Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_142248010.1 BK574_RS21120 D-glycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_002019605.1:WP_142248010.1 Length = 326 Score = 286 bits (731), Expect = 6e-82 Identities = 151/324 (46%), Positives = 216/324 (66%), Gaps = 6/324 (1%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAP-PRGVLLEKVREVDALVTLVTDKVDK 59 MKP VF+TR++PE+ + + + E+ +W+ P P VL +++ DAL +LV+D + Sbjct: 1 MKPYVFVTRKMPEHLLSDLYEIAEVGMWEHEDIPVPSEVLQKELERADALFSLVSDPLRS 60 Query: 60 ELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRI 119 + L PKLK+IA AVGYDNID+E AT +GI V +TP VLTD TADL FALLLA AR+I Sbjct: 61 QQLAKCPKLKVIANMAVGYDNIDVEHATNKGIVVCHTPDVLTDTTADLTFALLLATARKI 120 Query: 120 VEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYY 179 EA ++++ +W++ W P + G + KT+GIVG GRIG+A+AKRAKGF M+I+Y+ Sbjct: 121 PEATDYIKNDQWQQ----WSPYLLAGTDVHHKTIGIVGMGRIGEAVAKRAKGFDMEILYH 176 Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 +R+RK E E+++GA+Y FE LL++SD++ P T T + ++ + MK +AI IN Sbjct: 177 NRSRKMETEQQLGAKYCSFEELLQQSDYVVCLAPFTPVTKELFDQQAFQQMKNSAIFINA 236 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSATHEARE 298 SRG +V+ AL +AL++G I AGLDVF EEP N L +L NVV PHIGSAT E R+ Sbjct: 237 SRGGLVNEAALQEALEKGVIQAAGLDVFAEEPVRANHPLVQLPNVVAIPHIGSATVETRD 296 Query: 299 GMAELVAKNLIAFAKGEIPPNLVN 322 M ++ +N+ +G+ P VN Sbjct: 297 AMVKMTVENIKKVLEGKPPLAAVN 320 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: 257 Number of extensions: 9 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: 326 Length adjustment: 28 Effective length of query: 303 Effective length of database: 298 Effective search space: 90294 Effective search space used: 90294 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 Apr 09 2024. 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