Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Ac3H11_3014 Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2193 (272 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3014 Length = 261 Score = 202 bits (515), Expect = 5e-57 Identities = 107/246 (43%), Positives = 155/246 (63%) Query: 16 VATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHFSAGADLAWMQQS 75 VA + L++ NAF+ E+I E+ A V S P++R +++ G F AGA+L WM++ Sbjct: 14 VARITLTQPEVRNAFSDEVIAEITAAFTDVGSRPDVRAVVLAAEGPAFCAGANLNWMRRM 73 Query: 76 AELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQFC 135 A+ N+ DA +LAE++ + + PT+A VQG + G +GL++ACDMA+ D A FC Sbjct: 74 ADYTREENIADAGKLAEMLRVIYECPKPTVARVQGDVYAGGMGLVAACDMAVAVDTAGFC 133 Query: 136 LSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPAEVLDQQV 195 LSEV++GL PA ISP+V++A+G RAA RY LTAERFD A IG + A+ LD +V Sbjct: 134 LSEVKLGLIPATISPYVIRAMGARAAHRYFLTAERFDAAEALRIGFVHTVVAADQLDAKV 193 Query: 196 EQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARIRVSPEGQEGLRAFLQ 255 ++ + L SP A+RA K+L+ +V + L T IA IR S EG+EG+++FL Sbjct: 194 DELLKALTSASPNAVRACKKLVLQVAEREINAGLIAATVQGIADIRASDEGKEGVQSFLN 253 Query: 256 KRAPNW 261 KR PNW Sbjct: 254 KRKPNW 259 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: 182 Number of extensions: 6 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: 272 Length of database: 261 Length adjustment: 25 Effective length of query: 247 Effective length of database: 236 Effective search space: 58292 Effective search space used: 58292 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