Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_011940656.1 GURA_RS19650 phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_000016745.1:WP_011940656.1 Length = 539 Score = 201 bits (510), Expect = 5e-56 Identities = 112/323 (34%), Positives = 188/323 (58%), Gaps = 13/323 (4%) Query: 4 KVFITRQIPENGIKMIEKFYEIELWKDPKAP-PRGVLLEKVREVDALVTLVTDKVDKELL 62 KV +T ++ G+ ++ + +E+ D + + LL + + +A++T VD++LL Sbjct: 2 KVIVTDEVAPEGLALLAQDPRVEM--DIRLGLKKEELLAIIGDYEAIITRSGTNVDRDLL 59 Query: 63 ENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEA 122 + A KLK++A+ VG DN+D++ A+ RG+ V N P T++ A+ ALLLA R I +A Sbjct: 60 DAAKKLKMVARAGVGIDNVDVDYASARGVIVVNAPFGNTNSAAEHTMALLLAFYRNITKA 119 Query: 123 DAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRT 182 +A ++SGEWK++ F GY LKG+T G++G G++G +A R K F +++ Sbjct: 120 NASLKSGEWKRAP-------FTGYELKGRTAGVIGLGKVGGRVATRLKAFECEVLACDPY 172 Query: 183 RKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRG 242 + ++G V E + + D I++H PL ET MIGEKE+ +MK +LIN +RG Sbjct: 173 VAVKRAHDLGVRLVSHEEIYRNCDIITIHTPLNGETLDMIGEKEIAMMKEGVVLINAARG 232 Query: 243 AVVDTNALIKALKEGWIAGAGLDVFEEEPYYNE---ELFKLKNVVLAPHIGSATHEAREG 299 + + AL+ AL+ G +AGA +DV+ EEP E EL + +V+ PH+G+ T EA+ Sbjct: 233 GIFNEQALLNALQTGKVAGAAVDVWSEEPPRTELLKELIAQQRLVVTPHLGANTFEAQIN 292 Query: 300 MAELVAKNLIAFAKGEIPPNLVN 322 +A V++ ++ + + N VN Sbjct: 293 VAVDVSREILNYLDDQPLENAVN 315 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: 427 Number of extensions: 10 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: 331 Length of database: 539 Length adjustment: 32 Effective length of query: 299 Effective length of database: 507 Effective search space: 151593 Effective search space used: 151593 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 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