Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_086509102.1 BZY95_RS06205 2-deoxy-D-gluconate 3-dehydrogenase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_002151265.1:WP_086509102.1 Length = 250 Score = 156 bits (395), Expect = 3e-43 Identities = 92/246 (37%), Positives = 142/246 (57%), Gaps = 6/246 (2%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGAD-VAINYAHSDGPAQSCVAEIEALGQRAIAVK 62 L G+ +VTG + G+G+ A+ A+ GAD V +N ++SD + ++EALG+R +AV+ Sbjct: 6 LHGRVAMVTGCNKGLGQGLALALAEAGADIVGVNRSNSDETRE----KVEALGRRYVAVE 61 Query: 63 GDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFM 122 ++ T + VA+A+E+ G++D++++NAG L + E VNL A+F+ Sbjct: 62 AELGR-DTPEAIVARALESTGRLDMLINNAGAIRRAPALTFTEEDWEAVVDVNLKAAFFL 120 Query: 123 VQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRC 182 QA A+ +V +G G IV V+S+ + GG YT +K+G+ L + A HGI Sbjct: 121 AQAVARHLVERGAPGRIVNVASVLSFQGGIRVPAYTASKSGLLGLTRLLANEWAAHGITV 180 Query: 183 NSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242 N++ PG + T+ + D + + R P GR G PEDLAG ++FL SD AAYV G A Sbjct: 181 NAIAPGYMATDNTQALREDATRSAEILGRIPAGRWGTPEDLAGAVIFLCSDAAAYVNGHA 240 Query: 243 LLVDGG 248 L VDGG Sbjct: 241 LAVDGG 246 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: 132 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: 254 Length of database: 250 Length adjustment: 24 Effective length of query: 230 Effective length of database: 226 Effective search space: 51980 Effective search space used: 51980 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: 46 (22.3 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