Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_086511946.1 BZY95_RS21575 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_002151265.1:WP_086511946.1 Length = 257 Score = 157 bits (396), Expect = 3e-43 Identities = 94/254 (37%), Positives = 138/254 (54%), Gaps = 2/254 (0%) Query: 5 KVDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGA 64 +V+ G + + T+ NA++ A+++ELG + + A+VITG G++ F AGA Sbjct: 6 QVERTGAVGVITLYRPDAHNALNGALMRELGCALRAFEQDDAIGAMVITG-GERVFAAGA 64 Query: 65 DLKERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAP 124 D+KE ++ E D + + + + IAA+ G ALGGG ELA+ CDL +AA Sbjct: 65 DIKEIQSLTFSETY-LSDLITSDWEEVTRCRKPVIAAVAGMALGGGCELAMMCDLIIAAD 123 Query: 125 AAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEG 184 A G E+K+G +PG GGTQRL R +G +A DL LT R + A EA GL +R+ P Sbjct: 124 TARFGQPEIKVGTLPGAGGTQRLTRAIGKAKAMDLCLTGRLMAADEAERSGLVSRVVPAE 183 Query: 185 HLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGL 244 LL A A V + +AV K A++ L + + E R TED+ EG+ Sbjct: 184 RLLDEAMTAAAQVASMSAVAVRLNKEAVERAQETTLAEGVRFERRLLHASFATEDQKEGM 243 Query: 245 RAFAEKRAPVYKGR 258 +AF EKR PV++ R Sbjct: 244 QAFIEKRPPVWRHR 257 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: 134 Number of extensions: 5 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: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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 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