Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_097028846.1 CRO07_RS01150 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_900207575.1:WP_097028846.1 Length = 258 Score = 135 bits (341), Expect = 6e-37 Identities = 86/260 (33%), Positives = 136/260 (52%), Gaps = 3/260 (1%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60 M + TI +++ + +TL RP+ +NAL++ + EL +AV+QA RVI++TG+G+ Sbjct: 1 MGYRTIRIEEQDGVALVTLCRPEVMNALSSLMRAELLQAVTQAAQ--AARVIVLTGEGRG 58 Query: 61 FCAGADITQFNQLTPAEAWKFSKKGRE-IMDKIEALSKPTIAMINGYALGGGLELALACD 119 FC+G D+ L + + ++ E ++ I PT+A +NG A G G LALACD Sbjct: 59 FCSGQDLGDAQGLETPDFGRILREEYEPLLRAIATCPIPTLAAVNGPAAGAGANLALACD 118 Query: 120 IRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVN 179 + IAA+ A +G+ P GGT L R IG RA+ + DRI + A +G++ Sbjct: 119 VVIAAQSASFIQAFTRIGLIPDAGGTWTLPRQIGLARAMGATLFADRIGAQHAADWGMIY 178 Query: 180 RVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239 VP R A ++A + +K+ + + LALE+ ++ Sbjct: 179 EAVPDEAFPARWRDRAAQLATGPTTAYRALKQALRASSGNDFNQQLALEADLQASCGTSA 238 Query: 240 DKKEGVSAFLEKREPTFKGK 259 D +EGV+AFLEKR P F G+ Sbjct: 239 DFREGVAAFLEKRPPRFTGR 258 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: 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: 258 Length adjustment: 24 Effective length of query: 235 Effective length of database: 234 Effective search space: 54990 Effective search space used: 54990 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