Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011384972.1 AMB_RS13040 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::Q13825 (339 letters) >NCBI__GCF_000009985.1:WP_011384972.1 Length = 255 Score = 138 bits (347), Expect = 2e-37 Identities = 87/209 (41%), Positives = 125/209 (59%), Gaps = 8/209 (3%) Query: 82 LEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 141 L RG V + + N+LS+ LIK L A+D +++DK +R + +RSE FCAGA Sbjct: 6 LNTARRGAVFVVTLASPPVNALSRALIKDLHAAMDMVEADKTIRVLHLRSEQKA-FCAGA 64 Query: 142 DLKE-RAKMSSSEVGP----FVSKIRAVINDIANLPVPTIAAIDGLALGGGLELALACDI 196 DL E R +++ ++ FV ++ V+ I L + T+A + G A+GGGLELALACD Sbjct: 65 DLAEMRENLANPDLVDAQIAFVRDLQNVLKRIETLALATVAEVGGAAMGGGLELALACDF 124 Query: 197 RVAASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGKEAKAVGLISH 256 R+AA+ AK+ L E L +IPG GGTQRL R G ++AK LI A +LDG+ A+A+G++ Sbjct: 125 RMAANEAKLALPEVNLGLIPGAGGTQRLTRLCGPAIAKRLILGAEILDGQSAEAMGIVHW 184 Query: 257 VLEQNQEGDAAYRKALDLAREFLPQGPVA 285 + + D A A LA LP+ VA Sbjct: 185 SAPRAELADKAATLADRLAT--LPRAAVA 211 Lambda K H 0.318 0.135 0.386 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: 176 Number of extensions: 8 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: 339 Length of database: 255 Length adjustment: 26 Effective length of query: 313 Effective length of database: 229 Effective search space: 71677 Effective search space used: 71677 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: 48 (23.1 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