Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_013842150.1 DESRU_RS10835 NAD(P)-dependent oxidoreductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_000215085.1:WP_013842150.1 Length = 299 Score = 153 bits (387), Expect = 3e-42 Identities = 94/257 (36%), Positives = 144/257 (56%), Gaps = 12/257 (4%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L +KV I+TGG GIGRA+A+A A EGADV I Y ++ + + A IE LGR Sbjct: 53 LMNKVAIITGGDSGIGRAVAIAFAKEGADVVIVYLNEHQDAETTK-------ARIEQLGR 105 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGI-CPFHAFLDMPPEVLESTVAVN 121 R +A+ G++ Q+V T++ FG++D++ +NA + P + L++ E L T N Sbjct: 106 RCLALAGDLRNEAFSAQIVNQTMQCFGRLDIVVNNAAVQFPQQSILNISSEQLHDTFRTN 165 Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVAL 181 + FY+T+AA +K G +I++T+S++A G Y+ TK + S +S + +L Sbjct: 166 IYPLFYLTKAALPCLK---AGSSIISTASVTAYEGNKQLIDYSSTKGAIVSFTRSLSQSL 222 Query: 182 GPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 GIR N+V PG I T L + E K F P+ R G+P ++A +LASD A Sbjct: 223 VEQGIRVNAVAPGPIWTPLIPASFSAEQVKV-FGTDTPMKRAGQPFELAPAYVYLASDDA 281 Query: 242 RYVTGAALLVDGGLFVN 258 YVTG + V+GG+ V+ Sbjct: 282 SYVTGQVIHVNGGVMVS 298 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: 131 Number of extensions: 6 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: 299 Length adjustment: 26 Effective length of query: 234 Effective length of database: 273 Effective search space: 63882 Effective search space used: 63882 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 24 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