Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 8502147 DvMF_2858 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Miya:8502147 Length = 245 Score = 122 bits (306), Expect = 7e-33 Identities = 86/245 (35%), Positives = 124/245 (50%), Gaps = 7/245 (2%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65 + IVTG SRGIGRA A A+ G VV+ ++ + AL + + IA GG A+AV A Sbjct: 6 RNAIVTGGSRGIGRAIALRLAQDGFCVVVNYASN---APAALEVVDAIARTGGQAVAVPA 62 Query: 66 DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTV 125 D + E L AAA +AFG V V+VN+AGI P + K + TNL G + + Sbjct: 63 DVGETGDVEGLFAAAHDAFGQVGVVVNSAGIMPMLPIAGGDTAAFEKVLRTNLTGTFNVL 122 Query: 126 QAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRCN 185 AA + GG IIA+S+ Y +KAG+ L++ A L I N Sbjct: 123 SRAANALT---AGGRIIALSTSVIAKPFPGYGPYIASKAGVEGLVRVLANELRGRSITVN 179 Query: 186 AVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGASL 245 AV PG +ATD+ ++ E+ + PL RLG P+++AG + FL ++ + Sbjct: 180 AVAPGPVATDLFLNGKTE-EQIAAIGKLAPLERLGTPEEIAGVVSFLVGPEGGWINAQVV 238 Query: 246 LVDGG 250 V+GG Sbjct: 239 RVNGG 243 Lambda K H 0.319 0.136 0.383 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: 11 Number of successful extensions: 4 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: 256 Length of database: 245 Length adjustment: 24 Effective length of query: 232 Effective length of database: 221 Effective search space: 51272 Effective search space used: 51272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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