Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate CA265_RS09010 CA265_RS09010 3-phosphoglycerate dehydrogenase
Query= SwissProt::P53839 (350 letters) >FitnessBrowser__Pedo557:CA265_RS09010 Length = 315 Score = 119 bits (299), Expect = 8e-32 Identities = 92/292 (31%), Positives = 144/292 (49%), Gaps = 24/292 (8%) Query: 48 PQNKLSQVQVITRTARSVKNTGRFDEELALALPSSVVAVCHTGAGYDQIDVEPFKKRHIQ 107 PQ++L++ + A +V++ + +EL A+P+ + + G G D IDVE + + I Sbjct: 30 PQDQLAEA-LKNYDAITVRSATKVRKELIDAVPN-IKLIGRGGVGMDNIDVEYARSQGIN 87 Query: 108 VANVPDLVSNATADTHVFLLLGALRNFGIGNRRL-IEGNWPEAGPACGSPFGYDPEGKTV 166 V N P S + A+ L +R NR++ +EG+ G + GKT+ Sbjct: 88 VVNTPAASSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELSGKTI 147 Query: 167 GILGLGRIGRCILERLKPFGFENFIYHNRHQLPSEEEHGCEYVG------------FEEF 214 GI+G GRIGR + G Y PSE E E+ G +E Sbjct: 148 GIIGFGRIGRATAKVALGLGMNVLAYD---LYPSESEITLEFQGGKSVSIPIKTVSLDEV 204 Query: 215 LKRSDIVSVNVPLNHNTHHLINAETIEKMKDGVVIVNTARGAVIDEQAMTDALRSGKIRS 274 + SD S++ P ++ AE KMK+GV IVN +RG IDE A+ DAL SGK+ Sbjct: 205 ITGSDFFSLHTPFADKP--ILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVSF 262 Query: 275 AGLDVFEYEPKISKELLSMSQVLGLPHMGTHSVETRKK----MEELVVENAK 322 AGLDVF+ EP E+L+ ++ PH+G + E +++ + L++E+ K Sbjct: 263 AGLDVFDNEPTPLAEILTHPKISLTPHIGASTNEAQERIGTELATLIIEHFK 314 Lambda K H 0.317 0.136 0.396 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: 269 Number of extensions: 12 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: 350 Length of database: 315 Length adjustment: 28 Effective length of query: 322 Effective length of database: 287 Effective search space: 92414 Effective search space used: 92414 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: 49 (23.5 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