Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Pedo557:CA265_RS20005 Length = 259 Score = 178 bits (452), Expect = 9e-50 Identities = 99/244 (40%), Positives = 149/244 (61%), Gaps = 3/244 (1%) Query: 16 TIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAED 75 TI+ E NA+++ L EL +++ + +VR V++TGAG+KAF AGAD+KE + + Sbjct: 18 TINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEKAFVAGADIKEFSDYSGK 77 Query: 76 EVRAFLD-GLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVK 134 + G F AIE S FIAAING ALGGG ELA+AC +R+A+ A+LGL EV Sbjct: 78 QGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELAMACHIRIASDNAKLGLPEVT 137 Query: 135 LGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLA 194 LG+IPG GGTQRL +LVG G+A ++I TA I A +A +GL N + P+ L+ A + Sbjct: 138 LGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKIGLVNVVVPQADLIGKAEEML 197 Query: 195 ESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKRAPV 254 + + AP+A++ A ++ + + A E+ ++ + +T D EG+ AF EKR + Sbjct: 198 NVIKQRAPLAISAAIKSVI--ASINNTNGYATEIEEFGKCFETADFKEGVTAFVEKRKAI 255 Query: 255 YKGR 258 + G+ Sbjct: 256 FTGK 259 Lambda K H 0.319 0.136 0.380 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: 141 Number of extensions: 6 Number of successful extensions: 3 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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 (21.7 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