Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate AZOBR_RS02035 AZOBR_RS02035 3-ketoacyl-ACP reductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__azobra:AZOBR_RS02035 Length = 250 Score = 158 bits (399), Expect = 1e-43 Identities = 113/257 (43%), Positives = 140/257 (54%), Gaps = 20/257 (7%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSA--VAEVVAEIEAL 60 L K +VTGGSRGIG AIA+A A +GADVAI+Y RSA AEVV IEA Sbjct: 8 LVGKRALVTGGSRGIGAAIALALADKGADVAISY---------ERSAERAAEVVRAIEAK 58 Query: 61 GRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAV 120 GRR +AI+ + A LV TVEA G +D+L +NAGI +M +++ + V Sbjct: 59 GRRAVAIQADSADPSAMAALVGRTVEALGGLDILVNNAGIARQGMVAEMSLADIDALLNV 118 Query: 121 NLNGAFYVTQAAAQQMKLQGTGGAIVATSSISA--LVGGGMQTHYTPTKAGVHSLMQSCA 178 N+ A V QAA +K GG IV S A + G+ T Y+ TK+ +L A Sbjct: 119 NVRAAVLVAQAAIPHLK---DGGRIVFIGSCLADRITAPGV-TIYSMTKSAQTALTHGLA 174 Query: 179 VALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLAS 238 LGP I N V PG TD+N AD A + PLGR G+PEDVA V FLAS Sbjct: 175 RELGPRDITVNLVQPGATNTDMNP---ADGAHAEILRSQTPLGRYGQPEDVAAAVAFLAS 231 Query: 239 DRARYVTGAALLVDGGL 255 AR ++GA L VDGGL Sbjct: 232 PAARQISGATLTVDGGL 248 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: 157 Number of extensions: 10 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: 250 Length adjustment: 24 Effective length of query: 236 Effective length of database: 226 Effective search space: 53336 Effective search space used: 53336 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