Align Short-chain dehydrogenase (characterized, see rationale)
to candidate HSERO_RS11255 HSERO_RS11255 3-ketoacyl-ACP reductase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS11255 Length = 252 Score = 107 bits (266), Expect = 3e-28 Identities = 77/251 (30%), Positives = 126/251 (50%), Gaps = 6/251 (2%) Query: 3 LNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDP-QFWARLTGLQPRAALFQ 61 + LQDKV IVTGG SG G I+ A EGA VV E + + RA + Sbjct: 1 MRLQDKVAIVTGGGSGFGEGIAKAYAREGAAIVVADIGEAGGLRVVEEIKAAGGRAVFAK 60 Query: 62 LELQDEARCGEAVAETVRRFGRLDGLVNNAGVN--DSVGLDAGRNEFVASLERNLIHYYV 119 ++ A + +A + FG+LD +VNNAG + L+ +EF N+ ++ Sbjct: 61 ADVSKRADMDQLLATALEHFGKLDIVVNNAGTTHRNRPMLEVEEDEFDRVYAVNVKSIFL 120 Query: 120 MAHYCVPHLKATRG-AILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRV 178 A VP+ + G A +N++S + + + Y SKGA ++ ++ AA L D +RV Sbjct: 121 SAKTFVPYFRQVGGGAFINIASTAGIRPRPGLTWYNGSKGAVITTSKSMAAELGPDKIRV 180 Query: 179 NALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSH 238 N + P T L +++ + P+ + + + IP+G RF+T E++A+ ++L S + Sbjct: 181 NCVNPVISATGLLSEFMGVPDTPENRKKFVAT-IPMG-RFSTPEDIANACLYLGSDEAEF 238 Query: 239 TTGQWVFVDGG 249 TG + VDGG Sbjct: 239 VTGVCIEVDGG 249 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: 152 Number of extensions: 12 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: 252 Length adjustment: 24 Effective length of query: 234 Effective length of database: 228 Effective search space: 53352 Effective search space used: 53352 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