Align Short-chain dehydrogenase (characterized, see rationale)
to candidate Ac3H11_2762 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2762 Length = 255 Score = 93.6 bits (231), Expect = 4e-24 Identities = 75/252 (29%), Positives = 121/252 (48%), Gaps = 14/252 (5%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64 L + +++TGGASG+G + L GA+ V + + A+ G + ++++ Sbjct: 6 LAGRRILITGGASGMGEGLVRSLTGMGALVVSMDLNRERGEAVAKAAGAR---GFMEVDV 62 Query: 65 QDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGLDAGRNEFVASLER----NLIHYYVM 120 DE AV R G LD L++ AG+ S + +A E+ N ++M Sbjct: 63 ADEGSVARAVDAACTRLGGLDVLIHAAGIAPS---SPAQGTSLALWEKVFAVNATGTFLM 119 Query: 121 AHYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNA 180 PH++ G+I+N +S G N S Y A+KGA L+ TR A +RVNA Sbjct: 120 NRAVFPHMREQGGSIINFASAAGALGLPNKSAYSAAKGAVLAWTRTVAQEWGPYNIRVNA 179 Query: 181 LIPAEVMTPLYEKWIATFENPQ-EKLDAITSK-IPL-GKRFTTSEEMADMAVFLLSGRSS 237 + PA + TP+Y++ + Q DA+ ++ IPL GK ++++ + FL S + Sbjct: 180 IAPA-IWTPMYDQTRSEMSPEQLSAHDALMARVIPLGGKLGDMAQDLVPVLAFLASPGAR 238 Query: 238 HTTGQWVFVDGG 249 TGQ VDGG Sbjct: 239 FMTGQIFAVDGG 250 Lambda K H 0.318 0.134 0.394 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: 141 Number of extensions: 6 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: 258 Length of database: 255 Length adjustment: 24 Effective length of query: 234 Effective length of database: 231 Effective search space: 54054 Effective search space used: 54054 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 (21.7 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