Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate H281DRAFT_02741 H281DRAFT_02741 Enoyl-CoA hydratase/carnithine racemase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__Burk376:H281DRAFT_02741 Length = 260 Score = 137 bits (344), Expect = 3e-37 Identities = 90/257 (35%), Positives = 141/257 (54%), Gaps = 10/257 (3%) Query: 7 TSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAG 66 T + T + L+ P RNA+ +M A I AL+SV RD +RAVV+TG FCAG Sbjct: 5 TIQVTIESQVATIALNRPEKRNAITNEMRAELIAALESVSRDRDVRAVVLTGNGKGFCAG 64 Query: 67 GNLNRLLENRAKDPSVQA-----QSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLAL 121 G+++ + + R + P+ + ++ ++ L KP IAAV+GAAAG G +AL Sbjct: 65 GDVSGMAQ-RMEAPAGEVAFNGWSRQQIVHHTVNLLYSMPKPTIAAVNGAAAGLGADMAL 123 Query: 122 ACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELG 181 +CD I+A+ +A F SY R GL PDGGG +FL + + A E++ G+ + A ELG Sbjct: 124 SCDFILASHEASFTWSYIRRGLIPDGGGMYFLPRRVGLARAKELIFSGRKVDAKEALELG 183 Query: 182 VVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASL 241 + ++L+ P + A AWA EL + S ++A KT++ + LS H V + + ++ Sbjct: 184 IADRLSAPDSLIADAHAWAVELSQGSATALALGKTIL--NQSYELSAHQVFAQGSQAQAV 241 Query: 242 HH--REGLEGISAFLEK 256 + E + + AFL K Sbjct: 242 CYTSSEHRDSVLAFLNK 258 Lambda K H 0.317 0.132 0.377 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: 142 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: 262 Length of database: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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: 41 (21.7 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