Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate H281DRAFT_02542 H281DRAFT_02542 2-Methylisocitrate lyase, PEP mutase family
Query= curated2:Q9YFM7 (308 letters) >FitnessBrowser__Burk376:H281DRAFT_02542 Length = 290 Score = 216 bits (550), Expect = 5e-61 Identities = 117/262 (44%), Positives = 159/262 (60%), Gaps = 2/262 (0%) Query: 16 LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAMF 75 LR+ +E ++++VAPG ++ A L E+ GF Y++GA + + PD GL+TL+E+ Sbjct: 7 LRKQLESKELIVAPGAWDGISARLIEQAGFPVAYMTGAGVAAANGYPDFGLVTLTEMTAA 66 Query: 76 TSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKAL 135 +TR V +PVI DADTGFG A+NV RTV+E E +G AAIQIEDQ+ PK+CGHL+GK L Sbjct: 67 ARTLTRSVSIPVIADADTGFGNALNVRRTVQEYEISGVAAIQIEDQLFPKRCGHLEGKEL 126 Query: 136 ISPEDMVKKIIAAVGARRDA--LIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEALT 193 + + V+KI AA AR + LIVARTDAR V G + A+ER ++AGADI F EA Sbjct: 127 VQTTEFVEKIAAAAAARGEGGMLIVARTDARAVTGLDDAIERVNRALDAGADIAFVEAPQ 186 Query: 194 SLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETVL 253 S EE ARRV P L N+ GKTP I + E G++I I P + + A++ L Sbjct: 187 SAEEAAAIARRVNGPCLLNLVPGGKTPNIPLKDVAELGFRIAILPGLLLTSMMGAADLAL 246 Query: 254 REIMEKGTQKDILDKLYTRTEF 275 + G + D L R F Sbjct: 247 ATVRNTGRVEVRPDALPIRDLF 268 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: 237 Number of extensions: 10 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: 308 Length of database: 290 Length adjustment: 27 Effective length of query: 281 Effective length of database: 263 Effective search space: 73903 Effective search space used: 73903 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