Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate CA265_RS09910 CA265_RS09910 short-chain dehydrogenase/reductase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Pedo557:CA265_RS09910 Length = 280 Score = 93.2 bits (230), Expect = 5e-24 Identities = 66/204 (32%), Positives = 97/204 (47%), Gaps = 20/204 (9%) Query: 9 KGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNC--VFAP--AD 64 K V ITG + GLGL+ +L+ G S + KK NN F P + Sbjct: 3 KKKVWFITGASKGLGLSLVHQLLNAGQYVAA----TSRNIGELKKAVNNDGGKFLPLAVN 58 Query: 65 VTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMG 124 + +E+ V+ A+ KF R+DV +N AG + L +T + DVN+ G Sbjct: 59 LANEQSVEDAIKATIAKFERIDVVINNAGYGIGGSIEELSDAET------RNSFDVNVFG 112 Query: 125 TFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184 T NVIR + + + + G IIN AS+A G G A Y+A+K ++ ++ A Sbjct: 113 TLNVIRKASPYL------RAQRAGHIINIASIAGIAGATGWAVYAAAKSAVIALSEVSAE 166 Query: 185 DLAPIGIRVMTIAPGLFGTPLLTS 208 DL GI+V +APG F T LT+ Sbjct: 167 DLKEFGIKVTVVAPGAFRTSFLTA 190 Lambda K H 0.318 0.135 0.385 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: 144 Number of extensions: 7 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: 261 Length of database: 280 Length adjustment: 25 Effective length of query: 236 Effective length of database: 255 Effective search space: 60180 Effective search space used: 60180 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