Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate 8502217 DvMF_2927 tartronate semialdehyde reductase (RefSeq)
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__Miya:8502217 Length = 299 Score = 144 bits (363), Expect = 2e-39 Identities = 90/279 (32%), Positives = 132/279 (47%) Query: 3 VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62 +GF+GLGIMG M NLLK GF VT + R K + GA+ ESPA V I Sbjct: 4 IGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDVVIT 63 Query: 63 MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSG 122 ML + +V GG+ E G DMS++ S +I + K R ++ PVSG Sbjct: 64 MLPNSPEVRAVALGPGGIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAPVSG 123 Query: 123 SKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMN 182 + A DG L ++ G + F+ +P F + +G+VG G KL +++ + Sbjct: 124 GEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAASVVRVGEVGAGNVTKLANQIVVAGNIA 183 Query: 183 AFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRL 242 A SE LVLA ++G D + + G + + K P + + P F ++ KDM Sbjct: 184 AMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFRIRLHAKDMGN 243 Query: 243 ALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVI 281 L E V +P+AA E + + GLGD D A+I Sbjct: 244 VLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALI 282 Lambda K H 0.317 0.134 0.379 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: 175 Number of extensions: 5 Number of successful extensions: 1 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: 289 Length of database: 299 Length adjustment: 26 Effective length of query: 263 Effective length of database: 273 Effective search space: 71799 Effective search space used: 71799 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