Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate RR42_RS21135 RR42_RS21135 gluconate 5-dehydrogenase
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS21135 Length = 255 Score = 146 bits (369), Expect = 4e-40 Identities = 94/245 (38%), Positives = 132/245 (53%), Gaps = 2/245 (0%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 LEG+ LVTG + G+G+A A G AQ GA V + +++ + VA + A G RA + Sbjct: 8 LEGRVALVTGGAQGLGQAIAAGLAQAGAHVIVAARNAER-VHAAVAALAADGGRAEPLVL 66 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 DV D A T G++D++V+NAG + + + NL Y + Sbjct: 67 DVTDAAAVDAAFAHIDATHGRLDILVNNAGARNRSNMAHLNAADLREMLETNLVAPYALC 126 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183 + AAQ M R+G G IV VSSI+ V Y TK G+ +L ++ A LG+ G+ N Sbjct: 127 RHAAQLM-RRGRYGRIVNVSSIAGQVARANDVLYPATKGGLDALTRAMAADLGRDGVTVN 185 Query: 184 SVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAAL 243 +V PG TE N+ + D E++ RT LGR G PE++AG +VFLAS A+YVTG L Sbjct: 186 AVAPGYFATEPNQPMVDDAGVAEWLRQRTALGRWGQPEEIAGAVVFLASGAASYVTGHVL 245 Query: 244 LVDGG 248 VDGG Sbjct: 246 AVDGG 250 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: 137 Number of extensions: 6 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: 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