Align Short-chain alcohol dehydrogenase protein (characterized, see rationale)
to candidate CCNA_01885 CCNA_01885 short chain dehydrogenase
Query= uniprot:D8IS13 (254 letters) >FitnessBrowser__Caulo:CCNA_01885 Length = 258 Score = 130 bits (327), Expect = 3e-35 Identities = 87/256 (33%), Positives = 133/256 (51%), Gaps = 22/256 (8%) Query: 6 GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKPH-----LDELAGIAGVETHL 60 GRL G+ +T A++G+GRA+ L A EGA V D+ K H DE+ G L Sbjct: 9 GRLEGRVAAVTGASRGLGRATAALLAAEGAMVALLDL-KAHWAQAAADEIIAAGGKAVGL 67 Query: 61 -LDVTDDAAIKALVAKI----GTIDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFH 115 DV+D A+ A + + G DVL N A + + ++ D ++ + Sbjct: 68 GCDVSDREALTATLGAVNDAHGRFDVLVNNAMWNVYEPLAAIRPESLDRMVSVGFSGVIW 127 Query: 116 TIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVAQGIR 175 ++A P M A GSIVNIAS ++ + G+ N AY KA V G+T++ AA+ A IR Sbjct: 128 GMQAAAPLMAASGGGSIVNIASVSAQL-GIPNGIAYCGVKAGVAGMTRAAAAELGAMNIR 186 Query: 176 CNAICPGTIESPSLNQRISTQAKETGKSEEEVRAAFVGRQPMGRIGKAEEVAALALYLAS 235 NA+ P T+++ + + +S EE A +G+ P+GR+G E++A YLA Sbjct: 187 VNAVAPSTVDTEGVRRVVS----------EERIAMRIGQTPLGRLGTTEDIAKAVRYLAC 236 Query: 236 DESNFTTGSIHMIDGG 251 D+S+F TG + +DGG Sbjct: 237 DDSDFVTGQMLTVDGG 252 Lambda K H 0.317 0.130 0.365 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: 170 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: 254 Length of database: 258 Length adjustment: 24 Effective length of query: 230 Effective length of database: 234 Effective search space: 53820 Effective search space used: 53820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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