Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_040659684.1 ON16_RS04320 SDR family oxidoreductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000307265.1:WP_040659684.1 Length = 264 Score = 132 bits (332), Expect = 7e-36 Identities = 90/256 (35%), Positives = 130/256 (50%), Gaps = 15/256 (5%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L GK ++TG +GIG A + +GA VAI A+ E+ G++A K Sbjct: 10 LTGKVAVITGGGSGIGLGVAQLLSAYGAAVAI--VDVSDKAEEKAQEMRDAGRQAAFFKC 67 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 DV ++ VA VE FG++D++ +NAG+ A D+ + V L G + M Sbjct: 68 DVTSEESVTATVAAIVEKFGRIDILHNNAGVTVRKAMADLSEKEWDFVLDVGLKGLFLMS 127 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183 + +M + G GGSIV S L GG+ Y K G+ ++ ++ AI GK+ IR N Sbjct: 128 KHVIPEMQKVG-GGSIVNTGSGWGLKGGDLAAAYCAVKGGIVNVTRAMAIDYGKYNIRVN 186 Query: 184 SVLPGTILT-----------EINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLAS 232 SV PG +T EI D D + R PL R+G PED+A ++FL S Sbjct: 187 SVNPGDTVTAMMVSEGRQTGEIKSDADIDAFLKSCGSGR-PLARIGQPEDIANGVLFLCS 245 Query: 233 DMAAYVTGAALLVDGG 248 +A++VTGAAL+VDGG Sbjct: 246 GLASWVTGAALVVDGG 261 Lambda K H 0.318 0.133 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: 138 Number of extensions: 6 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: 254 Length of database: 264 Length adjustment: 24 Effective length of query: 230 Effective length of database: 240 Effective search space: 55200 Effective search space used: 55200 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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