Align SDR family oxidoreductase (characterized, see rationale)
to candidate 16525 b2426 putative oxidoreductase (VIMSS)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Keio:16525 Length = 263 Score = 161 bits (407), Expect = 1e-44 Identities = 99/255 (38%), Positives = 142/255 (55%), Gaps = 13/255 (5%) Query: 6 GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETH-----L 60 G+L GKT LIT A QGIG FAR GA +I DIS +E+LA H + Sbjct: 2 GKLTGKTALITGALQGIGEGIARTFARHGANLILLDISP-EIEKLADELCGRGHRCTAVV 60 Query: 61 LDVTDDDAIKALVA----KVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHT 116 DV D ++ A + K G +D+L N AG G+ L+ D DF ++N K +++ Sbjct: 61 ADVRDPASVAAAIKRAKEKEGRIDILVNNAGVCRLGSFLDMSDDDRDFHIDINIKGVWNV 120 Query: 117 IRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRC 176 +AVLP M+A+K G IV ++S + AY +KAA+VGLTKS+A ++ GIR Sbjct: 121 TKAVLPEMIARKDGRIVMMSSVTGDMVADPGETAYALTKAAIVGLTKSLAVEYAQSGIRV 180 Query: 177 NAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASD 236 NAICPG + +P + + I+ Q+ + + V PM R+ EV LA +LASD Sbjct: 181 NAICPGYVRTP-MAESIARQSNP--EDPESVLTEMAKAIPMRRLADPLEVGELAAFLASD 237 Query: 237 ESNFTTGSIHMIDGG 251 ES++ TG+ ++IDGG Sbjct: 238 ESSYLTGTQNVIDGG 252 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: 163 Number of extensions: 6 Number of successful extensions: 3 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: 263 Length adjustment: 24 Effective length of query: 230 Effective length of database: 239 Effective search space: 54970 Effective search space used: 54970 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 Apr 09 2024. 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