Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PfGW456L13_252 3-oxoacyl-[ACP] reductase (EC 1.1.1.100)
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_252 Length = 242 Score = 142 bits (359), Expect = 5e-39 Identities = 91/246 (36%), Positives = 139/246 (56%), Gaps = 10/246 (4%) Query: 7 KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66 ++VLVTG+S GIGRA A+ AQ G D+ ++ A++ AE+EALG+RA ++ DVA Sbjct: 3 ESVLVTGSSRGIGRAIALRLAQAGHDIVLHCRSGLADAEAVKAEVEALGRRARILQFDVA 62 Query: 67 DPQTAQDFVAKAVETFGKVDVMVSNAGIC---PFHAFLDMPVDVVERTFKVNLHGAYFMV 123 D ++ + VE G +V NAG+ F A + DVV RT NL G Y ++ Sbjct: 63 DRARCKEILEADVEAHGAYYGVVLNAGLTRDGAFPALSEEDWDVVMRT---NLDGFYNVL 119 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183 M+R+ G IV ++S+S L+G Q +Y+ +KAG+ ++ AI LGK I N Sbjct: 120 HPVMMPMIRRRAAGRIVCITSVSGLIGNRGQVNYSASKAGLIGAAKALAIELGKRKITVN 179 Query: 184 SVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAAL 243 V PG I T + +++ +E + + P R+G PE++AG + FL S A+Y+T L Sbjct: 180 CVAPGLIDTAMLDENVPVEELMKMI----PAQRMGTPEEVAGAVNFLMSAEASYITRQVL 235 Query: 244 LVDGGM 249 V+GG+ Sbjct: 236 AVNGGL 241 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: 7 Number of successful extensions: 2 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: 242 Length adjustment: 24 Effective length of query: 230 Effective length of database: 218 Effective search space: 50140 Effective search space used: 50140 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