Align Muconate cycloisomerase 1; EC 5.5.1.1; Cis,cis-muconate lactonizing enzyme I; MLE; Muconate cycloisomerase I (uncharacterized)
to candidate GFF2998 PGA1_c30470 mandelate racemase / muconate lactonizing enzyme
Query= curated2:P95608 (373 letters) >FitnessBrowser__Phaeo:GFF2998 Length = 321 Score = 82.8 bits (203), Expect = 1e-20 Identities = 95/307 (30%), Positives = 142/307 (46%), Gaps = 34/307 (11%) Query: 44 GVTGYGEGVVPGGPWWGGESVETMQAIVERYIVPVLLGRGVDEITGIMPDIERVVANARF 103 GVTG GE VP + GE++E++ A +E +P R E+ ++P A Sbjct: 37 GVTGCGE-CVPYARY--GETLESVTAEIEG--LPETFNRA--ELQSLLP--------AGA 81 Query: 104 AKAAVDVALHDAWARSLGVPVHTLLGGAFRKSVDVTWALGAAPAEEIIEEALDLVESKRH 163 A+ AVD AL D A+ G V L G K + L E + +A ++ Sbjct: 82 ARNAVDCALWDLEAKQAGKRVWELAGLPEPKPEITAYTLSLDSPENMQAQA---AKNAHR 138 Query: 164 FSFKLKMGALDPAVDTARVVQIAQALQGKAGVRIDVNARWDRLTALKYVPRLVEGGVELI 223 K+K+G D D AR+ + +A +A + +D N W P LV GV+L+ Sbjct: 139 PLLKIKLGTAD---DMARL-EAVRAGAPEARIIVDANEGWSAEVYADLAPHLVRLGVDLV 194 Query: 224 EQPTPGEQLEVLAELNRLVPVPVMADESVQTPHDALEVAR-RGAADVIALKTTKCGGLQK 282 EQP P + L + R PVPV ADES HD +A G DVI +K K GGL + Sbjct: 195 EQPLPAGEDAALLGMER--PVPVCADESC---HDRESLAALEGKYDVINIKLDKTGGLTE 249 Query: 283 SREVVAIAKAAGIACHGATSIEGPIGTAASIHFACAEPGIDFGTELFGPLLFSEELLQEP 342 + ++ A A G + +G++ ++ A T+L GPLL +E+ +EP Sbjct: 250 ALKLRDAALAQGF----EVMVGCMVGSSLAMAPATLVAQGAVVTDLDGPLLLAED-REEP 304 Query: 343 IRY-ADG 348 + + ADG Sbjct: 305 LDFDADG 311 Lambda K H 0.318 0.136 0.400 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: 234 Number of extensions: 13 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: 373 Length of database: 321 Length adjustment: 29 Effective length of query: 344 Effective length of database: 292 Effective search space: 100448 Effective search space used: 100448 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: 49 (23.5 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