Align Short-chain dehydrogenase (characterized, see rationale)
to candidate BPHYT_RS32935 BPHYT_RS32935 3-ketoacyl-ACP reductase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__BFirm:BPHYT_RS32935 Length = 248 Score = 83.6 bits (205), Expect = 4e-21 Identities = 78/254 (30%), Positives = 119/254 (46%), Gaps = 18/254 (7%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGA-IPVVFARSEPDPQ-FWARLTGLQPRAALFQL 62 LQ K+ +VTGG+ GIG A ++QLAAEGA + + ++ SE Q AR+ +A + Sbjct: 5 LQGKIALVTGGSRGIGAATAIQLAAEGATVALSYSSSEAAAQEVIARIEASGGKAIALKA 64 Query: 63 ELQDEARCGEAVAETVRRFGRLDGLVNNAG--VNDSVGLDAGRNEFVASLERNLIHYYVM 120 + D +AE + R GR+D LVNNA V +V A + F ++ N V Sbjct: 65 DQADAKAVKALIAEVIERLGRIDILVNNAAVFVTGTVAETADTSAFERQVKIN-YEAVVT 123 Query: 121 AHYCVPHLKATRGAILNVSSKTALTGQ-GNTSGYCASKGAQLSLTREWAAALRDDGVRVN 179 A + + G I+++SS A + Y A+K A ++ A L G+ VN Sbjct: 124 AIREASRVMDSGGRIISISSALAWRSTWPGLADYSATKRAIEGYSKGAARDLGPKGITVN 183 Query: 180 ALIPAEVMTPLYEKWIATFENPQEK--LDAITSKIPLGKRFTTSEEMADMAVFLLSGRSS 237 + T + NP + +A + LG RF EE+A + F+ S +S Sbjct: 184 VIGTGSTNTEM---------NPDDSPFAEAQAAATALG-RFGRPEEIASVIAFVASPAAS 233 Query: 238 HTTGQWVFVDGGYT 251 TG + VDGGY+ Sbjct: 234 FITGAIIPVDGGYS 247 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: 132 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: 248 Length adjustment: 24 Effective length of query: 234 Effective length of database: 224 Effective search space: 52416 Effective search space used: 52416 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: 46 (22.3 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