Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 3607683 Dshi_1092 carboxyvinyl-carboxyphosphonatephosphorylmutase (RefSeq)
Query= SwissProt::Q56062 (295 letters) >FitnessBrowser__Dino:3607683 Length = 293 Score = 168 bits (426), Expect = 1e-46 Identities = 102/274 (37%), Positives = 150/274 (54%), Gaps = 7/274 (2%) Query: 5 SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTL 64 S + R+ LA++ + +A A L + GY ++SG +A +G PDLG+ + Sbjct: 2 SAARTLRSLLAQDRCHVMPCCFDALSAKLIAQEGYDLTFMSGFAASASRIGAPDLGLMSY 61 Query: 65 DDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQVGAKRCG 124 +V+ R IT+ +PL+ D D G+G+ A NV RTV AKAG A++ IEDQ+ KRCG Sbjct: 62 GEVVDQARNITEAVDIPLIGDGDTGYGN-AMNVRRTVTGFAKAGCASVMIEDQLAPKRCG 120 Query: 125 HRPNKAIVSKEEMVDRIRAAVDARTD-----PNFVIMARTDALAVEGLEAALDRAQAYVD 179 H P KA+V ++E DRIRAAVDAR + + +I+ARTDA GL A+DRA + + Sbjct: 121 HTPGKAVVGRDEAFDRIRAAVDAREEIRAAGGDILILARTDARHEHGLAEAIDRAARFAE 180 Query: 180 AGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSA 239 GAD+LF EA + R P +ANI E GATP + A+A YPLS Sbjct: 181 LGADILFVEAPRTEAEMRTVCAELPGPKMANIVEGGATPDLPNAAMHDIGYAIAAYPLSL 240 Query: 240 FRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNEL 273 A +A + +R + + +++D + R + Sbjct: 241 MAAAMQAMVRTLRGMRDD-RRPDLMDFAELRTRI 273 Lambda K H 0.320 0.133 0.371 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: 210 Number of extensions: 12 Number of successful extensions: 5 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: 295 Length of database: 293 Length adjustment: 26 Effective length of query: 269 Effective length of database: 267 Effective search space: 71823 Effective search space used: 71823 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: 48 (23.1 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