Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (uncharacterized)
to candidate N515DRAFT_2996 N515DRAFT_2996 3-hydroxyisobutyrate dehydrogenase
Query= curated2:Q931R3 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_2996 Length = 286 Score = 82.4 bits (202), Expect = 2e-20 Identities = 84/276 (30%), Positives = 127/276 (46%), Gaps = 24/276 (8%) Query: 1 MTQQIGVIGLAVMGKNLAWNIESHGYSVSVFNRSSEKTDLMVEESKGKNIHPTYSLEEFV 60 MT + +GL MG +A +++S G +V NR+ K D + E G P LE+ Sbjct: 1 MTFKAAFVGLGAMGAPMAGHLKSKGLLHAVANRTQAKADALARE-LGVVAPP---LEQLA 56 Query: 61 NSLEKPRKILLMVQAGKATDATIDSLLPLLDDGDILIDGGNTNYQDTIRRNKA-LAQSAI 119 E I L V A ATID++LP L G +++D +T DT +R A LA + + Sbjct: 57 AQCE---VIALCVTADADVLATIDTMLPHLKRGAVVVD-HSTVAPDTAKRAAARLATAGV 112 Query: 120 NFIGMGVSGGEIGALTGP-SLMPGGQEEAYNKVADILDAIAAKAKDGASCVTYIGPNGAG 178 +F+ VSGG GA G S+M GG + +L+A A + VT++G GAG Sbjct: 113 DFLDAPVSGGVEGAKNGKLSVMVGGDAAVLERARPVLEAYALR-------VTHLGDVGAG 165 Query: 179 HYVKMVHNGIEYADMQLIAESYAMMKELLGMSHEDIAQTFKDWNAGELESYLIEITGDIF 238 K V+ + Q + E A + E LG+ E + T AG S+ +E G Sbjct: 166 QATKAVNQVLVAGIAQAVCEGLA-LGEALGLEAERLLPTL---GAGAAGSWFLEKRGATM 221 Query: 239 MKLDEN---KEALVEKILDTAGQKGTGKWTSINALE 271 ++ + + K AL+ K L + G T +E Sbjct: 222 LRDEFSVGFKLALLHKDLGIVKRIAEGAGTDRTVIE 257 Lambda K H 0.315 0.134 0.384 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: 212 Number of extensions: 7 Number of successful extensions: 2 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: 468 Length of database: 286 Length adjustment: 30 Effective length of query: 438 Effective length of database: 256 Effective search space: 112128 Effective search space used: 112128 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: 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