Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate WP_086508306.1 BZY95_RS01855 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= curated2:Q9YFM7 (308 letters) >NCBI__GCF_002151265.1:WP_086508306.1 Length = 291 Score = 196 bits (498), Expect = 5e-55 Identities = 112/270 (41%), Positives = 160/270 (59%), Gaps = 5/270 (1%) Query: 16 LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGS-LAMPDLGLITLSELAM 74 L+ + +IVVAPGVY+ A LA GF+ +YLSGA+I + L PD+GL+++SE+ Sbjct: 8 LKARLHAPEIVVAPGVYDALSASLAAEAGFDTVYLSGASIAYTQLGRPDIGLVSVSEVND 67 Query: 75 FTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA 134 S+I + V+VD DTGFG A+NV R+VR LERAGA AIQ+EDQ PK+CGHL+GK Sbjct: 68 VMSHIRERTELSVVVDCDTGFGNAMNVMRSVRMLERAGANAIQLEDQTYPKRCGHLRGKT 127 Query: 135 LISPEDMVKKIIAAVGARRD--ALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEAL 192 L+ +MV K+ AA+ AR LI+ RTDA VEG +A+ERA Y EAG D++F E + Sbjct: 128 LVPEGEMVGKLKAALDARASDATLIIGRTDAVAVEGTARAIERAHAYREAGVDMLFIEGI 187 Query: 193 TSLEEFREFAR--RVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASE 250 S ++ R + P++ANM E G TP +E G+ +VIFP RA + Sbjct: 188 RSDDDIASIMAEFRGRIPIMANMVEGGDTPLQNARALQEQGFSLVIFPGALVRAFTHMAS 247 Query: 251 TVLREIMEKGTQKDILDKLYTRTEFYDLIG 280 + GT +++ + +++G Sbjct: 248 QFFATLRRDGTTDAFRERMLDFGQLNEVLG 277 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: 239 Number of extensions: 14 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: 291 Length adjustment: 27 Effective length of query: 281 Effective length of database: 264 Effective search space: 74184 Effective search space used: 74184 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 24 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