Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate BPHYT_RS30440 BPHYT_RS30440 short-chain dehydrogenase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS30440 Length = 254 Score = 161 bits (408), Expect = 1e-44 Identities = 111/261 (42%), Positives = 144/261 (55%), Gaps = 17/261 (6%) Query: 2 LLKDKVVIVTGGS--RGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEA 59 LL KV +++GG+ RGIG A A AA GA +AI D D A E A I Sbjct: 6 LLDGKVAVISGGASPRGIGMATARKFAAHGARIAIF---DLD-----EKAAVEAAASIGP 57 Query: 60 LGRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVA 119 R + NV R Q V TV FG +D+L +NAGI FLD+ PE + + Sbjct: 58 EHRGYVC---NVTDRGACQAAVERTVADFGSIDILINNAGITQAAKFLDIDPESWDRILD 114 Query: 120 VNLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGM--QTHYTPTKAGVHSLMQSC 177 VNL G Y++QA QMK Q G+I SS+SA GGG+ HY+ KAGV L ++ Sbjct: 115 VNLRGVLYLSQAVVPQMKKQ-KSGSIGCMSSVSAQRGGGILGGPHYSAAKAGVLGLAKAM 173 Query: 178 AVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLA 237 A LG GIR N V PG I TD+NA ++D+ K+ IPL RLG P+DVA FLA Sbjct: 174 ARELGNDGIRVNCVTPGLIQTDINAGKISDD-KRVEILSGIPLNRLGVPDDVAGAFLFLA 232 Query: 238 SDRARYVTGAALLVDGGLFVN 258 SD + Y+TGA + V+GG+ ++ Sbjct: 233 SDLSSYITGAVIDVNGGMLIH 253 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: 4 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: 260 Length of database: 254 Length adjustment: 24 Effective length of query: 236 Effective length of database: 230 Effective search space: 54280 Effective search space used: 54280 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