Align SDR family oxidoreductase (characterized, see rationale)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Pedo557:CA265_RS08355 Length = 254 Score = 149 bits (375), Expect = 7e-41 Identities = 85/251 (33%), Positives = 141/251 (56%), Gaps = 9/251 (3%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTH----LEELASIAGVE-THLLD 62 L K ++T GIG+A + A++GA V ++ H L+E+ + GV ++ D Sbjct: 4 LKNKKAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAFSYGCD 63 Query: 63 VTDDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLP 122 V+D A+ A+ ++G +++L N AG G D+ +D +N K +++ + A +P Sbjct: 64 VSDHQAVAAVFNEIGNINILINNAGIAHIGKADTTDEADFDRVMRVNVKGVYNCLHAAIP 123 Query: 123 GMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPG 182 + G I+N+AS A+ + G+ +RF Y A+K AV +T SVA D++ + IRCN+I P Sbjct: 124 QIRLSGGGVIINMASIAALI-GLPDRFVYSAAKGAVKAITMSVAKDYIGENIRCNSISPA 182 Query: 183 TIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTT 242 + +P ++ + K + E+ QP+GR+ K EEV ALALYL SDE++F T Sbjct: 183 RVHTPFVDGFLQ---KNYPDNIPEMFEKLSKTQPIGRMAKPEEVGALALYLCSDEASFIT 239 Query: 243 GSIHMIDGGWS 253 G + IDGG++ Sbjct: 240 GCDYPIDGGFT 250 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: 166 Number of extensions: 9 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: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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