Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 204 bits (518), Expect = 2e-57 Identities = 110/244 (45%), Positives = 156/244 (63%), Gaps = 1/244 (0%) Query: 17 ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADITQFNQLTP 75 +TLNRP + NAL+A +LEE+++ + + + D IR +++TG G K FCAGAD+ + +T Sbjct: 17 MTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLKERRLMTE 76 Query: 76 AEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEIN 135 EA + ++ IE+L P IA+ING+ALGGGLELALACD+RIA A LGLPE Sbjct: 77 QEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAALGLPETG 136 Query: 136 LGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRKLA 195 L I PG GGTQRL R+IG G+A EM+ TG + ++A + GL+ R+ +L + LA Sbjct: 137 LAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLMNDAITLA 196 Query: 196 EKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKREPT 255 ++I K PI+L K+ + LD L +GL E + + TED+ EG+ AF EKR P Sbjct: 197 KQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKAFQEKRTPH 256 Query: 256 FKGK 259 ++GK Sbjct: 257 YRGK 260 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: 138 Number of extensions: 7 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: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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