Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate PfGW456L13_3824 Muconate cycloisomerase (EC 5.5.1.1)
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3824 Length = 424 Score = 733 bits (1891), Expect = 0.0 Identities = 377/382 (98%), Positives = 378/382 (98%) Query: 1 MLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 60 MLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG Sbjct: 43 MLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 102 Query: 61 NESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRL 120 NESPDSIKTNID HFAPLLIGQDS NVNAAMLRLERSIRGNTFAKSGIETALLDA GKRL Sbjct: 103 NESPDSIKTNIDTHFAPLLIGQDSNNVNAAMLRLERSIRGNTFAKSGIETALLDALGKRL 162 Query: 121 GLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLA 180 GLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLA Sbjct: 163 GLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLA 222 Query: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNA 240 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDL+EQPISRNNR GMARLNA Sbjct: 223 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLIEQPISRNNRAGMARLNA 282 Query: 241 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGG 300 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGG Sbjct: 283 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGG 342 Query: 301 TMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGL 360 TMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGL Sbjct: 343 TMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGL 402 Query: 361 SLDEERLAFFRRDKTSTAIHQA 382 SLDEERLAFFRRDKTSTAIHQA Sbjct: 403 SLDEERLAFFRRDKTSTAIHQA 424 Lambda K H 0.319 0.136 0.386 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: 603 Number of extensions: 14 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: 382 Length of database: 424 Length adjustment: 31 Effective length of query: 351 Effective length of database: 393 Effective search space: 137943 Effective search space used: 137943 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 (21.7 bits) S2: 50 (23.9 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