Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate GFF377 Psest_0378 Lactate dehydrogenase and related dehydrogenases
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__psRCH2:GFF377 Length = 309 Score = 186 bits (471), Expect = 8e-52 Identities = 114/301 (37%), Positives = 165/301 (54%), Gaps = 13/301 (4%) Query: 17 KMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAV 76 ++ ++ + LW+ A L E ++ +VT EL+ P LK I + V Sbjct: 17 ELASRYDILSLWQ---AETAARLDELADAIEVVVTGSRFGCSAELMARLPALKAIVSFGV 73 Query: 77 GYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEV 136 GYD ID+ A RGI ++NTP VL D ADLA L++ R++ AD FVR+G W + Sbjct: 74 GYDPIDVPAAQARGIAISNTPEVLNDCVADLAMGLIIDGRRQLSRADRFVRAGGWPSGNL 133 Query: 137 GWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYV 196 L + G LGI+G GRIG A+AKRA+GF M + Y++R + E V Sbjct: 134 P------LARRVTGSRLGILGLGRIGHAVAKRAEGFSMPVRYHNRRPLADCPYEYAGSLV 187 Query: 197 DFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKE 256 + L + +D + L +T ++ + L + P+ +L+N +RG+VVD AL++AL+ Sbjct: 188 E---LARWADVLLLTCVGGPQTRGLVSREVLDALGPDGLLVNVARGSVVDEPALVEALQA 244 Query: 257 GWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMAELVAKNLIAF-AKGE 315 G + GA LDVF EEP E L + NVVL PHIGSAT E R M +LV NL F A+G+ Sbjct: 245 GRLGGAALDVFAEEPQAPEALLGMDNVVLLPHIGSATRETRGAMEDLVLANLQRFLAEGQ 304 Query: 316 I 316 + Sbjct: 305 L 305 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: 207 Number of extensions: 9 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: 309 Length adjustment: 28 Effective length of query: 303 Effective length of database: 281 Effective search space: 85143 Effective search space used: 85143 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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