Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Ac3H11_4989 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4989 Length = 266 Score = 138 bits (348), Expect = 1e-37 Identities = 80/251 (31%), Positives = 126/251 (50%) Query: 9 KKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADIT 68 ++EG + + NRP+ LNA++ + AV +DP +R +++ G G+ F AG D+ Sbjct: 16 EREGAIATLRFNRPEALNAIDVPMANAFLAAVQTVAADPAVRAVVLCGNGRGFMAGGDLA 75 Query: 69 QFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQ 128 A + + ++ P +A ++G A G GL L L D IAAE + Sbjct: 76 TLRADPVQSAIDILTPLNAALLLLAQMNAPVVAQVHGVAAGAGLSLLLMADYVIAAEGTR 135 Query: 129 LGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLE 188 L L INLG G + L R++G +ALE+ + GD DA + GLVNRVVP A L+ Sbjct: 136 LNLAYINLGTSCDVGASWALPRIVGVRQALEIALLGDAFTADDALRLGLVNRVVPAAELD 195 Query: 189 QETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAF 248 T LA+++A ++ +K ++ +D L LA E + TED + GV AF Sbjct: 196 SATAALAQRLASGPTLAYGAMKRLMRASMDHTLPEQLAAEKDAFVHCAGTEDFRAGVEAF 255 Query: 249 LEKREPTFKGK 259 ++ +F G+ Sbjct: 256 HLRQSASFAGR 266 Lambda K H 0.315 0.135 0.382 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: 136 Number of extensions: 4 Number of successful extensions: 2 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: 259 Length of database: 266 Length adjustment: 25 Effective length of query: 234 Effective length of database: 241 Effective search space: 56394 Effective search space used: 56394 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: 42 (22.0 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