Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_003548339.1 RL_RS29885 crotonase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_000009265.1:WP_003548339.1 Length = 258 Score = 144 bits (363), Expect = 2e-39 Identities = 93/249 (37%), Positives = 132/249 (53%), Gaps = 11/249 (4%) Query: 16 TIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATM--- 72 T+D R NA+ A +EL + + + D+ VV+TGAG++AFCAGADLK + Sbjct: 15 TLDRPERMNAVDAATEQELETIWREIEARDDISCVVLTGAGERAFCAGADLKGGSGSSGL 74 Query: 73 ---AEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELG 129 A V F GL FR D IA +NG ALGGG E+ L CD+ +AA A G Sbjct: 75 DYWAASRVNGF-GGL--AFR--RSLDVPVIARVNGFALGGGFEMVLGCDIVIAAQTARFG 129 Query: 130 LTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAV 189 L E ++G +P GG L R + RA ++LT R+ +AAE G+ N + P L A Sbjct: 130 LPEARVGRMPLDGGMVLLQRKIAFNRAMAVMLTGRQFSAAEMAGFGVVNEVVPAIELDAA 189 Query: 190 AYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAE 249 +V AP+++ K ++ L +A AL + L++ED LEG+ AF + Sbjct: 190 VDRWVADIVACAPLSLRAIKQTVNRTGHLSPAEAQALRTPALVKALQSEDALEGVAAFQQ 249 Query: 250 KRAPVYKGR 258 KRAPV++GR Sbjct: 250 KRAPVWRGR 258 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: 143 Number of extensions: 7 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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