Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate 8500725 DvMF_1468 adenylosuccinate lyase (RefSeq)
Query= curated2:Q9I6Q8 (459 letters) >FitnessBrowser__Miya:8500725 Length = 432 Score = 159 bits (403), Expect = 1e-43 Identities = 126/419 (30%), Positives = 195/419 (46%), Gaps = 12/419 (2%) Query: 19 MRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAACRAELYDPLALAEAVATA 78 M +++ R + LD E A+ A R GV+ A + I +D + E Sbjct: 10 MARIWTLENRFRAWLDVELAVCEAWHRLGVIGADDMRVIREKAD---FDVDRILEIEQET 66 Query: 79 GNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRALALLEQDLQRLAE 138 + I + A+ +V + R++HLG TS D +D+ L L +A L+ + +RL Sbjct: 67 RHDVIAFLTAVEEKVGP----SARFIHLGCTSSDIVDTANGLLLAQAGELILKGFERLLS 122 Query: 139 VLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRELRPRLLVLQFGG 198 L A + GRT HA P + G+K+AG RH R R+ + V + G Sbjct: 123 TLETLAFANKGRLCMGRTHGIHAEPTSFGLKMAGFHAEFQRHVARFRDGLESVRVGKISG 182 Query: 199 ASGTLAALGEQALPVAAALAEELGLAL-PEQPWHTQRDRLVEFASVLGLVAGSLGKFGRD 257 A GT A L + V A E LGLA+ P QRDR F + L L AG + + + Sbjct: 183 AVGTYAMLDPR---VEAIACEILGLAVDPISTQVIQRDRHAHFFTSLALAAGGVERLCVE 239 Query: 258 VSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATRAPGLVSTLFAAMPQEH 317 + L +TE E E G+ GSS MPHK+NP+S+ + + M H Sbjct: 240 LRHLQRTEVLEAEEGFAKGQKGSSAMPHKKNPISAENMTGLSRLIRTNSLAAMENMALWH 299 Query: 318 ERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRRNLGLTHGLVLAEAVSI 377 ER + E +P+ L+ L + GLL L V + M RNL ++GL ++ V + Sbjct: 300 ERDISHSSVERVIMPDSTILMDYVLHRLSGLLSNLRVIPENMDRNLAGSYGLYYSQRVLL 359 Query: 378 ALARR-IGREAAHHLVEQCCRRAVEQRRELRAVLGEEARVSAELSGDELDRLLDPAHYL 435 AL + R+ A+ +V++C ++ E R+ ++ +A +SA L+ LD L DP +YL Sbjct: 360 ALVESGMARQEAYVMVQRCAMQSWETRKPFPDMVRADADISARLAPSVLDELFDPGYYL 418 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: 384 Number of extensions: 9 Number of successful extensions: 4 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: 432 Length adjustment: 32 Effective length of query: 427 Effective length of database: 400 Effective search space: 170800 Effective search space used: 170800 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