Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_068462532.1 APY04_RS10945 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_001541235.1:WP_068462532.1 Length = 251 Score = 120 bits (301), Expect = 3e-32 Identities = 82/249 (32%), Positives = 124/249 (49%), Gaps = 5/249 (2%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L DK +VTG++ GIG A A +GA V + +D AGA A + A G A A Sbjct: 4 LKDKIALVTGSAAGIGLATIERLAAEGAHVYV----TDVDGAGAEKAAAALVAKGLHATA 59 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 + D + LV A + G +DV+VNNAGI F +M +++ NL+G Sbjct: 60 MTVDVSRGQDVTALVRAIEQQHGRLDVVVNNAGINVRTDFRNMSDADWVRLREVNLDGMV 119 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 + MK G+ ++I ++SI G Y TK + +L + A+ P+GI Sbjct: 120 RIARDTFPLMKASGKA-SLINLASIMGHRGMRTLAAYGATKGAMSALTRGLAVEYAPFGI 178 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 R NA+ PG I T + + L + + + PL R G +D+A ++F ASD + Y+TG Sbjct: 179 RVNALAPGFIETALTERVLRIEAFSKALLEQTPLRRFGSGEDVANAVLFFASDESAYITG 238 Query: 243 ASLLVDGGL 251 A L +DGG+ Sbjct: 239 AELAIDGGM 247 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: 154 Number of extensions: 11 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: 256 Length of database: 251 Length adjustment: 24 Effective length of query: 232 Effective length of database: 227 Effective search space: 52664 Effective search space used: 52664 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: 47 (22.7 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