Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Pf1N1B4_5593 4-hydroxycinnamoyl CoA hydratase/lyase (Enoyl-CoA hydratase/lyase) (EC 4.2.1.17)
Query= reanno::pseudo5_N2C3_1:AO356_01590 (273 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5593 Length = 276 Score = 116 bits (290), Expect = 6e-31 Identities = 71/205 (34%), Positives = 116/205 (56%), Gaps = 7/205 (3%) Query: 15 GVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHFSAGADLAWMQQ 74 G+A + L+R K NA + + RE+I L+ + DP+ L++ G G+ ++AG DL + Sbjct: 18 GIAWVILNRPEKRNAMSPTLNREMIDVLETLEQDPDAGVLVLTGAGEAWTAGMDLK--EY 75 Query: 75 SAELDYHTNLDDA---RELAELMYNLAKLKI-PTLAVVQGAAFGGALGLISACDMAIGAD 130 E+D + RE ++ + L ++ PT+A+V G FGG + ACD+AI AD Sbjct: 76 FREVDAGPEILQEKIRREASQWQWKLLRMYAKPTIAMVNGWCFGGGFSPLVACDLAICAD 135 Query: 131 EAQFCLSEVRIGLAPA-VISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPVE 189 EA F LSE+ G+ P ++S + +G R + Y +T + F GQ+A E+GL++ES P+ Sbjct: 136 EATFGLSEINWGIPPGNLVSKAMADTVGHRQSLYYIMTGKTFGGQKAAEMGLVNESVPLA 195 Query: 190 TLDQQVEQWIDNLLLNSPAAMRASK 214 L + + NLL +P +RA+K Sbjct: 196 QLREVTIELARNLLEKNPVVLRAAK 220 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: 175 Number of extensions: 9 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: 273 Length of database: 276 Length adjustment: 25 Effective length of query: 248 Effective length of database: 251 Effective search space: 62248 Effective search space used: 62248 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