Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_037374751.1 A3GO_RS0105700 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000428045.1:WP_037374751.1 Length = 263 Score = 149 bits (375), Expect = 7e-41 Identities = 92/251 (36%), Positives = 128/251 (50%), Gaps = 4/251 (1%) Query: 11 EQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEM 70 + G+ + RPE LNA+N L EL +L EQ + R ++LTG+ +AF GAD+K Sbjct: 13 DDGIAELRFNRPERLNAVNEALYAELQEQLGRLEQMPDVRVILLTGAGRAFCVGADMKAH 72 Query: 71 AERDLVGILEDPRVAHWQRIAAF----SKPLIAAVNGFCLGGGCELAMHADILIAGEDAR 126 E + Q++ +KP++AAVNG+ LG G E+A+ AD ++ AR Sbjct: 73 GEATRSAYQRRQYLNAEQQVCRAIRESAKPVVAAVNGYALGAGAEMAIAADFILMKASAR 132 Query: 127 FGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTI 186 G PEI +G G G T L R VG + A ++V G+ ID A R GL S + Sbjct: 133 IGLPEITIGTFLGGGVTHTLPRLVGLAKARELVFLGEKIDGAEALRIGLASRCFADDRFD 192 Query: 187 ERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAF 246 E A R +A AP +++LAK L A + L+ E T A T D EG+ AF Sbjct: 193 EEVRAFCRQLALGAPHSMQLAKRQLNHALQQGFDNALQAELEGMTFCATTRDWQEGVDAF 252 Query: 247 QEKRRPEFTGR 257 +EKR P F GR Sbjct: 253 REKRAPRFEGR 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: 183 Number of extensions: 12 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: 257 Length of database: 263 Length adjustment: 24 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 24 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