Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_012645265.1 GEOB_RS00800 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::F4JML5 (301 letters) >NCBI__GCF_000022265.1:WP_012645265.1 Length = 260 Score = 150 bits (380), Expect = 2e-41 Identities = 96/257 (37%), Positives = 135/257 (52%), Gaps = 6/257 (2%) Query: 41 EFVKLNRLSGSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVP 100 EF+ L + D ++ ++L+RP T N +N + L AF Q VV+I S + Sbjct: 4 EFITLKK----DDRVLTISLNRPPT-NPLNGVFGQELFKAFSEAEQMEDITVVIITSALE 58 Query: 101 GVFCAGADLKERRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALAC 160 F AGAD+KE +E + L+ + + + IAAI G ALGGG E+ALAC Sbjct: 59 KAFIAGADIKEMAAQDAAEAEQFSKLLQGANNILNRMKKIVIAAINGHALGGGCELALAC 118 Query: 161 DLRICGEN-AVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGL 219 D R+ A+ GLPE GL IIPGAGGTQRL RLVG S + +++ GR + EA GL Sbjct: 119 DYRLMTSGKALIGLPEAGLGIIPGAGGTQRLPRLVGLSKALDILLRGRTMSPQEALAIGL 178 Query: 220 VNICVTAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLN 279 V+ + + ++ AQ++ A+ K A+ EGI+ + L VE + Sbjct: 179 VDKLIEPENFQAEVMQFAQELAAGAGKALGYIKAAVYEGIDFPLEQALAVERKYSAENSK 238 Query: 280 TQDRLEGLAAFAEKRKP 296 T D EGL AF EKR+P Sbjct: 239 THDAKEGLTAFVEKRRP 255 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: 163 Number of extensions: 9 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: 301 Length of database: 260 Length adjustment: 26 Effective length of query: 275 Effective length of database: 234 Effective search space: 64350 Effective search space used: 64350 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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