Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_048081445.1 EJ01_RS05790 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000745485.1:WP_048081445.1 Length = 258 Score = 144 bits (362), Expect = 2e-39 Identities = 88/255 (34%), Positives = 144/255 (56%), Gaps = 11/255 (4%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L+GK +VTGAS G+G AA AQ GADVA+ A +S EIE+ G +A+AV+ Sbjct: 7 LKGKVAVVTGASGGLGADAARAYAQEGADVAL-LARRKERLESLAEEIESAGVKALAVQC 65 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 DVAD ++ ++ + + ++ FGK+D++++NAGI + V+ ++ VN+ G + + Sbjct: 66 DVADEESVENAIDEVIKYFGKIDILLNNAGIAVRGGVHSLSVEDWDKGMDVNVKGIFLVS 125 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTH----YTPTKAGVHSLMQSTAIALGKHG 179 + M++ + G IV SSI+++ G + + Y +KA V L A + GK+G Sbjct: 126 KYVLPHMMKNNY-GKIVNTSSINSIAGDKSEMFIRHVYNASKAAVRGLTMGMACSYGKYG 184 Query: 180 IRCNSVLPGTILTEINKDDLADQEKREYMEART---PLGRLGAPEDLAGPIVFLASDMAA 236 I N+V P +E+ + L E E++E + PL R +L GPI+FL+S+ ++ Sbjct: 185 ITVNAVAPALFESEMTSNTLFKSE--EFLERYSNVVPLNRPAKKGELNGPIIFLSSEASS 242 Query: 237 YVTGAALLVDGGMYV 251 Y+TG + VDGG V Sbjct: 243 YITGQTIFVDGGFSV 257 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: 119 Number of extensions: 5 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: 254 Length of database: 258 Length adjustment: 24 Effective length of query: 230 Effective length of database: 234 Effective search space: 53820 Effective search space used: 53820 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: 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