Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 3607131 Dshi_0553 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Dino:3607131 Length = 255 Score = 144 bits (364), Expect = 1e-39 Identities = 81/245 (33%), Positives = 139/245 (56%), Gaps = 2/245 (0%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L+ KT LVTGAS+GIGRA A A GAD+ + A+I+ G++ A+ G Sbjct: 9 LQDKTALVTGASSGIGRAIAEVFADAGADI-VGQGRDLDRLTDLGAQIKTTGRQFAAITG 67 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 D+ADP Q+ +A+ FGK+D++V++AGI + +D +RT VNL + + Sbjct: 68 DLADPDQTQNVADRALAAFGKIDILVNSAGIAVTGPVTNYDLDDWQRTLAVNLTAPFILS 127 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183 +A M+++ G I+ +SS + ++ + Y +K G+++L +S H ++ N Sbjct: 128 KAVMPGMMQRKQG-KIINISSQTGVIALKDHAAYATSKGGLNALTKSLMTEAAPHNVQVN 186 Query: 184 SVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAAL 243 ++ P +LTE+ K+ + E+++ ARTPLGR G P ++A ++LAS + V GA + Sbjct: 187 AICPTVVLTEMGKELWSAPERKDPFIARTPLGRFGEPIEIADMALYLASPASDLVNGAVM 246 Query: 244 LVDGG 248 +++GG Sbjct: 247 MIEGG 251 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: 150 Number of extensions: 5 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: 254 Length of database: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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 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