Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase
Query= reanno::Pedo557:CA265_RS09125 (258 letters) >FitnessBrowser__azobra:AZOBR_RS18155 Length = 248 Score = 94.4 bits (233), Expect = 2e-24 Identities = 72/243 (29%), Positives = 121/243 (49%), Gaps = 9/243 (3%) Query: 13 IATITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGD-AFSAGADLAYLQQ 71 +ATIT++RP+K NA+ P++ A+L AA + + DD ++ V+L G AF G+D+ L Sbjct: 5 VATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDIRELD- 63 Query: 72 LQYNTFEENVADSNHLKKLFTTIYYLPKVVIAQVEGHAIAGGCGLATICDIVFATPESNF 131 +Y+T + + + I L K IA V G+A GG A CDI A+ + F Sbjct: 64 -RYDT----AWNFRNREDYCDAIRGLRKPSIAAVNGYAFGGGLETAMSCDIRIASENAQF 118 Query: 132 GYTEVKIGFV-PAIVSCFLKEKVSESIAKEILLTGKIFSAEEALKYNLINFVTNSSDIHQ 190 G E+K+G++ V+ FL + S A ++LTG A++AL + L++ V + + Sbjct: 119 GAPEIKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPADRLLA 178 Query: 191 IVREFALSLCSGSSGNSLMITKQLITQTTNPLLEKCLETAVQINARVRESEDFKKGISSF 250 +E A + S + + L T P +EK +E + + D +G ++F Sbjct: 179 RAQEIAAIVASRAPIAAETAKLNLKAAHTMP-VEKAIEYERDLQTICFATADAAEGRAAF 237 Query: 251 LNK 253 K Sbjct: 238 KEK 240 Lambda K H 0.318 0.133 0.367 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: 122 Number of extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 234 Effective length of database: 224 Effective search space: 52416 Effective search space used: 52416 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: 46 (22.3 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