Align Short-chain dehydrogenase (characterized, see rationale)
to candidate Ac3H11_2732 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2732 Length = 278 Score = 100 bits (249), Expect = 3e-26 Identities = 86/253 (33%), Positives = 117/253 (46%), Gaps = 19/253 (7%) Query: 6 QDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTG-LQPRAALFQLEL 64 +D+V IVTGGASGIG A +L AEGA VV ++ + + A L L PRA+ + Sbjct: 15 KDQVAIVTGGASGIGEATCRRLVAEGATVVV---ADVNAERAAALASELGPRASAQVFDA 71 Query: 65 QDEARCGEAVAETVRRFGRLDGLVNNAGVN-------DSVGLDAGRNEFVASLERNLIHY 117 D V TV RFGRLD L NNA ++ D +D + + NL Y Sbjct: 72 ADVRSIERLVQGTVERFGRLDVLHNNAALSSPAIHAKDKNAIDIEFEVWDQVMAVNLRGY 131 Query: 118 YVMAHYCVPHLKATRG-AILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGV 176 Y +P + A G AI+N +S +G Y SK A + LTR+ A GV Sbjct: 132 LAGCKYALPTMIAQGGGAIVNTASTGGFSGDITRMAYSVSKAAIIGLTRQIATHHGAQGV 191 Query: 177 RVNALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRS 236 R NA+ P V+TP T +D + + L F E++A + FL SG + Sbjct: 192 RCNAVAPGLVLTP------GTRGAAASVIDVMQRHL-LVPEFGEPEDIAALVCFLASGEA 244 Query: 237 SHTTGQWVFVDGG 249 + GQ DGG Sbjct: 245 RYINGQTYIADGG 257 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: 147 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: 258 Length of database: 278 Length adjustment: 25 Effective length of query: 233 Effective length of database: 253 Effective search space: 58949 Effective search space used: 58949 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