Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834 Length = 256 Score = 153 bits (387), Expect = 3e-42 Identities = 94/261 (36%), Positives = 139/261 (53%), Gaps = 18/261 (6%) Query: 6 IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGA 65 + ++ G + + LNR +K NAL+ + + A+ + E D + VI+ITG F AGA Sbjct: 5 VVVERNGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGDSVFAAGA 64 Query: 66 DIT--------QFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALA 117 D+ Q +L + W K + KP IA ++G+ALG G ELA+ Sbjct: 65 DLNLLVDKGAQQVAELDLGQYWAPVAKSQ----------KPLIAAVSGFALGAGCELAMM 114 Query: 118 CDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGL 177 CDI +A A+ G PE +GI PG GGTQRL R +GK A M++ G+ + + A + GL Sbjct: 115 CDILVADNSARFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQLGL 174 Query: 178 VNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFS 237 V+ +V + LA+ A P +L IK V+ G D L LALE+ + ++F Sbjct: 175 VSELVTEGSALARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLLFD 234 Query: 238 TEDKKEGVSAFLEKREPTFKG 258 T+DK EG+ AFL+KR P + G Sbjct: 235 TQDKTEGMRAFLDKRPPRYTG 255 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: 125 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: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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