Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_040658761.1 ON16_RS01385 glucose 1-dehydrogenase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000307265.1:WP_040658761.1 Length = 245 Score = 151 bits (382), Expect = 1e-41 Identities = 99/246 (40%), Positives = 131/246 (53%), Gaps = 10/246 (4%) Query: 7 KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66 K LVTG GIGRA A A+ G DVA+NY S A+ V E+ G RA A + DVA Sbjct: 3 KVALVTGGGRGIGRAIARKLAEQGYDVAVNYQQSRAVAEELVNELRQAGCRAGAFQADVA 62 Query: 67 DPQTAQDFVAKAVETFGKVDVMVSNAGIC-PFHAFLDMPVDVVERTFKVNLHGAYFMVQA 125 +P + + G V+ +V+NAGI P F D+ + R F VN+ G +++A Sbjct: 63 EPNAVKAMLHAVETELGPVETLVNNAGIALPGGLFQDVDDETWNRAFAVNVGGMRNVIRA 122 Query: 126 AAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSV 185 M+ + GSIV +SSI L G + Y TKA V L +S A+ L IR N+V Sbjct: 123 VLPHMLHEKR-GSIVNLSSIWGLRGASCEVTYACTKAAVVGLTRSLALELAPSHIRVNAV 181 Query: 186 LPGTILTEINKDDLADQEKREYMEA---RTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242 PG I T D+ RE M+A TPLGRLG PED+A + FLA + A+++TG Sbjct: 182 APGCIDT-----DMVSSLGRETMDALAQDTPLGRLGTPEDIAAAVAFLAGEDASFITGQV 236 Query: 243 LLVDGG 248 L DGG Sbjct: 237 LTADGG 242 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: 141 Number of extensions: 6 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: 254 Length of database: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 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