Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_011938637.1 GURA_RS08815 phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_000016745.1:WP_011938637.1 Length = 541 Score = 203 bits (517), Expect = 7e-57 Identities = 114/323 (35%), Positives = 190/323 (58%), Gaps = 13/323 (4%) Query: 4 KVFITRQIPENGIKMIEKFYEIELWKDPKAP-PRGVLLEKVREVDALVTLVTDKVDKELL 62 KV +T ++ + G++++++ +EL D + + LL + + + ++T VDK+LL Sbjct: 2 KVIVTDEVAQEGLELLKQDPRVEL--DIRLGLKKEELLAIIGDYEVIITRSGTTVDKDLL 59 Query: 63 ENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEA 122 + KLK++A+ VG DN+DI+ A+ +G+ V N P T++ A+ A ALLL+ R I +A Sbjct: 60 DAGKKLKMVARAGVGIDNVDIDYASSKGVIVVNAPFGNTNSAAEHAMALLLSFCRNITKA 119 Query: 123 DAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRT 182 +A ++SGEWK++ F G LKGKT G++G G++G +A R K F ++ Sbjct: 120 NASLKSGEWKRAP-------FTGVELKGKTAGVIGLGKVGGRVATRLKAFECDVLGCDPY 172 Query: 183 RKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRG 242 + ++G + V E + K D I+ H PL +ET +M+GEKE+ +MK ILIN +RG Sbjct: 173 IAVKRAHDLGVKLVSHEEIYKNCDIITFHTPLNEETRNMVGEKEIAMMKDGVILINAARG 232 Query: 243 AVVDTNALIKALKEGWIAGAGLDVFEEEPYYNE---ELFKLKNVVLAPHIGSATHEAREG 299 +++ AL+ ALK G + GA +DV+ EEP +E EL +V+ PH+G+ T EA+ Sbjct: 233 GIINEQALLNALKGGKVFGAAMDVWSEEPPKSETLKELISQDKLVVTPHLGANTFEAQIN 292 Query: 300 MAELVAKNLIAFAKGEIPPNLVN 322 +A V+K ++ + + N VN Sbjct: 293 VAVDVSKEILNYLDEQPLENAVN 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: 403 Number of extensions: 11 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: 541 Length adjustment: 32 Effective length of query: 299 Effective length of database: 509 Effective search space: 152191 Effective search space used: 152191 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