Align glyoxylate reductase (EC 1.1.1.26); glycerate dehydrogenase (EC 1.1.1.29); hydroxypyruvate reductase (EC 1.1.1.81) (characterized)
to candidate BWI76_RS12790 BWI76_RS12790 lactate dehydrogenase
Query= BRENDA::Q9C9W5 (386 letters) >FitnessBrowser__Koxy:BWI76_RS12790 Length = 329 Score = 112 bits (281), Expect = 1e-29 Identities = 77/242 (31%), Positives = 114/242 (47%), Gaps = 25/242 (10%) Query: 63 CDGVIGQLTEDWGETLFSALSKAGGKAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTET 122 C+ V + +D + L G K + G+NNVD++AA + G+ V P E Sbjct: 45 CEAVCIFVNDDGSRPVLEELKAHGVKYIALRCAGFNNVDLDAAKELGLRVVRVPAYSPEA 104 Query: 123 TAELAASLSLAAARRIVEADEFMRGGLY--EGWLPHLFVGNLLKGQTVGVIGAGRIGSAY 180 AE A + ++ RRI A + R + EG G + G+T GVIG G+IG A Sbjct: 105 VAEHAIGMMMSLNRRIHRAYQRTRDANFSLEG-----LTGFTMHGKTAGVIGTGKIGVAA 159 Query: 181 ARMMVEGFKMNLIYFDLYQSTRLEKFVTAYGQFLKANGEQPVTWKRASSMEEVLREADLI 240 R++ +GF M L+ FD Y S Y +E + RE+D+I Sbjct: 160 LRIL-KGFGMRLLAFDPYPSAAALDMGVEY-----------------VDLETLYRESDVI 201 Query: 241 SLHPVLDKTTYHLVNKERLAMMKKEAILVNCSRGPVIDEAALVEHLKENPMFRVGLDVFE 300 SLH L YHL+N MK +++N SRG +ID A ++ LK + +G+DV+E Sbjct: 202 SLHCPLTDENYHLLNHAAFERMKDGVMIINTSRGALIDSQAAIDALKHQKIGALGMDVYE 261 Query: 301 EE 302 E Sbjct: 262 NE 263 Lambda K H 0.318 0.135 0.399 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: 257 Number of extensions: 12 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: 386 Length of database: 329 Length adjustment: 29 Effective length of query: 357 Effective length of database: 300 Effective search space: 107100 Effective search space used: 107100 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 (21.7 bits) S2: 49 (23.5 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