Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_002117405.1:WP_085770280.1 Length = 246 Score = 122 bits (306), Expect = 7e-33 Identities = 76/246 (30%), Positives = 135/246 (54%), Gaps = 7/246 (2%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L GKT LVTGAS+G+G A A Q GA V ++ + ++ E++ +RA + Sbjct: 4 LTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREA-LETLAGELK---ERAHILPC 59 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 +++D + A G VD++V+NAGI F+ M + + VNL A+ + Sbjct: 60 NLSDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLS 119 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183 +A + M+R+ HG I+ ++S++ VG Q +Y+ KAG+ + +S A + G+ N Sbjct: 120 RAVLRGMMRKRHG-RIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVN 178 Query: 184 SVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAAL 243 V PG I + + + + ++ +RE + P+ R G+ +++ +++LASD AA++TG L Sbjct: 179 CVAPGVIESPMTQ--VLNEAQRERLLKLIPMERFGSADEIGAAVLYLASDEAAFITGQTL 236 Query: 244 LVDGGM 249 ++GGM Sbjct: 237 HINGGM 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: 99 Number of extensions: 5 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: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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 Apr 09 2024. 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