Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate GFF2840 HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Marino:GFF2840 Length = 247 Score = 149 bits (376), Expect = 5e-41 Identities = 88/251 (35%), Positives = 137/251 (54%), Gaps = 4/251 (1%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60 M+ L+GK LVTGAS GIGR A+ AQ GADVAINY + EIEA G RA++ Sbjct: 1 MQDLKGKVALVTGASRGIGRHIALQLAQRGADVAINYRSRQSEGEEVAKEIEATGVRALS 60 Query: 61 VKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAY 120 K D++ A+ V + E +G++D++V+NAGI + + D NL Y Sbjct: 61 FKADLSKMPEARSLVRQVQEQWGRIDILVNNAGITKDKSMKKLTDDDWNDVLDTNLGSVY 120 Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180 + M+ Q + G I+ ++S G Q +Y +K G+ + ++ A+ + K+ I Sbjct: 121 ATCSEVLKIMMDQKY-GRIINITSFVGQAGNFGQANYAASKGGIIAFTKTLALEMAKYNI 179 Query: 181 RCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTG 240 N++ PG TE+ + RE + AR P+GR G PE++A +VFLA++ Y+TG Sbjct: 180 TVNAIAPGFTETEMLAQ--VPENIREQIIARVPMGRFGKPEEIARAVVFLAAE-GDYITG 236 Query: 241 AALLVDGGMYV 251 + V+GG+Y+ Sbjct: 237 QQINVNGGVYM 247 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: 124 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: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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 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