Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate PfGW456L13_2984 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2984 Length = 257 Score = 217 bits (553), Expect = 2e-61 Identities = 119/262 (45%), Positives = 166/262 (63%), Gaps = 8/262 (3%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60 + +ETI + G + ITLNRP LNALNA+++ EL++A+ E+D I I++TG KA Sbjct: 1 VSYETILLETHGRVGLITLNRPQALNALNAQIVSELNQALDGFEADSNIGCIVLTGSKKA 60 Query: 61 FCAGADITQFNQLTPAEAW---KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALA 117 F AGADI + +LT + + FS D++ KP IA +NG+ALGGG ELAL Sbjct: 61 FAAGADIKEMAELTYPQIYIDDLFSDS-----DRVANRRKPIIAAVNGFALGGGCELALM 115 Query: 118 CDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGL 177 CD +A + A+ G PEINLG+ PG GGTQRLTR +GK +A+EM ++G I +AE+ G+ Sbjct: 116 CDFILAGDNARFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGI 175 Query: 178 VNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFS 237 V R+VP L E K+A IAKKS ++KE VNR + L G+ E + F+ Sbjct: 176 VARIVPSDELLDEALKVAALIAKKSLPIAMMVKESVNRAFEVSLAEGVRFERRVFHAAFA 235 Query: 238 TEDKKEGVSAFLEKREPTFKGK 259 T+D+KEG++AF+ KRE F+GK Sbjct: 236 TQDQKEGMAAFIAKREAEFQGK 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: 178 Number of extensions: 9 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