Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Dsui_2448 Dsui_2448 3-oxoacyl-(acyl-carrier-protein) reductase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__PS:Dsui_2448 Length = 246 Score = 130 bits (327), Expect = 2e-35 Identities = 84/253 (33%), Positives = 125/253 (49%), Gaps = 25/253 (9%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGL---------AGKPVEARKLD 55 L G+ AL+T A +GIG A A AR GA V+ T DG AG L+ Sbjct: 2 LQGQIALVTGASRGIGKAVALELARLGATVVGTATSDDGAGKISAYLAEAGAKGRGALLE 61 Query: 56 VRD----DAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIR 111 VRD DA I AL E GAV +L N AG + +++WD D N+KA++R+ + Sbjct: 62 VRDQAQVDALIAALEKEFGAVSILVNNAGITRDNLAMRMKDDEWDAVIDTNLKAVFRLSK 121 Query: 112 AFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNA 171 A + M+ G IIN++S G P + Y A+KA V G+T+S+A + +R + N Sbjct: 122 AVMRGMMKARAGRIINITSVVGHA-GNPGQANYCAAKAGVSGMTRSLARELGSRNITVNC 180 Query: 172 ICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDES 231 + PG + + + A D + + P+GR+G PE+IAA +L S + Sbjct: 181 VAPGFIDTDMTK-----------ALDDKQKEGLLGNIPLGRLGSPEDIAAAVAFLASPAA 229 Query: 232 SFTTGHAHVIDGG 244 + TG ++GG Sbjct: 230 GYVTGSTIHVNGG 242 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: 157 Number of extensions: 8 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: 246 Length adjustment: 24 Effective length of query: 223 Effective length of database: 222 Effective search space: 49506 Effective search space used: 49506 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 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