Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate PfGW456L13_2433 Phenylacetate degradation enoyl-CoA hydratase PaaB (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2433 Length = 263 Score = 166 bits (420), Expect = 5e-46 Identities = 92/263 (34%), Positives = 143/263 (54%), Gaps = 4/263 (1%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60 M FE I E + ++LNRPD+LN+ N ++ E+ A+ Q +P++RV+++TG+G+ Sbjct: 1 MNFEHILFSIEAGVALLSLNRPDQLNSFNTQMHGEVKEALKQVRQNPDVRVLLLTGEGRG 60 Query: 61 FCAGADITQFN----QLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELAL 116 FCAG D++ N P K ++ ++ L P I +NG A G G + L Sbjct: 61 FCAGQDLSDRNVAPGSAVPDLGESIEKFYNPLIRQLRDLPMPVICAVNGVAAGAGANIPL 120 Query: 117 ACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYG 176 ACD+ +AA A +G+ P GGT L R++G RA + + G+R+ + AE++G Sbjct: 121 ACDLVLAARSASFIQAFCKIGLIPDSGGTWTLPRLVGMARAKALALLGNRLSAEQAEQWG 180 Query: 177 LVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVF 236 L+ + V A L E KLA +A + LALIK +N + + L LE + Sbjct: 181 LIYQCVEDAELRDEALKLARHLATQPTYGLALIKRSLNASMSNSFDEQLELEKDLQRLAG 240 Query: 237 STEDKKEGVSAFLEKREPTFKGK 259 +ED +EGV AF+EKR P+FKG+ Sbjct: 241 RSEDYREGVGAFMEKRTPSFKGR 263 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: 158 Number of extensions: 4 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: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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