Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate 3608349 Dshi_1751 Enoyl-CoA hydratase/isomerase (RefSeq)
Query= reanno::Phaeo:GFF1711 (348 letters) >FitnessBrowser__Dino:3608349 Length = 348 Score = 389 bits (998), Expect = e-113 Identities = 198/347 (57%), Positives = 246/347 (70%), Gaps = 2/347 (0%) Query: 1 MSDIDIRITGRAGRITLTRSKALNALSYDMCMAVDAALKAWADDDAVDLVVMDAEGEKAF 60 MSDI IRI GRAGRITL R +ALNAL+Y+MC+A+DAAL+AWA+D V LV+++ GEKAF Sbjct: 1 MSDIAIRIDGRAGRITLNRPRALNALTYEMCLAIDAALRAWAEDPEVALVLIEGAGEKAF 60 Query: 61 CAGGDIAELYQTGTSGDYDYGRRFWRDEYRMNARIFEYPKPVLSFLQGFVMGGGVGLGCH 120 AGGDI E+Y+TGT GDY YGRRFWRDEYRMNARI YPKPV+SFLQGF MGGGVG+GCH Sbjct: 61 SAGGDIVEMYETGTRGDYSYGRRFWRDEYRMNARIAGYPKPVVSFLQGFTMGGGVGVGCH 120 Query: 121 GTHRIVGDSTKIAMPEVGIGLIPDVGGTLMLALAPGRLGEYLGLTGARMTAADAIYAGFA 180 G+HRIVG++++IAMPE GIGLIPDVGGT +LA APGRLGEY G+TGARM DA+ GFA Sbjct: 121 GSHRIVGETSQIAMPECGIGLIPDVGGTYLLARAPGRLGEYYGMTGARMGPGDAVLTGFA 180 Query: 181 DHYVPETRWPNLISELEQTGRADLLAESAETAPAGTLAPMYDDIGRNFGGETLTDILTAL 240 HY+P+ W + L +TG + + P +AP +I +F ++ AL Sbjct: 181 SHYLPQADWDAAKAALVETGTVTEMEAACPAPPEARIAPFCAEIDADFNYVFGVEVEAAL 240 Query: 241 DHDDSSFADATLKTLRRNAPLSMAATVELLHRLRLGNMGIRKALELEYRFTHRAMEKGDF 300 D D+ F+ L LRR APLS A+ + L+ R+ G +R+AL EYR+T RA E GDF Sbjct: 241 DTRDTEFSRNALLGLRRGAPLSTASALHLI-RMARGYADLREALRHEYRWTWRAAEHGDF 299 Query: 301 LEGIRAQIIDKDRQPKWQYAD-RDVPATAVSQMLMPLATQTLQFEEE 346 +EGIRAQ+IDKDR P+WQ+A +V V M+ L L FE E Sbjct: 300 IEGIRAQVIDKDRTPRWQHAKLGNVTPEDVRAMVATLGPDELTFEGE 346 Lambda K H 0.320 0.137 0.406 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: 345 Number of extensions: 8 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: 348 Length of database: 348 Length adjustment: 29 Effective length of query: 319 Effective length of database: 319 Effective search space: 101761 Effective search space used: 101761 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 (21.8 bits) S2: 49 (23.5 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