Align Short-chain dehydrogenase (characterized, see rationale)
to candidate AZOBR_RS05905 AZOBR_RS05905 putative 3-oxoacyl-[acyl-carrier-protein] reductase (3-ketoacyl-acyl carrier protein reductase)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__azobra:AZOBR_RS05905 Length = 263 Score = 116 bits (290), Expect = 5e-31 Identities = 89/251 (35%), Positives = 125/251 (49%), Gaps = 17/251 (6%) Query: 7 DKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLELQD 66 ++V +V+GG+ G+G + +L EG F+R P A + LQ R+ Q Sbjct: 23 ERVAVVSGGSRGLGFVLVQRLLDEGWGVATFSRGTPG----ADIEALQARSGSRLFWQQA 78 Query: 67 EARCGEAVAE----TVRRFGRLDGLVNNAGVNDSVGLDAGRNEFVAS-LERNLIHYYVMA 121 + R E++ VRRFGR+D L+NNA + L R VA + NL+ ++ Sbjct: 79 DLRLPESLHSFAKAVVRRFGRIDLLINNAALLTEGLLATTRGTTVADVIAANLVGPIALS 138 Query: 122 HYCV-PHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNA 180 CV P ++ RG I+NVSS ++ G S Y ASK TR A L +RVN+ Sbjct: 139 QACVKPMMQQRRGTIVNVSSINSVRGHPGVSIYTASKAGLDGFTRSMARELGPLNIRVNS 198 Query: 181 LIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTT 240 ++P T L A E+ D I + PL KR E+AD+A+FL S RSS T Sbjct: 199 IVPGFFETDLVAALTA------ERRDRIARRTPL-KRVAEIGEIADVAMFLASDRSSFVT 251 Query: 241 GQWVFVDGGYT 251 GQ + VDGGYT Sbjct: 252 GQTIIVDGGYT 262 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: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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 Apr 09 2024. 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