Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011842152.1 RSPH17029_RS16015 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_000015985.1:WP_011842152.1 Length = 655 Score = 116 bits (291), Expect = 1e-30 Identities = 75/174 (43%), Positives = 97/174 (55%), Gaps = 8/174 (4%) Query: 24 NAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAEDEVRAFLDG 83 NA+ A+ + L L + + VRAVV+T G + F GAD+ E E Sbjct: 25 NALGLAVRQRLTALTAELEADESVRAVVLTAEG-RVFVGGADIAEFDRPPE------APH 77 Query: 84 LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKLGIIPGGGG 143 L AIE S +IAA+NGAALGGG ELAL C R+ A A LGL E LG+IPG GG Sbjct: 78 LPDVIAAIEASRKPWIAALNGAALGGGAELALGCHYRIFADTARLGLPETSLGLIPGAGG 137 Query: 144 TQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAESV 197 TQRL R +G A ++I R ++AAEA GLA+R+A G L+ A A ++ Sbjct: 138 TQRLPRRIGLAPAIEVITAGRTLSAAEAREAGLADRIA-AGELIPEALAFARTL 190 Score = 27.7 bits (60), Expect = 6e-04 Identities = 23/78 (29%), Positives = 32/78 (41%), Gaps = 14/78 (17%) Query: 89 RAIEKSDCVFIAAINGAALGGGTELALAC---DLRVAAPAAEL---GL--------TEVK 134 R IE I G +G G ALA ++R+ E GL +VK Sbjct: 283 RGIEPVPLTRAGVIGGGTMGSGIAAALAAAGLEVRLTETGPEALAAGLERVEAIFEAQVK 342 Query: 135 LGIIPGGGGTQRLARLVG 152 G+ G T+R+AR+ G Sbjct: 343 RGLTDRAGATERMARVTG 360 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: 404 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 258 Length of database: 655 Length adjustment: 31 Effective length of query: 227 Effective length of database: 624 Effective search space: 141648 Effective search space used: 141648 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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