Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate N515DRAFT_0930 N515DRAFT_0930 methylglutaconyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__Dyella79:N515DRAFT_0930 Length = 264 Score = 124 bits (311), Expect = 2e-33 Identities = 88/257 (34%), Positives = 132/257 (51%), Gaps = 9/257 (3%) Query: 9 APEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADI- 67 A GVR +T+ RP+ NA + L+ EL LA A +D RAVVLTG+ +F+AGAD+ Sbjct: 8 ADRAGVRTVTMNRPQVHNAFDDSLIAELTDALAAAGRDENVRAVVLTGAGASFSAGADLN 67 Query: 68 --KEMAERDLVGILEDP-RVAHWQRIAAF-SKPLIAAVNGFCLGGGCELAMHADILIAGE 123 + MA+ ED R+A R F KP +A VNG GGG L DI I + Sbjct: 68 WMRGMAKASEAENREDSLRLAALMRTLQFLPKPTVARVNGAAYGGGVGLIACCDIAIGVD 127 Query: 124 DARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPE 183 A+FG E+ LG++P A + ++ A+G + ++ L+G+ DA AQR GL+ + E Sbjct: 128 SAKFGLTEVKLGLVP-AVISPYVIAAIGLRQSRRLFLTGELFDASTAQRIGLLHQCVRAE 186 Query: 184 LTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAG---TADRA 240 + + A+ P+A AK L+ D A R +R ++A +A+ Sbjct: 187 ELDDALAGVLAAFAKAGPVAQAQAKRLALRVAGQDQAQAERIDRENAELIARLRVSAEGQ 246 Query: 241 EGIRAFQEKRRPEFTGR 257 EG+ AF +KR +T + Sbjct: 247 EGLGAFLDKRAAAWTAQ 263 Lambda K H 0.320 0.134 0.374 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: 162 Number of extensions: 9 Number of successful extensions: 3 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: 257 Length of database: 264 Length adjustment: 25 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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: 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