Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_076581564.1 BB347_RS11510 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_001971705.1:WP_076581564.1 Length = 261 Score = 183 bits (464), Expect = 4e-51 Identities = 107/260 (41%), Positives = 154/260 (59%), Gaps = 12/260 (4%) Query: 5 TIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVS--QAESDPEI--RVIIITGKGKA 60 T+E ++ + +TLNRPD LNAL+ +L E++ ++ + ++D EI RV++++G Sbjct: 9 TVEFDEDTGVGRVTLNRPDALNALSGQLREDIVESLRLLEEQNDDEIALRVVVVSGAAGN 68 Query: 61 FCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDI 120 FCAGADIT+F +P R I P IA I GY LGGGLE A+ACD Sbjct: 69 FCAGADITEFEDASPG-----GSPERTHYQFIMDFPVPVIAKIEGYCLGGGLETAMACDF 123 Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180 R A E+A+LGLPE++LGI PG GG Q ++ + G A E+ MTGD I A++ G+VNR Sbjct: 124 RFADEDARLGLPEVDLGIIPGAGGVQYISELAGPAAAKEIAMTGDHISATRADELGIVNR 183 Query: 181 VVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTED 240 V +L++ T+K AEKIA K P+++ IK + L G+ ++ + + +TED Sbjct: 184 VPD--DLDEATQKFAEKIASKPPLAIQTIKNSARISTQTSLKEGIDYDNKVFEPLLATED 241 Query: 241 KKEGVSAFLE-KREPTFKGK 259 KEG AF E EP FKG+ Sbjct: 242 HKEGARAFAEDDYEPEFKGR 261 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: 163 Number of extensions: 8 Number of successful extensions: 4 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: 261 Length adjustment: 24 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 24 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