Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_10120 AO356_10120 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::P07896 (722 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10120 Length = 408 Score = 296 bits (758), Expect = 1e-84 Identities = 161/413 (38%), Positives = 243/413 (58%), Gaps = 22/413 (5%) Query: 296 VSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKII--TFTLEKEASRAHQN 353 + V+G GTMGRGI + A G++V V+++P+ L+ A + T+ R Q+ Sbjct: 8 IQRAAVVGAGTMGRGIVMCLANAGVAVQWVDNNPQMLEQALVAVAETYAHGVRQGRIDQD 67 Query: 354 GQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALN 413 + ++ + + VDLV+EAV+E++ LK+ +F EL L KP A L +NTSAL+ Sbjct: 68 EADARIARVTRADDYAAIREVDLVIEAVYENLELKQSIFRELDGLLKPEAILASNTSALD 127 Query: 414 VDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVG 473 +D IA+ T RP V+G HFFSPAH+M+LLE++ +S + + L +++GK+ V+ G Sbjct: 128 IDAIAAVTRRPAQVLGLHFFSPAHIMKLLEIVRGAQTSKAVLDAALVLGQRMGKVSVISG 187 Query: 474 NCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIR 533 NC+GF+GNRML PY + +L EG+ P VD L+ FGF MGPFR+ D+ G+D+ W+ R Sbjct: 188 NCHGFIGNRMLHPYVLEARKMLLEGAFPHQVDAALQGFGFAMGPFRMYDVVGIDLEWRAR 247 Query: 534 K--GQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKP 591 + G+G P + + + LCE GRFGQK+G G+Y Y+ P R + Sbjct: 248 ELAGKGQDAPEV---------------QVDNRLCELGRFGQKSGNGYYHYE-PGSRQAEH 291 Query: 592 DPWLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLH 651 D + + Q E ++R I EEILERCL +L+NE +IL+EG+A ID++YL+ Sbjct: 292 DVEVDALVLQVSEALGFQRREIGPEEILERCLLALVNEGAKILQEGIAESAHAIDLVYLN 351 Query: 652 GYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704 GYG+P KGGPM +A GL + +L + + D Q +P+ + L AQG Sbjct: 352 GYGFPADKGGPMAWADEQGLEAIHARLLELETKQGD--QWKPARVIGELAAQG 402 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: 688 Number of extensions: 39 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: 408 Length adjustment: 35 Effective length of query: 687 Effective length of database: 373 Effective search space: 256251 Effective search space used: 256251 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