Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__SB2B:6938034 Length = 706 Score = 118 bits (296), Expect = 4e-31 Identities = 76/226 (33%), Positives = 122/226 (53%), Gaps = 12/226 (5%) Query: 48 LSGSDSGIIEVNLDRP-VTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAG 106 LS D GI + +D P T N + + + + I D+S + +++ S F AG Sbjct: 7 LSRRDDGIALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKADSFVAG 66 Query: 107 ADLKERRTMSPSEVHTYVNSL-RYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRIC 165 AD+ +E ++ ++F+ +E L+IP +AAI GA LGGGLE+ALAC R+C Sbjct: 67 ADISMLDACETAEDARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALACHQRVC 126 Query: 166 GENA--VFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNIC 223 +++ + G+PE L ++PG GGTQRL RL+G + + +L+ TG+++ +A GLV+ Sbjct: 127 SDSSKTMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKMGLVDDV 186 Query: 224 VTAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEV 269 V + AIEMA LA K +K + + + T + G V Sbjct: 187 VPESILLDTAIEMA--------LAGKKTRKPLKQPLVTKLLEGTPV 224 Lambda K H 0.318 0.134 0.373 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: 390 Number of extensions: 11 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 706 Length adjustment: 33 Effective length of query: 268 Effective length of database: 673 Effective search space: 180364 Effective search space used: 180364 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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