Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012756545.1 RLEG_RS04380 SDR family oxidoreductase
Query= BRENDA::Q84X95 (319 letters) >NCBI__GCF_000023185.1:WP_012756545.1 Length = 266 Score = 112 bits (279), Expect = 1e-29 Identities = 73/193 (37%), Positives = 111/193 (57%), Gaps = 12/193 (6%) Query: 54 AIITGPTDGIGKAFAFQLAQKGLHLVLVARNPDKLKAVSDSIQAKHSTTQIKTVLMDFSG 113 A++TG + GIG +A +LA+KG L+LVAR D+LKA+SD + A H T+++ V D + Sbjct: 10 ALVTGASAGIGAIYAARLAEKGYDLILVARRADRLKALSDKLGAAHG-TKVEVVEADLTK 68 Query: 114 DIDAGVRRIKEAI-EGLEVGILINNAGVS--YPYAKYFHEVDEELLGNLIKINVEGTTKV 170 D D V R+++ + E + +L+NNAG S P AK EE +I +NV T++ Sbjct: 69 DAD--VNRVEKVLKENSAITLLVNNAGNSTLAPVAK----TTEEDAAAMIALNVTALTRL 122 Query: 171 TQAVLVNMLKRKRGAIVNMGSGAAALIPSYPFYSVYAGAKTYVDQFSRCLHVEYKKSGID 230 T AVL L R GAI+N+ S + P ++Y+G K YV FSR L E ++ + Sbjct: 123 THAVLPAFLSRNHGAIINVAS--VLSFHALPISAIYSGTKGYVMNFSRGLQQELAETNVR 180 Query: 231 VQCQVPLYVATKM 243 +Q +P AT++ Sbjct: 181 LQLVMPAATATEL 193 Lambda K H 0.322 0.137 0.402 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: 156 Number of extensions: 8 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: 319 Length of database: 266 Length adjustment: 26 Effective length of query: 293 Effective length of database: 240 Effective search space: 70320 Effective search space used: 70320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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