Align 3-methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Pf6N2E2_1149 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
Query= metacyc::MONOMER-16071 (271 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1149 Length = 368 Score = 62.0 bits (149), Expect = 2e-14 Identities = 46/147 (31%), Positives = 70/147 (47%), Gaps = 2/147 (1%) Query: 3 DFSTLEVIRDPRG-FATLWLSREDKNNAFNAQMIRELIVAIDQLAEDASLRFVLLRGRG- 60 D + EV+ + R L L+R NA M+R L +D A D +R V+LRG G Sbjct: 14 DTAAYEVLVEVRNHIGHLTLNRPAGLNALTLGMVRSLQQQLDSWALDPQIRAVVLRGAGE 73 Query: 61 RHFSAGADLAWMQQSAQLDFNTNLDDAHELGELMYALHRLKAPTLAVVQGAAFGGALGLI 120 + F AG D+ + S + + D E L +H + P +A++ G GG +GL Sbjct: 74 KAFCAGGDIRSLYDSHKQGDTLHEDFFVEEYALDLTIHHYRKPIVALMDGFVLGGGMGLA 133 Query: 121 SCCDMAIGAEDAQLCLSEVRIGLAPAV 147 D+ + E ++L + EV IG P V Sbjct: 134 QGADLRVVTERSRLGMPEVGIGYFPDV 160 Lambda K H 0.321 0.135 0.394 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: 214 Number of extensions: 6 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: 271 Length of database: 368 Length adjustment: 27 Effective length of query: 244 Effective length of database: 341 Effective search space: 83204 Effective search space used: 83204 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 (21.9 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