Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate CA265_RS00310 CA265_RS00310 oxidoreductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__Pedo557:CA265_RS00310 Length = 246 Score = 137 bits (344), Expect = 3e-37 Identities = 100/258 (38%), Positives = 136/258 (52%), Gaps = 22/258 (8%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L DK+ +VTGGSRGIG AI AAEGA V Y ++ A+A VVAE+EA G Sbjct: 4 LTDKIALVTGGSRGIGAAIVKRLAAEGAKVIFTY------AHSAEKALA-VVAEVEAAGG 56 Query: 63 RVIAIEGN--VAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAV 120 +A++ + +A TG V T+ FG++DVL +NAGI AF + E +AV Sbjct: 57 VAVALKASSTIAGEVTGA--VAKTIADFGRIDVLVNNAGIYIGKAFEEHTLEDYNEIMAV 114 Query: 121 NLNGAFYVTQAAAQQMKLQGTGGAIVAT-SSISALVGGGMQTHYTPTKAGVHSLMQSCAV 179 N+ F AA + M GG I+ S++ G T YT +K+ + + A Sbjct: 115 NVQAVFVAALAAVKAMP---EGGRIITIGSNMGDNAVGPETTLYTMSKSALQGFTRGLAR 171 Query: 180 ALGPYGIRCNSVMPGTIATDLNAQD--LADEAKKAYFEKRIPLGRLGRPEDVADCVTFLA 237 LG I N V PG I TD+N D LAD + R+ L G ED+A V+F+A Sbjct: 172 DLGARKITVNLVQPGPINTDMNPADAPLAD-----FLRTRMALPDYGTVEDIASFVSFIA 226 Query: 238 SDRARYVTGAALLVDGGL 255 S+ ARY+TG+ L +DGGL Sbjct: 227 SEEARYITGSFLTIDGGL 244 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: 175 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: 246 Length adjustment: 24 Effective length of query: 236 Effective length of database: 222 Effective search space: 52392 Effective search space used: 52392 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 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