Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 116 bits (290), Expect = 5e-31 Identities = 84/255 (32%), Positives = 125/255 (49%), Gaps = 30/255 (11%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEAR----------KL 54 L + AL+T A +GIG A A A GA+V G A + V A K Sbjct: 6 LTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKA 65 Query: 55 DVRDDAAIKALAAEI----GAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMI 110 DV ++ ++AL A + G +DVL N AG +L +DW DLN+ ++ Sbjct: 66 DVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCS 125 Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170 RA ML + G IIN++S + G P + YSA+KA VIGLTK+VA + +RG+ N Sbjct: 126 RAAAKIMLKQRSGRIINIASVVGEM-GNPGQANYSAAKAGVIGLTKTVAKELASRGITVN 184 Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSD- 229 A+ PG +A+ + A L+ + P+GR G+ E+A + +L +D Sbjct: 185 AVAPGFIATD------MTSELAAEKLLEVI--------PLGRYGEAAEVAGVVRFLAADP 230 Query: 230 ESSFTTGHAHVIDGG 244 +++ TG IDGG Sbjct: 231 AAAYITGQVINIDGG 245 Lambda K H 0.320 0.133 0.381 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: 129 Number of extensions: 9 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: 247 Length of database: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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 (21.8 bits) S2: 46 (22.3 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