Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_086511176.1 BZY95_RS17490 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_002151265.1:WP_086511176.1 Length = 257 Score = 201 bits (511), Expect = 1e-56 Identities = 113/248 (45%), Positives = 150/248 (60%), Gaps = 1/248 (0%) Query: 6 VDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65 VD G + + TI+ NA++ A+L EL L+T + D+RA++ITGAG+KAF AGAD Sbjct: 9 VDNAGVVRL-TINRPKALNALNSAVLTELEALLTELEKRSDLRALLITGAGEKAFVAGAD 67 Query: 66 LKERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPA 125 + E T +E RAF RT + +E +A +NG LGGG ELALACD VA+ Sbjct: 68 ITEMRTKTPEEARAFASQALRTIKRLETLPVPVVALVNGFCLGGGCELALACDWAVASDN 127 Query: 126 AELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGH 185 A G EV LG+IPG GGTQRL R VGP A DL+ T R+I+A EA +GL NR+ P+ Sbjct: 128 AIFGQPEVLLGVIPGFGGTQRLPRRVGPAMALDLVTTGRKIDAQEALRIGLVNRVMPQAE 187 Query: 186 LLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLR 245 L A A L + + N P+AV +AK A+ +G +LD ALALE + ++ EG+ Sbjct: 188 LEAYAEELTKQLAGNGPLAVRSAKQAVHDGMDQDLDSALALETSLFALGFAGSEQKEGMS 247 Query: 246 AFAEKRAP 253 AF EKR P Sbjct: 248 AFVEKRKP 255 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: 141 Number of extensions: 5 Number of successful extensions: 1 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: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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