Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate AO353_21585 AO353_21585 hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21585 Length = 316 Score = 167 bits (424), Expect = 2e-46 Identities = 102/269 (37%), Positives = 152/269 (56%), Gaps = 15/269 (5%) Query: 45 EVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDAT 104 ++DA++T + + + LKII GY+ +D++ A+ RGI VTN GV + Sbjct: 45 QIDAVLTRGPLGLYADEIAALANLKIICVIGAGYEQVDLQAASDRGITVTNGAGVNASSV 104 Query: 105 ADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQA 164 AD A ALLL++ R I DA VR GEW K + L GK LG++G G +G A Sbjct: 105 ADHAMALLLSLVRDIPRCDAAVRRGEWPK---------IMRPSLAGKRLGVLGLGAVGMA 155 Query: 165 LAKRA-KGFGMKIIYYSRTRKPEAEEEIGAEYVDFET-LLKESDFISLHVPLTKETYHMI 222 +AKRA GF M + Y+SR + +I ++ T L + SDF+ + P T H++ Sbjct: 156 IAKRAANGFDMTVSYHSR----QLLSDIPYDFCSTPTELARVSDFLIVCTPGGIGTQHLV 211 Query: 223 GEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKN 282 ++ L + P ++N +R +VV T+ L+ AL++ IAGA LDVF+EEP + L L N Sbjct: 212 NKQVLDALGPQGFIVNIARASVVATSDLVSALEQRRIAGAALDVFDEEPQVPDALKVLSN 271 Query: 283 VVLAPHIGSATHEAREGMAELVAKNLIAF 311 V+L PH+ + EA +G ELV +NL+AF Sbjct: 272 VILTPHVAGLSPEATKGTVELVGQNLMAF 300 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: 214 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: 316 Length adjustment: 28 Effective length of query: 303 Effective length of database: 288 Effective search space: 87264 Effective search space used: 87264 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