Align SDR family oxidoreductase (characterized, see rationale)
to candidate AO356_20240 AO356_20240 short-chain dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20240 Length = 272 Score = 130 bits (326), Expect = 4e-35 Identities = 88/256 (34%), Positives = 135/256 (52%), Gaps = 15/256 (5%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASI---AGVETHLL-- 61 RL K VL+T AAQGIG A FA + AR++ +DI +E +A+ G + H L Sbjct: 18 RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQA 77 Query: 62 DVTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTI 117 DV+ ++A+ + G +DVL NCAG + LE ++ W F ++ ++ Sbjct: 78 DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 Query: 118 RAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCN 177 +AVLP M+ + GSI+NIAS SS + F Y +K ++GLT+++ ++ +G+R N Sbjct: 138 KAVLPQMIEQGVGSIINIASVHSS-HIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 Query: 178 AICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDE 237 AI PG IE+ +++ R + P R+G+ EVA A++LASDE Sbjct: 197 AIAPGYIET-----QLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDE 251 Query: 238 SNFTTGSIHMIDGGWS 253 + F S IDGG S Sbjct: 252 APFINASCITIDGGRS 267 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: 137 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: 254 Length of database: 272 Length adjustment: 25 Effective length of query: 229 Effective length of database: 247 Effective search space: 56563 Effective search space used: 56563 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