Align SDR family oxidoreductase (characterized, see rationale)
to candidate 7026324 Shewana3_3466 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__ANA3:7026324 Length = 292 Score = 136 bits (342), Expect = 6e-37 Identities = 87/265 (32%), Positives = 134/265 (50%), Gaps = 13/265 (4%) Query: 1 MSASTGRLAGKTVLITAAAQGIGRASTELFAREGARVIATDIS-KTHLEELASIAGVETH 59 M+ L GK LIT + GIG A+ + A +G +I + + LA+ + H Sbjct: 27 MAVEHSSLKGKVGLITGSTSGIGLATAHVLAEQGCHLILHGLMPEAEGRRLAAEFAEQYH 86 Query: 60 L------LDVTDDDAIKAL----VAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLN 109 + D+ D ++I A V +G++D+L N AG N+ W+ +N Sbjct: 87 IHTYFSNADLRDPESIHAFMDAGVKALGSIDILVNNAGIQHTENVAHFPIDKWNDIIAIN 146 Query: 110 AKAMFHTIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADF 169 + FHTI+ +P M K+ G I+NIAS V V N+ AY A+K +VGLTK VA + Sbjct: 147 LSSAFHTIQQAVPAMAEKRWGRIINIASVHGLVASV-NKAAYCAAKHGIVGLTKVVAIEC 205 Query: 170 VSQGIRCNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFV-ARQPMGRIGKAEEVAA 228 QGI NAICPG +++P +N++I A G S DE + V A+QP+ + ++ Sbjct: 206 AEQGITVNAICPGWVDTPLINKQIEAIASNKGLSYDEAKYQLVTAKQPLPEMLDPRQIGE 265 Query: 229 LALYLASDESNFTTGSIHMIDGGWS 253 L+L S + TG+ +DG W+ Sbjct: 266 FVLFLCSSAARGITGASLAMDGAWT 290 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: 169 Number of extensions: 5 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: 292 Length adjustment: 25 Effective length of query: 229 Effective length of database: 267 Effective search space: 61143 Effective search space used: 61143 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