Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate 3607274 Dshi_0689 isocitrate lyase family protein (RefSeq)
Query= curated2:Q9YFM7 (308 letters) >FitnessBrowser__Dino:3607274 Length = 292 Score = 214 bits (546), Expect = 1e-60 Identities = 125/259 (48%), Positives = 163/259 (62%), Gaps = 8/259 (3%) Query: 25 IVVAPGVYNPAVALLAERMGFEALYLSGAAITGS-LAMPDLGLITLSELAMFTSYITRVV 83 IV+APGVY+ A LAE GF ALYLSGAA++ + L PD+GL +++E+ S I V Sbjct: 16 IVMAPGVYDALTASLAEAAGFPALYLSGAAVSYTRLGRPDIGLTSVTEMTETLSLIRDRV 75 Query: 84 RVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKALISPEDMVK 143 P+I+DADTGFG A+N +RT+R ERAGA A+QIEDQ PK+CGHL K LI ++M Sbjct: 76 STPIIIDADTGFGNALNAQRTMRLYERAGANALQIEDQAYPKRCGHLADKTLIPAQEMAG 135 Query: 144 KIIAAVGARRDA--LIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEALTSLEEFREF 201 KI A AR A LI+ARTDA VEGFE A ERA+ Y+EAGADI+F EA S + Sbjct: 136 KIRAMADARHAAQTLIIARTDAVAVEGFEAAQERAETYLEAGADILFIEAPQSEAQLTAI 195 Query: 202 ARRV--KAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETVLREIMEK 259 A+R + PLLANM E G+TP + + GY +VIFP RA + +E + E Sbjct: 196 AQRFRGRVPLLANMVEGGETPMKSARELEALGYALVIFPGGIVRALARTAEAYYLSLSET 255 Query: 260 GTQKDILDKLYTRTEFYDL 278 G+ D+++ +F DL Sbjct: 256 GSNAAFRDRMF---DFQDL 271 Lambda K H 0.321 0.137 0.378 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: 256 Number of extensions: 15 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: 308 Length of database: 292 Length adjustment: 27 Effective length of query: 281 Effective length of database: 265 Effective search space: 74465 Effective search space used: 74465 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