Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_108359319.1 B9Z44_RS10090 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_003063475.1:WP_108359319.1 Length = 259 Score = 150 bits (380), Expect = 2e-41 Identities = 91/245 (37%), Positives = 136/245 (55%), Gaps = 2/245 (0%) Query: 12 IEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERAT 71 + + T++ + NA++ ++ ELG+ + ++ + +VITG+ +KAF AGAD+ AT Sbjct: 15 VGVITLNRPKQLNALNAGLMVELGQALKDFDANEAIGCMVITGS-EKAFAAGADIGAMAT 73 Query: 72 MAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLT 131 + +V D + R + I IAA++G ALGGG ELA+ CD +AA A+ G Sbjct: 74 YSFADVYKN-DYITRDWETIRSIRKPVIAAVSGFALGGGCELAMMCDFIIAADNAKFGQP 132 Query: 132 EVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAY 191 E+KLGIIPG GGTQRL R VG +A DL LT R ++A EA GL +R+ P L+ Sbjct: 133 EIKLGIIPGAGGTQRLPRAVGKSKAMDLALTGRMMDATEAERAGLVSRVVPLDKLMEETL 192 Query: 192 GLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKR 251 G A + + IA AK +++ L D + E R + + T D+ EG+ AF KR Sbjct: 193 GAALMICGYSQIAAMAAKESVNRAFEGTLADGVMFERRLFHALFATADQKEGMDAFVNKR 252 Query: 252 APVYK 256 +K Sbjct: 253 PADFK 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: 129 Number of extensions: 6 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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