Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate Pf1N1B4_3809 Oxidoreductase, short chain dehydrogenase/reductase family
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3809 Length = 248 Score = 140 bits (354), Expect = 2e-38 Identities = 96/259 (37%), Positives = 132/259 (50%), Gaps = 26/259 (10%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L KV ++ GGSRGIG AI AAEGA VA Y + E+ I + G Sbjct: 6 LSGKVALIQGGSRGIGAAIVKRLAAEGATVAFTYVSST-------AKAEELQNSITSAGG 58 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVNL 122 +AI+ + A + V+ TVEAFG++D+L +NAG+ + D E + T+A+N+ Sbjct: 59 NALAIKADSADAVAIRNAVKVTVEAFGRLDILVNNAGVLAVASLEDFKLEDFDQTLAINV 118 Query: 123 NGAFYVTQAAAQQMKLQGTGGAIVATSSISA----LVGGGMQTHYTPTKAGVHSLMQSCA 178 F TQ AA+ M GG IV S +A GGG Y +K+ + L + A Sbjct: 119 RSVFIATQEAAKHMT---EGGRIVNIGSTNAERMPFAGGG---PYAMSKSALVGLTKGLA 172 Query: 179 VALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPL---GRLGRPEDVADCVTF 235 LGP GI N+V PG + TD+N A + E IPL GR GR E++A V + Sbjct: 173 RDLGPRGITINNVQPGPVDTDMN------PASGDFAESLIPLMAVGRYGRVEEIASFVAY 226 Query: 236 LASDRARYVTGAALLVDGG 254 L A Y+TGA+L +DGG Sbjct: 227 LVGPEAGYITGASLTIDGG 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: 161 Number of extensions: 11 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: 248 Length adjustment: 24 Effective length of query: 236 Effective length of database: 224 Effective search space: 52864 Effective search space used: 52864 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