Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 7024269 Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__ANA3:7024269 Length = 709 Score = 115 bits (287), Expect = 4e-30 Identities = 76/227 (33%), Positives = 117/227 (51%), Gaps = 12/227 (5%) Query: 44 KLNRLSGSDSGIIEVNLDRP-VTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGV 102 K L+ + GI + +D P T N + E + I +D+S R +++ S Sbjct: 3 KTFNLTRREDGIAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKKDS 62 Query: 103 FCAGADLKERRT-MSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACD 161 F AGAD+ + + +F+ +EAL+IP +AAI GA LGGGLE+ALAC Sbjct: 63 FVAGADISMLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALACH 122 Query: 162 LRICGENA--VFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGL 219 R+C ++ + G+PE L ++PG GGTQRL RLVG + + +++ TG++I +A GL Sbjct: 123 QRVCSDDGKTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKMGL 182 Query: 220 VNICVTAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASG 266 VN V + A+EMA LA K K + + + + G Sbjct: 183 VNDVVPQTILLQTAVEMA--------LAGKRTAKPVKKSLVNQLLEG 221 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: 396 Number of extensions: 18 Number of successful extensions: 4 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: 301 Length of database: 709 Length adjustment: 33 Effective length of query: 268 Effective length of database: 676 Effective search space: 181168 Effective search space used: 181168 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