Align Muconate cycloisomerase 1; EC 5.5.1.1; Cis,cis-muconate lactonizing enzyme I; MLE; Muconate cycloisomerase I (uncharacterized)
to candidate SMa0056 SMa0056 dehydratase/enolase
Query= curated2:Q43931 (370 letters) >FitnessBrowser__Smeli:SMa0056 Length = 377 Score = 66.2 bits (160), Expect = 1e-15 Identities = 70/207 (33%), Positives = 106/207 (51%), Gaps = 26/207 (12%) Query: 32 LIKIITEDGIVGWGEATTIGGLNYGEESPESVKANIDTYFKPLLLSIKA--PLNVAQTLK 89 ++++ T+ GIVG GE +GG G ES E+ + KP LL N+ + Sbjct: 37 IVEVETDVGIVGLGE---MGG---GGESAEAAFRAL----KPYLLGHDTFELENLRFMIC 86 Query: 90 LIRKSINGNRFAK-CAIQTALLEIQAKRLNVPVSELLGGRIRDRLP----VLWTLASGDT 144 S+ NR AI+ A L+I K L VPV +LLGG++RD +P + + L + DT Sbjct: 87 NPTASLYNNRTQMHAAIEFACLDIMGKFLGVPVCDLLGGKMRDAVPFASYMFFRLPNKDT 146 Query: 145 -DKDIAEAKKMIE----LKRHNTF---KLKIGSNPLQHDVDHVIAIKKALGPEISVRVDV 196 + + A ++IE LK+ F KLK G P ++++ A KALGP+ SVR D Sbjct: 147 GEGETRTADQLIEQTLALKKKCGFTSHKLKSGVFPPDYELEVFRAWAKALGPD-SVRYDP 205 Query: 197 NRAWSELECVKGIQQLQDGGIDLIEQP 223 N A+S E ++ + ++D D E P Sbjct: 206 NAAFSVEEAIRFAKGIEDLNNDYYEDP 232 Lambda K H 0.318 0.136 0.384 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: 312 Number of extensions: 11 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: 370 Length of database: 377 Length adjustment: 30 Effective length of query: 340 Effective length of database: 347 Effective search space: 117980 Effective search space used: 117980 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: 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