Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_012275357.1 SHAL_RS01130 crotonobetainyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_000019185.1:WP_012275357.1 Length = 261 Score = 148 bits (373), Expect = 1e-40 Identities = 97/257 (37%), Positives = 135/257 (52%), Gaps = 6/257 (2%) Query: 6 VDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65 V G I T+D + NAI E+GE+ ++R +ITGAG++ F AG D Sbjct: 7 VTRNGAILEITLD-RPKANAIDAKTSFEMGEVFLAFREDPELRVAIITGAGERFFSAGWD 65 Query: 66 LKERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPA 125 LK A E F G I D IAA+NG A GGG ELALA D+ + + Sbjct: 66 LKAAAE-GEAPDADFGPGGFAGLTEIFDLDKPVIAAVNGYAFGGGFELALAADMIICSEN 124 Query: 126 AELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGH 185 A L E KLGI+P GG RL +L+ P +L++T R + A EA G+ NR+ Sbjct: 125 ASFALPEAKLGIVPDSGGMLRLPKLLPPAIVNELMMTGRGMGAEEALRWGVVNRVVESDK 184 Query: 186 LLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDAL----ALELRKYEEILKTEDRL 241 L+ A LA+ + + AP+A+A K E + L +++ A L+ Y +L++ED L Sbjct: 185 LMDSARELAQQIAQGAPLAIAAIKEIYRETSELSVEEGYRHIRAGGLKNYPSVLRSEDAL 244 Query: 242 EGLRAFAEKRAPVYKGR 258 EG AF+EKR PV+KGR Sbjct: 245 EGPLAFSEKRDPVWKGR 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: 143 Number of extensions: 7 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: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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