Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate CCNA_02658 CCNA_02658 3-hydroxybutyryl-CoA dehydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Caulo:CCNA_02658 Length = 265 Score = 164 bits (415), Expect = 2e-45 Identities = 98/261 (37%), Positives = 143/261 (54%), Gaps = 8/261 (3%) Query: 6 IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQA-ESDPEIRVIIITGKGKAFCAG 64 I T+K G++ +TLNRPD +NAL A + A +A D +IR +I+TG GKAF AG Sbjct: 4 ILTEKRGHIAILTLNRPDAMNALGAPGDGDQVAAACEAINDDQDIRCVILTGAGKAFSAG 63 Query: 65 ADITQFNQLTPAEAWK-------FSKKGREIMDKIEALSKPTIAMINGYALGGGLELALA 117 D+ A + K I+ I L P+IA +NG A+G G ++A Sbjct: 64 GDVKAMKAREGAFGGNGVKVRDGYRKNIHRIVRAIYGLEVPSIAAVNGAAIGLGCDVACM 123 Query: 118 CDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGL 177 DIRIAA+ A+ G+ + LG+ PG GG + R IG RA E++ TGD I A ++GL Sbjct: 124 TDIRIAADTARFGVTFLKLGLIPGDGGAWLMPRTIGMSRAAELLFTGDVIDAAKAAEWGL 183 Query: 178 VNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFS 237 +++ VP +L E LAE+IA++ P +L + K ++ G + + + + + + Sbjct: 184 ISKAVPAGDLMGEALALAERIAQQPPHALRMAKSLLKHGQTASYDTLMEMSAAAQAIAHH 243 Query: 238 TEDKKEGVSAFLEKREPTFKG 258 TED EGV A LEKR P FKG Sbjct: 244 TEDHMEGVDAILEKRSPVFKG 264 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: 140 Number of extensions: 5 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: 259 Length of database: 265 Length adjustment: 25 Effective length of query: 234 Effective length of database: 240 Effective search space: 56160 Effective search space used: 56160 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