Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf1N1B4_267 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_267 Length = 263 Score = 117 bits (293), Expect = 2e-31 Identities = 90/259 (34%), Positives = 125/259 (48%), Gaps = 29/259 (11%) Query: 14 VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKE---- 69 V +I L R NA + LL+EL+ E D+E R V+ G + F AG D+ Sbjct: 17 VLMIGLDRVAKRNAFDLNLLNELSLAYGEFEADSEARVAVVFGHGEHFTAGLDLVSAGAA 76 Query: 70 MAER--------DLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIA 121 +AE D G+L PRV SKP+I A G+CL G EL + ADI + Sbjct: 77 LAEGWQAPPGGCDPWGVLAGPRV---------SKPVIVAAQGYCLTVGIELMLAADINLC 127 Query: 122 GEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTL 181 + RF Q E+ GI P G T RL + G AM+ +L+G DA A GLV EV Sbjct: 128 ASNTRFAQKEVQRGIFPFGGATLRLHQVAGWGNAMRWLLTGDEFDAHDALHLGLVQEVMA 187 Query: 182 PELTIERALAIARVIAQKAPLAVRL----AKEALLKAEDTDLASGLRFERHAFTVLAGTA 237 E + RA+ +A IA++APL V+ A++A + E T + ++ L + Sbjct: 188 SEDLLPRAIELAERIARQAPLGVQATLMSARQARYEGEMTAAQALPALVKN----LLNSE 243 Query: 238 DRAEGIRAFQEKRRPEFTG 256 D EG+R+ EKR F G Sbjct: 244 DAKEGVRSMIEKRPGVFKG 262 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: 164 Number of extensions: 10 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 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