Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_028321571.1 H567_RS0111905 SDR family oxidoreductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000422285.1:WP_028321571.1 Length = 269 Score = 144 bits (364), Expect = 1e-39 Identities = 94/259 (36%), Positives = 142/259 (54%), Gaps = 17/259 (6%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAE--IEALGQRAIAV 61 L GKT LVTGAS+G GR+ A+ A+ GADV I+ + P + E ++A G+R + + Sbjct: 10 LSGKTALVTGASSGFGRSFALTLAEAGADVVIS---ARNPERLTETEDLLKATGRRVLKI 66 Query: 62 KGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHA-FLDMPVDVVERTFKVNLHGAY 120 GD++ P+ + +AV FG +D+ V+NAG+ F +M ++ + VNL G + Sbjct: 67 FGDMSVPEDVSRMIDEAVSVFGHLDIAVNNAGLLTRPVRFHEMTLEDWNQVISVNLTGVF 126 Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEY----QTHYTPTKAGVHSLMQSTAIALG 176 +Q +M+ Q GGSI+ +SS+ LVG + + +Y +K GV L + A+ Sbjct: 127 LCMQQEIGRMLHQQAGGSIINISSVLGLVGLDADLNPRVNYIASKHGVIGLTRQAAVEYA 186 Query: 177 KHGIRCNSVLP----GTILTEINKDDLADQEKREY---MEARTPLGRLGAPEDLAGPIVF 229 GIR N++ P GT L + D +QE+ E M ARTP+ R G E+L G ++F Sbjct: 187 DRGIRVNAMAPAWHSGTSLAKARSDIQTEQEQAEREMRMLARTPMKRRGRLEELQGMLLF 246 Query: 230 LASDMAAYVTGAALLVDGG 248 LASD + Y TG DGG Sbjct: 247 LASDASTYTTGQVFASDGG 265 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: 115 Number of extensions: 9 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: 269 Length adjustment: 25 Effective length of query: 229 Effective length of database: 244 Effective search space: 55876 Effective search space used: 55876 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