Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate PfGW456L13_2434 Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2434 Length = 257 Score = 196 bits (499), Expect = 3e-55 Identities = 105/243 (43%), Positives = 150/243 (61%), Gaps = 2/243 (0%) Query: 17 ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPA 76 ITL RP LNAL +LL EL ++ A++DP+ R +++TG KAF AGADI + + Sbjct: 17 ITLQRPQALNALTTELLGELAAELNIAQADPDTRAVVLTGSRKAFAAGADIKEMAERDLV 76 Query: 77 EAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEINL 136 ++ I SKP IA +NG+ALGGG ELA+ DI IA E+A+ G PEINL Sbjct: 77 GILDDPRQAS--WQAITRFSKPLIAAVNGFALGGGCELAMHADIIIAGEDARFGQPEINL 134 Query: 137 GIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRKLAE 196 GI PG GGTQRL R +GK A++M++TG+ I + A++ GLV+ V + +A Sbjct: 135 GIMPGAGGTQRLLRAVGKSMAMQMVLTGESIDARQAQRVGLVSEVTQPEFTVERALHIAH 194 Query: 197 KIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKREPTF 256 IA K+P+++ L KE + + +D+ L +GL E + V+ T D+ EG++AF EKR PTF Sbjct: 195 SIAAKAPLAVRLAKEALLKAMDTDLATGLRFERHAFTVLAGTRDRDEGIAAFQEKRSPTF 254 Query: 257 KGK 259 G+ Sbjct: 255 TGQ 257 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: 148 Number of extensions: 6 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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