Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate CCNA_00006 CCNA_00006 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Caulo:CCNA_00006 Length = 262 Score = 160 bits (404), Expect = 3e-44 Identities = 93/234 (39%), Positives = 132/234 (56%), Gaps = 2/234 (0%) Query: 24 NAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAEDEVRAFLDG 83 NA++ A+L EL + + + V +V+TG+ KAF AGAD+KE + ++ D Sbjct: 30 NALNTALLGELAQALAAAQADDSVGCIVLTGSA-KAFAAGADIKEMSDKTYAQMFK-ADF 87 Query: 84 LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKLGIIPGGGG 143 RAIE+ IAA+ G ALGGG ELA+ CD +AA A+ G E+ LG+ PG GG Sbjct: 88 FTAGARAIEQCRKPIIAAVAGYALGGGCELAMMCDFILAADTAKFGQPEINLGVAPGIGG 147 Query: 144 TQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAESVVENAPI 203 TQRL R VG +A D+ILT R + A EA GL +R+ P L+ +A + +P+ Sbjct: 148 TQRLTRFVGKSKAMDMILTGRMMGAEEAERSGLVSRIFPADSLVDETLAIAAKIAGQSPL 207 Query: 204 AVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKRAPVYKG 257 AVA K ++ L +ALE R + + ED+ EG+ AF EKR P++KG Sbjct: 208 AVAMNKELVEAAYETTLTTGVALERRLFHSLFAFEDQKEGMTAFVEKRKPLFKG 261 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: 137 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: 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