Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate CA265_RS09125 CA265_RS09125 methylglutaconyl-CoA hydratase
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__Pedo557:CA265_RS09125 Length = 258 Score = 118 bits (296), Expect = 1e-31 Identities = 82/263 (31%), Positives = 135/263 (51%), Gaps = 15/263 (5%) Query: 4 ENIIL-EKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSF 62 EN++L + E++A + INRP+ NALN + E+ A ++D V+++I+ +GD +F Sbjct: 2 ENLVLYQVAERIATITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGD-AF 60 Query: 63 VAGADIAFMQNLSAMEAREFGALG---QKVFRLIEAMEKPVIAAVNGFALGGGCELAMCC 119 AGAD+A++Q L E A +K+F I + K VIA V G A+ GGC LA C Sbjct: 61 SAGADLAYLQQLQYNTFEENVADSNHLKKLFTTIYYLPKVVIAQVEGHAIAGGCGLATIC 120 Query: 120 DFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLV 179 D A + FG EV +G P L V +AK++L T + +A+EA + L+ Sbjct: 121 DIVFATPESNFGYTEVKIGFVPAIVSC-FLKEKVSESIAKEILLTGKIFSAEEALKYNLI 179 Query: 180 NKVVQPEELLPEVKKIAGRILSKG-----QLAVRLSKAAANEGMQTDIDRAMSIEADAFG 234 N V ++ V++ A + S + +L N ++ ++ A+ I A Sbjct: 180 NFVTNSSDIHQIVREFALSLCSGSSGNSLMITKQLITQTTNPLLEKCLETAVQINARV-- 237 Query: 235 LCFATQDQKEGMTAFLEKRKANF 257 ++D K+G+++FL K K N+ Sbjct: 238 --RESEDFKKGISSFLNKEKINW 258 Lambda K H 0.319 0.136 0.378 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: 160 Number of extensions: 7 Number of successful extensions: 5 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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