Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2193 (272 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 87.0 bits (214), Expect = 4e-22 Identities = 72/241 (29%), Positives = 100/241 (41%), Gaps = 8/241 (3%) Query: 26 KNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRG-KHFSAGADLAWMQQSAELDYHTNL 84 K NA + R + L DP LR +I G G K F AG DL +D + Sbjct: 22 KANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAGWDLKAAASGDAVDGDYGV 81 Query: 85 DDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQFCLSEVRIGLA 144 L EL L P + V G GG L + + D+ I A+ A F L E+R G Sbjct: 82 GGFGGLQELR----DLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHATFALPEIRSGTV 137 Query: 145 PAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPAEVLDQQVEQWIDNLLL 204 S + + I A LT D A G ++E PAE L ++ + L Sbjct: 138 ADAASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLMERAWELARLLES 197 Query: 205 NSPAAMRASKELLREVGNGALTPALRRYTENAIA---RIRVSPEGQEGLRAFLQKRAPNW 261 P A KE++RE A+ + T+ A R+ S + EG RAF +KR+P W Sbjct: 198 GPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEGARAFAEKRSPIW 257 Query: 262 Q 262 + Sbjct: 258 K 258 Lambda K H 0.318 0.133 0.382 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: 120 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: 272 Length of database: 260 Length adjustment: 25 Effective length of query: 247 Effective length of database: 235 Effective search space: 58045 Effective search space used: 58045 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Apr 09 2024. 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