Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate Synpcc7942_0315 Synpcc7942_0315 adenylosuccinate lyase
Query= curated2:Q9I6Q8 (459 letters) >FitnessBrowser__SynE:Synpcc7942_0315 Length = 431 Score = 186 bits (471), Expect = 2e-51 Identities = 135/430 (31%), Positives = 213/430 (49%), Gaps = 14/430 (3%) Query: 9 LFDAYFMAAPMRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAACRAELYDP 68 L + Y + A M +++D +L+ L E A+ A+A G +PA AV I+A +DP Sbjct: 1 LIERYTLPA-MGGLWTDTYKLKTWLQVEIAVCEAQAELGYIPADAVETIKAKAN---FDP 56 Query: 69 LALAEAVATAGNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRALAL 128 + E + I + + V +A RY+HLG TS D +D+GL LQ+ ++ L Sbjct: 57 ARVLEIEQEVRHDVIAFLTNVNEYVG----DAGRYIHLGMTSSDVLDTGLALQMVASVDL 112 Query: 129 LEQDLQRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRELR 188 L + + L + + QA++H +T + GR+ HA P+T G KLAG L + R+R RL ++R Sbjct: 113 LLAETENLIQAIRWQAQQHRETVMIGRSHGIHAEPITFGFKLAGWLAEMLRNRDRLVQVR 172 Query: 189 PRLLVLQFGGASGTLAALGEQALPVAAALAEELGLALPEQPWH-TQRDRLVEFASVLGLV 247 + V + GA GT A + + V A ++LGL RDR E+ VL LV Sbjct: 173 QSVAVGKISGAVGTYANIEPR---VEALTCQKLGLEPDTASTQVVSRDRHAEYVQVLALV 229 Query: 248 AGSLGKFGRDVSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATRAPGLVS 307 A SL +F ++ L +++ EV E G+ GSS MPHKRNP+ S + A G Sbjct: 230 AASLERFSVEIRNLQRSDVLEVEEFFAKGQKGSSAMPHKRNPIRSERISGLARVIRGYAV 289 Query: 308 TLFAAMPQEHERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRRNLGLTH 367 + HER + E LP+ + L + L++ L+V + M RNL Sbjct: 290 AALENVALWHERDISHSSVERMMLPDCSATLHFMLVEMTELVKTLQVYPENMTRNLNRYG 349 Query: 368 GLVLAEAVSIALA-RRIGREAAHHLVEQCCRRA-VEQRRELRAVLGEEARVSAELSGDEL 425 G+V ++ V +AL + + RE A+ +V+ A + RA++ + V A LS E+ Sbjct: 350 GVVFSQRVLLALVDKGLSREEAYRIVQSNAHSAWNHEGGNFRALIEADPTVQAHLSAAEI 409 Query: 426 DRLLDPAHYL 435 + H+L Sbjct: 410 EDCFAAQHHL 419 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: 370 Number of extensions: 11 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: 431 Length adjustment: 32 Effective length of query: 427 Effective length of database: 399 Effective search space: 170373 Effective search space used: 170373 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