Align Short-chain dehydrogenase (characterized, see rationale)
to candidate Synpcc7942_1573 Synpcc7942_1573 3-oxoacyl-(acyl-carrier protein) reductase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__SynE:Synpcc7942_1573 Length = 266 Score = 117 bits (292), Expect = 3e-31 Identities = 85/260 (32%), Positives = 131/260 (50%), Gaps = 20/260 (7%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWAR----LTGLQ------ 54 L +++ +VTG + GIG I+++LA+EGA V+ RS P+ R G Q Sbjct: 4 LDNQIALVTGSSQGIGQEIAIRLASEGASVVIDYRSHPEGAEETRKQVEAAGAQCHLAKD 63 Query: 55 --PRAALFQLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL-DAGRNEFVASLE 111 P + Q +L D + VAE+++ FG+LD LVNNAG+ + ++ L Sbjct: 64 HAPEGYVVQADLGDVTQVRNLVAESIKHFGKLDILVNNAGMERRAPFWEVTEADYDMVLN 123 Query: 112 RNLIHYYVMAHYCVPHLKATR--GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAA 169 NL + A V HL T+ G I+N+SS N + YC SKG +TR+ A Sbjct: 124 VNLKGAFFAAQALVQHLLETKRPGKIINISSVHEELPFPNFASYCLSKGGIKMMTRDLAV 183 Query: 170 ALRDDGVRVNALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAV 229 L + G+ +N + P + TP+ + NP E L+A+ IPL KR +++A + + Sbjct: 184 ELGEYGITINNVAPGAIETPINTNLL---NNPTE-LNALLGNIPL-KRLGKPKDIASLVL 238 Query: 230 FLLSGRSSHTTGQWVFVDGG 249 FL S + + TG +F DGG Sbjct: 239 FLASPDADYITGTTIFADGG 258 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: 149 Number of extensions: 5 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: 266 Length adjustment: 25 Effective length of query: 233 Effective length of database: 241 Effective search space: 56153 Effective search space used: 56153 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