Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate GFF2282 PS417_11635 3-carboxy-cis,cis-muconate cycloisomerase
Query= curated2:Q9I6Q8 (459 letters) >FitnessBrowser__WCS417:GFF2282 Length = 451 Score = 373 bits (957), Expect = e-108 Identities = 211/451 (46%), Positives = 275/451 (60%), Gaps = 4/451 (0%) Query: 2 SDVPANQLFDAYFMAAPMRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAAC 61 S V + LF F A MR VFSD+ ++ ++ E ALARAEAR GV+P A I Sbjct: 3 STVFDSALFRDMFGTAEMRGVFSDKALIERYIEVEVALARAEARCGVIPTDAAEQIATLS 62 Query: 62 RAELYDPLALAEAVATAGNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQ 121 + E D + G +PLV+ L + EA RYVH GAT+QD MD+ +VLQ Sbjct: 63 QYEALDLALMQHETEIVGYPILPLVEQLSKICG----EAGRYVHWGATTQDIMDTAVVLQ 118 Query: 122 LRRALALLEQDLQRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHR 181 +R ALA++E+D+Q + +LA AER+ DTP+AGRT LQHA P+T G K A L RH Sbjct: 119 VRAALAIVERDIQTVRGLLAGLAERYRDTPMAGRTHLQHALPITFGYKCAVWLSMFDRHA 178 Query: 182 QRLRELRPRLLVLQFGGASGTLAALGEQALPVAAALAEELGLALPEQPWHTQRDRLVEFA 241 +RL ELRPR+ + QF GA+GTLA+LG++ L V AL ELGL +P+ WH RD L E Sbjct: 179 ERLVELRPRVEIGQFAGAAGTLASLGDKGLEVQEALMSELGLGVPQATWHVARDGLAETL 238 Query: 242 SVLGLVAGSLGKFGRDVSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATR 301 + LGLV GSLGK D+ ++M +E GEV+EP GRG SSTMP KRNP+S ++ AAA Sbjct: 239 NFLGLVTGSLGKIALDIMMMMTSELGEVYEPFVKGRGASSTMPQKRNPISCELMYAAAKG 298 Query: 302 APGLVSTLFAAMPQEHERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRR 361 + AM Q+ ERS G W AEW +PE L A +L QA +L GLEV +RMR+ Sbjct: 299 VRQHAGLMLDAMIQDFERSTGPWQAEWIAIPEAFALSAASLGQATFMLAGLEVRPERMRK 358 Query: 362 NLGLTHGLVLAEAVSIALARRIGREAAHHLVEQCCRRAVEQRRELRAVLGEEARVSAELS 421 NL +T GL++AEAV + LA +GR+ AH +V CR A +Q L L + +A+L Sbjct: 359 NLDMTQGLIVAEAVMMGLAPALGRQVAHDVVYAACRMANDQGTSLLDALLAQGEATAQLD 418 Query: 422 GDELDRLLDPAHYLGQARAWVERALAEHHAL 452 EL RL DPA+YLG A V+ ALA A+ Sbjct: 419 LAELQRLTDPANYLGLAPQMVDIALARQGAV 449 Lambda K H 0.320 0.133 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: 481 Number of extensions: 19 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: 459 Length of database: 451 Length adjustment: 33 Effective length of query: 426 Effective length of database: 418 Effective search space: 178068 Effective search space used: 178068 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: 51 (24.3 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