Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate BPHYT_RS25360 BPHYT_RS25360 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__BFirm:BPHYT_RS25360 Length = 256 Score = 179 bits (454), Expect = 5e-50 Identities = 98/243 (40%), Positives = 138/243 (56%) Query: 16 WITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTP 75 W+TL+RP +N+LN ++ L + +D +RV+++TG G+AFCAGAD+ + + T Sbjct: 13 WLTLDRPAAMNSLNREMATGLIAQLKAWRNDDAVRVLVVTGNGRAFCAGADLIEAAEATQ 72 Query: 76 AEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEIN 135 +F + E D + A KP IA +NG AL GGLE+ LACD+ +AAE A+LG N Sbjct: 73 PGRREFLELIVEFFDTLRAFPKPVIAAVNGLALAGGLEVVLACDVVLAAESARLGDAHSN 132 Query: 136 LGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRKLA 195 G++PG GG L R + A ++ TGD + + + YGLVN V+ A L + LA Sbjct: 133 FGVFPGAGGAAILPRKVPANVARYLLFTGDAMSAAELKGYGLVNEVLADAELRPRAQALA 192 Query: 196 EKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKREPT 255 K AKKSP+ LA +K V N D L E + + D +EG+ AF EKREP Sbjct: 193 HKFAKKSPLVLARMKRVANETADKSAADALRHELLELRNHQRSYDVQEGLRAFAEKREPQ 252 Query: 256 FKG 258 FKG Sbjct: 253 FKG 255 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: 147 Number of extensions: 3 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: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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