Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate HSERO_RS20665 HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS20665 Length = 262 Score = 152 bits (383), Expect = 9e-42 Identities = 90/243 (37%), Positives = 135/243 (55%), Gaps = 3/243 (1%) Query: 16 TIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAED 75 T++ + RNA+ L+E+ + R VR VVI+G +KAF AGADL E + +D Sbjct: 23 TLNRPALRNALRNQSLREIVAALARAEEDDSVRVVVISG-NEKAFAAGADLNEM--IHKD 79 Query: 76 EVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKL 135 + LD + +RAI + +AA+NG ALG G EL + D+ +AA A++G E+ + Sbjct: 80 AIATQLDVRAQYWRAIARFPKPILAAVNGYALGAGCELLMHADIAIAARGAKIGQPEINV 139 Query: 136 GIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAE 195 G +PG GGTQRL R VG A ++L+ I+A +A GL + + L LA Sbjct: 140 GTLPGAGGTQRLIRTVGKPLAMKMVLSGEFISADQALQAGLVAEVVDDDATLERTLALAH 199 Query: 196 SVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKRAPVY 255 S+ + +P+AV AK A+ + L L+ L E + + + + DR EG+ AF EKRA V+ Sbjct: 200 SIAQKSPLAVRLAKEAMLQSFELGLEAGLLFERKSFSLMAASADRQEGIAAFQEKRAAVF 259 Query: 256 KGR 258 GR Sbjct: 260 SGR 262 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: 115 Number of extensions: 3 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: 262 Length adjustment: 24 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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 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