Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_086510640.1 BZY95_RS14570 phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_002151265.1:WP_086510640.1 Length = 416 Score = 161 bits (408), Expect = 2e-44 Identities = 105/297 (35%), Positives = 151/297 (50%), Gaps = 14/297 (4%) Query: 31 PKAPPRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRG 90 P + L+EKVR+ L ++ + + A KL + + +G + +D+ A RG Sbjct: 39 PTSLDEAALIEKVRDAHFLGIRSRTQLTERVFAAAEKLNAVGCFCIGTNQVDLNAALIRG 98 Query: 91 IYVTNTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKG 150 I V N P T + A+L A + + R I E +A G W KS H +G Sbjct: 99 IPVFNAPYSNTRSVAELVLAEAIMLLRGIPEKNARAHQGGWLKSAKNSHEA-------RG 151 Query: 151 KTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISL 210 KTLGIVG+G IG L+ A+ G +I+Y K + E LL +D +SL Sbjct: 152 KTLGIVGYGNIGAQLSVLAESLGFNVIFYDVVTKLGMGN--ANQVASLEELLARADVVSL 209 Query: 211 HVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEE 270 HVP T MIG+ +L LMKP+ ILIN SRG+VV L +AL+ G + GA +DVF E Sbjct: 210 HVPELPSTKWMIGKDQLVLMKPSGILINASRGSVVVIEDLAEALQAGRLYGAAIDVFPVE 269 Query: 271 PYYNEELF-----KLKNVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPNLVN 322 P N+E F + NV+L PH+G +T EA+E + V++ LI ++ VN Sbjct: 270 PKGNDEEFVSPLRGIPNVILTPHVGGSTLEAQENIGIEVSEKLITYSDNGTTVTSVN 326 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: 304 Number of extensions: 13 Number of successful extensions: 4 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: 416 Length adjustment: 30 Effective length of query: 301 Effective length of database: 386 Effective search space: 116186 Effective search space used: 116186 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 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