Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 147 bits (370), Expect = 3e-40 Identities = 104/251 (41%), Positives = 142/251 (56%), Gaps = 17/251 (6%) Query: 6 KVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGRRVI 65 +V IVTGG++GIG A AAEGA I DV R A+A AE+ AL R Sbjct: 21 RVCIVTGGAQGIGEACVRRFAAEGAKPVIV-----DVDDARGQALA---AELGALYVRC- 71 Query: 66 AIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVNLNGA 125 +V + LV + A G++DVL +NAGI FL++ ++ + VNL G+ Sbjct: 72 ----DVGDKAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGS 127 Query: 126 FYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVALGPYG 185 F V QA A+ M G GGAIV SS++ ++ Y +K GV+ L + A+AL Sbjct: 128 FLVGQAVARAMVTSG-GGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKN 186 Query: 186 IRCNSVMPGTIATDLNAQDL--ADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRARY 243 IR N+V PGTIAT+L A+ + +DEAK+ R P+ RLG+P ++AD V +LASD A Y Sbjct: 187 IRVNAVAPGTIATELAAKAVLTSDEAKRKIMS-RTPMKRLGQPSEIADVVAWLASDAASY 245 Query: 244 VTGAALLVDGG 254 VTG + VDGG Sbjct: 246 VTGEIVTVDGG 256 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: 171 Number of extensions: 12 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: 267 Length adjustment: 25 Effective length of query: 235 Effective length of database: 242 Effective search space: 56870 Effective search space used: 56870 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: 47 (22.7 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