Align SDR family oxidoreductase (characterized, see rationale)
to candidate 202371 SO3263 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__MR1:202371 Length = 255 Score = 99.0 bits (245), Expect = 8e-26 Identities = 79/253 (31%), Positives = 126/253 (49%), Gaps = 27/253 (10%) Query: 11 KTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAG-----VETHLLDVTD 65 K VLIT ++GIG + FA G V T ++ H ++ S+A V LD + Sbjct: 14 KLVLITGGSRGIGAGIAKAFAEAGYWVAITYLN--HQDKAVSLANILGDKVAAFALDQSK 71 Query: 66 DDAIKALVAKVG-----TVDVLFNCAGYVAAGNILECDDKAWDFS--FNLNAKAMFHTIR 118 ++IK + +V ++DVL N G +A D A DF+ N N + F + Sbjct: 72 PESIKQCITEVEKYFNRSIDVLIN-NGAIAQEKPFS-DITADDFTTMLNTNLRGPFLLAQ 129 Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNA 178 A +P M G I+NI S G N+ Y A+KA ++ L++S+A + GIR N Sbjct: 130 ACIPAMQQHGFGRIINIGSIGGQWGGY-NQVHYAAAKAGLINLSQSIAKIYSRDGIRTNT 188 Query: 179 ICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDES 238 I G + + ++T+A GK + A P+GR+GK E++A++AL+LAS +S Sbjct: 189 IAIGLVATEMTEHELTTEA---GKQK-------AAAIPVGRLGKVEDIASIALFLASQDS 238 Query: 239 NFTTGSIHMIDGG 251 ++ +G +GG Sbjct: 239 DYLSGQTLNANGG 251 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: 140 Number of extensions: 13 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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