Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_017559746.1 C892_RS0126925 phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_000341205.1:WP_017559746.1 Length = 529 Score = 233 bits (594), Expect = 8e-66 Identities = 124/321 (38%), Positives = 194/321 (60%), Gaps = 10/321 (3%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 KP V + ++ G+ ++E +E+ + R LL + +VDAL+ +VD E Sbjct: 3 KPSVLVAEELSPAGLALLEGDFEV---RHTTGADRSQLLPALADVDALIVRSATQVDAEA 59 Query: 62 LENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121 L APKLK++A+ VG DN+D++ ATK G+ V N P + A+ A LLLA AR Sbjct: 60 LAAAPKLKVVARAGVGLDNVDVDAATKAGVLVVNAPTSNIISAAEQAVNLLLASARNTAP 119 Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSR 181 A + +GEWK+S+ + G + KT+G+VG GRIG +A+R FG K+I Y Sbjct: 120 AHNALVNGEWKRSK-------YTGVEVYDKTVGVVGLGRIGALVAQRLAAFGTKLIAYDP 172 Query: 182 TRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241 +P ++G E V + LL+ SDFI++H+P +K+T +IG++ L +KP+ +IN +R Sbjct: 173 FVQPARAAQMGVEMVSLDELLQRSDFITVHLPKSKDTLGLIGDEALHKVKPSVRVINAAR 232 Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMA 301 G ++D +AL +A+KEG +AGAG+DV+ EP + LF+ +NVV+APH+G++THEA+E Sbjct: 233 GGILDEDALYRAIKEGRVAGAGIDVWASEPCTDSPLFEFENVVVAPHLGASTHEAQEKAG 292 Query: 302 ELVAKNLIAFAKGEIPPNLVN 322 V +++ GE P+ VN Sbjct: 293 TQVVRSVKLALAGEFVPDAVN 313 Lambda K H 0.317 0.137 0.392 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: 374 Number of extensions: 15 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: 331 Length of database: 529 Length adjustment: 32 Effective length of query: 299 Effective length of database: 497 Effective search space: 148603 Effective search space used: 148603 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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