Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate PfGW456L13_3427 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3427 Length = 272 Score = 204 bits (520), Expect = 1e-57 Identities = 105/260 (40%), Positives = 169/260 (65%), Gaps = 6/260 (2%) Query: 4 ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFC 62 + + +++ + W+ L RP ++NA+N ++ + + +A++ + DP+IRVI+I G+G + FC Sbjct: 15 DAVRLERDAMVGWVVLTRPRQINAINDEIRQGVPQALALLQQDPDIRVIVIRGEGDRGFC 74 Query: 63 AGADITQFNQLTPAEAWKFSKKGREI--MDKIEALSKPTIAMINGYALGGGLELALACDI 120 AGADI + + P + + ++ + ++ ++ ++KP IA I+GY +GGGLEL LACDI Sbjct: 75 AGADIKE--RRGPESSLQVRQRMENVRWIETLDGITKPVIAAIHGYCMGGGLELVLACDI 132 Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180 R AA +A LPE LG+ PG GGTQRL+RV+ G+AL+M++TGDR+ + A++ GLV+R Sbjct: 133 RFAAPDAVFALPETGLGLIPGGGGTQRLSRVVAPGQALDMLLTGDRVGAEQAQRIGLVSR 192 Query: 181 VV-PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239 + ANL QE R A++IA K P + A +K+ L+ L GL LE + ++ T+ Sbjct: 193 LASDSANLVQEVRAFAQRIASKPPTASAFVKQAARAALEMDLKRGLDLELDLFALLAPTK 252 Query: 240 DKKEGVSAFLEKREPTFKGK 259 D +E AF E+REP F G+ Sbjct: 253 DAREAAQAFSERREPRFTGE 272 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: 169 Number of extensions: 7 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: 272 Length adjustment: 25 Effective length of query: 234 Effective length of database: 247 Effective search space: 57798 Effective search space used: 57798 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