Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate N515DRAFT_2826 N515DRAFT_2826 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Dyella79:N515DRAFT_2826 Length = 247 Score = 141 bits (356), Expect = 1e-38 Identities = 89/245 (36%), Positives = 136/245 (55%), Gaps = 9/245 (3%) Query: 9 IVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGADAA 68 +VTGASRGIG A A E A QGA V+ G+ +GA ++ E +A GG + + Sbjct: 11 LVTGASRGIGAAIADELAAQGATVI----GTATSESGAAAIGERLAPHGGQGRVL--NVT 64 Query: 69 DLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTVQAA 128 + + E LV A + G++ +LVNNAGI + M E + + TNL Y +A Sbjct: 65 EPGAIEALVDAIGKDVGALSILVNNAGITRDQLLMRMRDEDWQAILDTNLTSVYRASKAV 124 Query: 129 ARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRCNAVL 188 R M + R G I++++S+ L G Q++Y KAG+++ +S A +G GI N V Sbjct: 125 MRGMMK-ARKGRIVSIASVIGLTGNPGQSNYAAAKAGIIAFSKSLAREIGSRGITVNVVA 183 Query: 189 PGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGASLLVD 248 PG I TD+ + E ++ + ++ LGRLGE D+A + FLAS A Y+TG +L V+ Sbjct: 184 PGFIDTDMTR--ALPEESKQALLGQIALGRLGEAQDIAKAVAFLASPAAAYITGETLHVN 241 Query: 249 GGLFV 253 GG+++ Sbjct: 242 GGMYM 246 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: 170 Number of extensions: 14 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: 247 Length adjustment: 24 Effective length of query: 232 Effective length of database: 223 Effective search space: 51736 Effective search space used: 51736 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 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