Align Uncharacterized protein YbdD (characterized, see rationale)
to candidate AZOBR_RS18100 AZOBR_RS18100 hypothetical protein
Query= uniprot:P0AAS9 (65 letters) >FitnessBrowser__azobra:AZOBR_RS18100 Length = 67 Score = 75.5 bits (184), Expect = 7e-20 Identities = 36/62 (58%), Positives = 41/62 (66%), Gaps = 1/62 (1%) Query: 4 SLAKAGKYLGQAAKLMIGMPDYDNYVEHMRVNHPDQTPMTYEEFFRERQDARYGGKGGAR 63 +L++ Y Q AKLMIG+PDYD Y+EHMR HPDQ MTY EF R ARYG G A Sbjct: 7 NLSRFRGYFEQTAKLMIGVPDYDTYLEHMRTRHPDQPAMTYTEFLDNRLQARYGA-GKAG 65 Query: 64 CC 65 CC Sbjct: 66 CC 67 Lambda K H 0.322 0.139 0.437 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: 41 Number of extensions: 2 Number of successful extensions: 1 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: 65 Length of database: 67 Length adjustment: 5 Effective length of query: 60 Effective length of database: 62 Effective search space: 3720 Effective search space used: 3720 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: 37 (20.1 bits) S2: 37 (18.9 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