Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Dsui_0981 Dsui_0981 enoyl-CoA hydratase/carnithine racemase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2193 (272 letters) >FitnessBrowser__PS:Dsui_0981 Length = 263 Score = 216 bits (551), Expect = 3e-61 Identities = 114/247 (46%), Positives = 160/247 (64%), Gaps = 1/247 (0%) Query: 16 VATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHFSAGADLAWMQQS 75 V L L++ ++NAF+ ++ E+ L + +DP +R +++ GK F AGADL WM+++ Sbjct: 14 VGILTLNKPDRHNAFDETLMAEITAGLKQLEADPAVRVVVLSATGKSFCAGADLNWMKRA 73 Query: 76 AELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQFC 135 A NL DA LAEL+ L L PT+A VQG A+GG +GL++ACD+A+ + +A F Sbjct: 74 AGYTPEQNLADAGNLAELLRTLNTLAKPTVARVQGPAYGGGVGLVAACDVAVASYDAMFA 133 Query: 136 LSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPA-EVLDQQ 194 L+EV++GL PAVISP+V+ A+GER RRY LTAERF +GLL E P+ E LD+ Sbjct: 134 LTEVKLGLIPAVISPYVIAALGERQCRRYFLTAERFSAAEGYRLGLLHEIVPSEEQLDEA 193 Query: 195 VEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARIRVSPEGQEGLRAFL 254 V + +D LL N PAA ASKEL+R V N + A+ T I +R S EG+EG+ AFL Sbjct: 194 VGEIVDKLLKNGPAAQAASKELIRAVANQPIDDAVIADTARRITAMRASAEGREGIAAFL 253 Query: 255 QKRAPNW 261 +KR P+W Sbjct: 254 EKRKPHW 260 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: 209 Number of extensions: 10 Number of successful extensions: 2 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: 263 Length adjustment: 25 Effective length of query: 247 Effective length of database: 238 Effective search space: 58786 Effective search space used: 58786 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 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