Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_015738970.1 ADEG_RS04855 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_000024605.1:WP_015738970.1 Length = 247 Score = 179 bits (455), Expect = 4e-50 Identities = 112/255 (43%), Positives = 146/255 (57%), Gaps = 10/255 (3%) Query: 1 MLLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEAL 60 M L KV +VTG SRGIGRAIA A AA GA V INY R +VV I++ Sbjct: 1 MKLGGKVALVTGASRGIGRAIAEALAASGAKVVINY-------LAREEEALQVVNGIKSA 53 Query: 61 GRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAV 120 G +A +VA Q+LV TV+ +GK+D+L +NAGI + L M E + +AV Sbjct: 54 GGEAVAHRADVAQAPEAQELVEFTVKHYGKIDILVNNAGITRDNLLLRMKDEDWDKVLAV 113 Query: 121 NLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVA 180 NL GAF T+AA + M ++ G I+ SS+ L G Q +Y KAG+ ++ A Sbjct: 114 NLKGAFLTTRAAVRFM-VKSRWGRIINISSVVGLSGNAGQANYAAAKAGLIGFTKALAKE 172 Query: 181 LGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDR 240 LGP I N+V PG I TD+ A L +E K+ +R LGR GRPE+VA VTFLAS+ Sbjct: 173 LGPRNITVNAVAPGFILTDMTA-SLPEEVKQELL-RRCALGRFGRPEEVAALVTFLASEE 230 Query: 241 ARYVTGAALLVDGGL 255 A Y+TG + VDGGL Sbjct: 231 AGYITGQVISVDGGL 245 Lambda K H 0.319 0.134 0.386 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: 9 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: 260 Length of database: 247 Length adjustment: 24 Effective length of query: 236 Effective length of database: 223 Effective search space: 52628 Effective search space used: 52628 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 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