Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF3899 Psest_3969 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::P07896 (722 letters) >FitnessBrowser__psRCH2:GFF3899 Length = 412 Score = 296 bits (757), Expect = 2e-84 Identities = 154/385 (40%), Positives = 232/385 (60%), Gaps = 16/385 (4%) Query: 296 VSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKII--TFTLEKEASRAHQN 353 + + V+G GTMGRGI +S A G+ V ++++P+ L+ A + T+ R + Sbjct: 8 IQTAAVIGAGTMGRGIVMSLANAGVQVRWLDNNPEMLERALGTVADTYAHNVRQGRIDEA 67 Query: 354 GQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALN 413 A+ + + ++ + L+ VDLV+EAV+E++ LK+K+F EL + KP L +NTSAL+ Sbjct: 68 QAAARRACISKAADYQALADVDLVIEAVYENLELKQKIFRELDGIVKPAGILASNTSALD 127 Query: 414 VDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVG 473 +D IA+ T RP+ V+G HFFSPAH+M+LLE++ +S + L K++GK+ V+ G Sbjct: 128 LDAIAAVTKRPEQVVGLHFFSPAHIMKLLEIVRGAKTSKAVLDASTELGKRMGKVSVIAG 187 Query: 474 NCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIR 533 NC GF+GNRMLA Y + +L EG+ P VD L+ FGF MGPFR+ D+ G+D+ W+ R Sbjct: 188 NCQGFIGNRMLATYVREARMMLLEGAYPHQVDAALQGFGFAMGPFRMYDVVGIDLEWRAR 247 Query: 534 KGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDP 593 + G K + + + LCE GRFGQK+ G+Y+Y + R + DP Sbjct: 248 ELAG-------------KGQDEVEVQVDNRLCELGRFGQKSRMGYYRYAEG-SRQAEHDP 293 Query: 594 WLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGY 653 + + + E ++R I EEILERCL +L+NE +ILEEGMA ID +YL+GY Sbjct: 294 EVDALVQRESERLGFQRREIGSEEILERCLLALVNEGAKILEEGMAESSADIDTVYLYGY 353 Query: 654 GWPRHKGGPMFYAASVGLPTVLEKL 678 G+P GGPM +A GLP + ++L Sbjct: 354 GFPAEVGGPMTWADRQGLPAIRDRL 378 Lambda K H 0.319 0.136 0.405 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: 676 Number of extensions: 32 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: 722 Length of database: 412 Length adjustment: 35 Effective length of query: 687 Effective length of database: 377 Effective search space: 258999 Effective search space used: 258999 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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