Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate RR42_RS22765 RR42_RS22765 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= curated2:Q9YFM7 (308 letters) >FitnessBrowser__Cup4G11:RR42_RS22765 Length = 281 Score = 210 bits (534), Expect = 4e-59 Identities = 108/244 (44%), Positives = 155/244 (63%), Gaps = 2/244 (0%) Query: 15 VLRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAM 74 +LR+ ++ +++APG Y+ A L E+ GF A Y++GA + + PD GL+T+SE+ Sbjct: 6 ILRQRLQAPGMIIAPGAYDAIGARLIEQAGFSACYMTGAGTSAARGFPDFGLLTMSEMVE 65 Query: 75 FTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA 134 + + R V +P+I DADTG+G +NV RTVRE E G AAI IEDQV PK+CGHL GK Sbjct: 66 NAAVMARSVSIPLIADADTGYGNQLNVTRTVREYEARGVAAIHIEDQVAPKRCGHLDGKE 125 Query: 135 LISPEDMVKKIIAAVGARR--DALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEAL 192 ++S E+ V KI AAV ARR D +I+ARTDAR + G E+A+ RA +EAGAD+ F EA Sbjct: 126 VVSREEFVSKIRAAVQARRTPDFVIIARTDARAMLGLEEAIWRANAALEAGADLAFVEAT 185 Query: 193 TSLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETV 252 ++EE R V+ P L N+ G+TP + + GYK+ I P +A+++A + Sbjct: 186 QTIEEVAAVPRLVRGPCLLNVVPGGRTPIFDLREAEVMGYKLAILPGLMLKAAIQAGDEA 245 Query: 253 LREI 256 L E+ Sbjct: 246 LAEL 249 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: 251 Number of extensions: 5 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: 281 Length adjustment: 26 Effective length of query: 282 Effective length of database: 255 Effective search space: 71910 Effective search space used: 71910 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