Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF3367 PGA1_c34200 carnitinyl-CoA dehydratase CaiD
Query= reanno::pseudo6_N2E2:Pf6N2E2_2193 (272 letters) >FitnessBrowser__Phaeo:GFF3367 Length = 261 Score = 88.2 bits (217), Expect = 2e-22 Identities = 67/219 (30%), Positives = 96/219 (43%), Gaps = 8/219 (3%) Query: 48 DPNLRFLLIRGRG-KHFSAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLA 106 DP LR ++ G G K F G DL +D + + L EL + P +A Sbjct: 45 DPELRVAILTGGGEKFFCPGWDLKAAADGDAVDGNYGVGGFGGLQELR----DMNKPVIA 100 Query: 107 VVQGAAFGGALGLISACDMAIGADEAQFCLSEVRIGLAPAVISPFVVQAIGERAARRYAL 166 V G A GG L L + DM + AD A F L E+R G S + + I A L Sbjct: 101 AVNGIACGGGLELALSADMIVAADHATFALPEIRSGTVADAASIKLPKRIPYHIAMELLL 160 Query: 167 TAERFDGQRAKEIGLLSESYPAEVLDQQVEQWIDNLLLNSPAAMRASKELLREVGNGALT 226 T FD + A GL++E A+ L + + L P A KE++R+ + Sbjct: 161 TGRWFDAEEAHRWGLVNEIVTADQLLDRAWELARLLASGPPLVYAAIKEIVRDAEDSKFQ 220 Query: 227 PALRRYTENAIARIRV---SPEGQEGLRAFLQKRAPNWQ 262 A+ R T+ + + V S + EG RAF +KR P W+ Sbjct: 221 DAMNRITKRQLRSVDVLYDSEDQMEGARAFAEKRDPVWK 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: 122 Number of extensions: 3 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: 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