VMDAAP L+VIS + G D ID A +RGI V G AVAE T LI+A Sbjct: 60 VSARVMDAAPILRVISKHGTGIDSIDSQAAQQRGIAVKAAAGANAPAVAEHTWALIMACA 119 Query: 119 RRIVEADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKILYY 178 + +V D+ +R G WDK + EL+G+T+GLVGLG IG A ++ + +L + Sbjct: 120 KNVVGLDQRMREGHWDKSTHKSL----ELQGRTLGLVGLGAIGRRVAAVAAALGMPVLAH 175 Query: 179 DIERRWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLIN 238 D + + V + DLDTL +SD+VS+H PLT E H+IN + L +MK A L+N Sbjct: 176 DPYAKEAPQGV----QLVDLDTLFAQSDVVSLHCPLTAENKHMINAQSLARMKDGAILVN 231 Query: 239 TARGPVVDTEALVKALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIEAR 298 TARG ++D +AL+ AL G + A LD FE+EP HPL + N VL+PHI T +A Sbjct: 232 TARGGLIDEQALIAALDSGKLRAAGLDSFEKEPFTAPHPLQRVGNAVLSPHIGGVTSDAY 291 Query: 299 QRMAELAARNLIAVL 313 M AA N++AVL Sbjct: 292 IAMGTGAASNVLAVL 306 Lambda K H 0.319 0.137 0.404 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: 209 Number of extensions: 13 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: 339 Length of database: 308 Length adjustment: 28 Effective length of query: 311 Effective length of database: 280 Effective search space: 87080 Effective search space used: 87080 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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