Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate N515DRAFT_0851 N515DRAFT_0851 hypothetical protein
Query= BRENDA::Q84X96 (319 letters) >FitnessBrowser__Dyella79:N515DRAFT_0851 Length = 267 Score = 81.6 bits (200), Expect = 2e-20 Identities = 58/191 (30%), Positives = 97/191 (50%), Gaps = 12/191 (6%) Query: 54 AIITGPTDGIGKAFAFQLAQKGLNLVLVARNPDKLKDVSDSIQAKYSNTQIKTVVMDFSG 113 A+ITG + GIG +A +LA++G +L+LVARN +L D+ A+ + + F Sbjct: 9 ALITGASTGIGAVYADRLARRGHDLILVARNRQRLDDL-----ARRLTDETGRSIQVFPA 63 Query: 114 DI--DGGVRRIKEAIEG-LEVGILINNAGVSYPYAKYFHEVDEEMLGNLIKINVEGTTKV 170 D+ GV +++ + + +L+NNAG+ E D + +I++N+ T++ Sbjct: 64 DLGNPAGVAGVEQLLRSDRSISMLVNNAGMG--ATAPLLESDVARMTQMIELNIGALTRL 121 Query: 171 TQAVLVNMLKRKRGAIVNMGSGAAALIPSYPFYSVYAGAKTYVDQFSRCLHVEYKKSGID 230 T A + ++R G ++N+ S A+ P VY G K YV F+R L E G+ Sbjct: 122 TYAAVPGFVERGGGTVINIAS-VVAIAPEL-LNGVYGGTKAYVLAFTRSLQHELAAQGVR 179 Query: 231 VQCQVPLYVAT 241 VQ +P AT Sbjct: 180 VQAVLPGATAT 190 Lambda K H 0.322 0.138 0.405 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: 160 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: 319 Length of database: 267 Length adjustment: 26 Effective length of query: 293 Effective length of database: 241 Effective search space: 70613 Effective search space used: 70613 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