Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_27920 AO356_27920 p-hydroxycinnamoyl CoA hydratase/lyase
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27920 Length = 276 Score = 113 bits (282), Expect = 5e-30 Identities = 73/224 (32%), Positives = 114/224 (50%), Gaps = 16/224 (7%) Query: 4 TLSVDAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAA 63 T+ VD E+G+ +TL RPE NA++ L E+ L EQD +VLTG+ A+ A Sbjct: 10 TVKVDI-EEGIAWVTLNRPEKRNAMSPTLNREMIDVLETLEQDPAAGVLVLTGAGDAWTA 68 Query: 64 GADIKEMAERDLVG-------ILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHA 116 G D+KE G I + W+ + ++KP IA VNG+C GGG + Sbjct: 69 GMDLKEYFREVDAGPEILQEKIRREASQWQWKLLRMYAKPTIAMVNGWCFGGGFSPLVAC 128 Query: 117 DILIAGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLV 176 D+ I ++A FG EIN GI PG ++ + VG ++ +++G+ + A GLV Sbjct: 129 DLAICADEATFGLSEINWGIPPGNLVSKAMADTVGHRQSLYYIMTGKTFGGQKAAEMGLV 188 Query: 177 SE----VTLPELTIERALAIARVIAQKAPLAVRLAKEALLKAED 216 +E L E+T+E +AR + +K P+ +R AK + + Sbjct: 189 NESVPLAQLREVTVE----LARNLLEKNPVVLRAAKHGFKRCRE 228 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: 151 Number of extensions: 5 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: 276 Length adjustment: 25 Effective length of query: 232 Effective length of database: 251 Effective search space: 58232 Effective search space used: 58232 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 Apr 09 2024. 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