Align SDR family oxidoreductase (characterized, see rationale)
to candidate GFF2780 HP15_2724 short-chain dehydrogenase/reductase SDR
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Marino:GFF2780 Length = 286 Score = 128 bits (322), Expect = 1e-34 Identities = 98/259 (37%), Positives = 136/259 (52%), Gaps = 20/259 (7%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLL--DVT 64 RL GKT LIT AA+GIG A FA +GA VI +DI + L + ++ H L DV+ Sbjct: 22 RLDGKTALITGAARGIGEAIAIQFAEQGATVIVSDIDDQMGQALVDSSKLDMHYLHLDVS 81 Query: 65 DDD----AIKALVAKVGTVDVLFNCAGYV----AAG--NILECDDKAWDFSFNLNAKAMF 114 D+ K++ + G +D+L N AG +AG + D +W+ N + Sbjct: 82 DESQWITCAKSIEDQFGGLDILVNNAGITGFLESAGPHDPEHLDLASWETVHATNLNGVA 141 Query: 115 HTIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQG- 173 + + M + ++ SIVNI+S + V G+ AY +SKA V TKSVA +G Sbjct: 142 LGCKYGIKLMKSSRSASIVNISSRSGLV-GIPGAAAYASSKAGVRNHTKSVALHCAEKGY 200 Query: 174 -IRCNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALY 232 IRCN+I PG I SP + G++ + A A P+GR+GK E+VA ALY Sbjct: 201 PIRCNSIHPGAIMSPMWEAMLGE-----GEAREAAIAEVEAGVPIGRMGKPEDVAYAALY 255 Query: 233 LASDESNFTTGSIHMIDGG 251 LASDESN+ TG IDGG Sbjct: 256 LASDESNYVTGIELNIDGG 274 Lambda K H 0.316 0.129 0.359 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: 178 Number of extensions: 14 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: 286 Length adjustment: 25 Effective length of query: 229 Effective length of database: 261 Effective search space: 59769 Effective search space used: 59769 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