Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_092056804.1 BQ4888_RS09680 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_900111775.1:WP_092056804.1 Length = 245 Score = 163 bits (413), Expect = 3e-45 Identities = 101/256 (39%), Positives = 150/256 (58%), Gaps = 11/256 (4%) Query: 2 LLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALG 61 + KD+V IVTG SRGIG++I++A AA GA + D D++ A +VAE++A G Sbjct: 1 MAKDRVAIVTGASRGIGKSISLALAACGAKIVAV---DIDLA-----ATEAMVAELKANG 52 Query: 62 RRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVN 121 IA++GNV +++V+ VEAFG+VD+L +NAGI L M E ++ + VN Sbjct: 53 TEAIAVQGNVTLSADAEKMVQAAVEAFGRVDILVNNAGITRDALLLRMKDEDWDAVLNVN 112 Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVAL 181 L GAF ++AAA+ M Q G I+ +S+ +G Q +Y +KAG+ L +S A L Sbjct: 113 LKGAFLCSRAAAKVMSKQ-RYGRIINIASVVGQMGNAGQANYCASKAGLMGLTRSNAREL 171 Query: 182 GPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 + N+V PG IATD+ D E + +IPL RLG ED+A V FLA +++ Sbjct: 172 ARRNVTVNAVAPGFIATDMT--DALPEKTREELAAQIPLERLGSAEDIAHAVVFLAQEKS 229 Query: 242 RYVTGAALLVDGGLFV 257 Y+TG L V+GG+++ Sbjct: 230 GYITGQVLAVNGGMYM 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: 153 Number of extensions: 11 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: 245 Length adjustment: 24 Effective length of query: 236 Effective length of database: 221 Effective search space: 52156 Effective search space used: 52156 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: 46 (22.3 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