Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_041939495.1 FRAAL_RS19180 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000058485.1:WP_041939495.1 Length = 245 Score = 159 bits (402), Expect = 5e-44 Identities = 94/249 (37%), Positives = 136/249 (54%), Gaps = 8/249 (3%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L + +VTG +RGIGRA AR GA VV+GH E A SL E+ GG + Sbjct: 5 LAGRRALVTGGTRGIGRAVVLGLARAGATVVVGHQRQTEE---AESLRRELKDTGGDHLL 61 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 V AD AD +L+ A G +D++VN+ G + D+P + + + + TNL + Sbjct: 62 VQADVADPAQITELIEATGTHLGGLDIVVNSVGTISHIPYADLPLDAWTQVLATNLTATH 121 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 Q A + G G+++ + S + +VG ++ HYT K GL+ L +S + LG GI Sbjct: 122 LVTQGALPLL---GESGSVVNIGSGAGVVGVPLRAHYTAAKTGLIGLTRSLSKELGSRGI 178 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 R N V PG I TD + R T+R+PLGRLGE D++A ++FLASD++ YV G Sbjct: 179 RVNLVSPGVIETD--QAAGMPEAARTAYTNRIPLGRLGEADEVAAVVLFLASDVSSYVNG 236 Query: 243 ASLLVDGGL 251 A+ VDGG+ Sbjct: 237 ATFTVDGGI 245 Lambda K H 0.319 0.136 0.383 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: 182 Number of extensions: 16 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: 256 Length of database: 245 Length adjustment: 24 Effective length of query: 232 Effective length of database: 221 Effective search space: 51272 Effective search space used: 51272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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