Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate GFF546 Psest_0551 PEP phosphonomutase and related enzymes
Query= curated2:Q9YFM7 (308 letters) >FitnessBrowser__psRCH2:GFF546 Length = 287 Score = 133 bits (335), Expect = 4e-36 Identities = 93/242 (38%), Positives = 131/242 (54%), Gaps = 7/242 (2%) Query: 17 RELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGA-AITGSLAMPDLGLITLSELAMF 75 REL+ V++P A +A +GFE L G+ A LA PD LITLSE Sbjct: 14 RELLNADRCFHTASVFDPMSARIAADLGFEVGILGGSVASLQVLAAPDFNLITLSEFVEQ 73 Query: 76 TSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKAL 135 + I RV ++PV+ DAD G+G A+NV RTV ELERAG +A+ IED ++P K G + L Sbjct: 74 ATRICRVAQLPVLADADHGYGNALNVMRTVSELERAGISALTIEDTLLPPKFGR-RSTDL 132 Query: 136 ISPEDMVKKIIAAVGARRD--ALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEALT 193 I + V KI AA+ AR D I+ RT+A GV GFE+ + RAQ Y +AGAD I + Sbjct: 133 IGMFEAVGKIRAALEARVDPEMAIIGRTNA-GVIGFEEVIARAQAYEKAGADAICLVGIE 191 Query: 194 SLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETVL 253 + A ++ PL+ + +G + G +IV+ + A++KA+ L Sbjct: 192 DFDHLESIASQLSKPLM--LVTYGNPNLRDNARLASLGVRIVVNGHAAYFAAIKATYDCL 249 Query: 254 RE 255 RE Sbjct: 250 RE 251 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: 186 Number of extensions: 10 Number of successful extensions: 3 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: 287 Length adjustment: 26 Effective length of query: 282 Effective length of database: 261 Effective search space: 73602 Effective search space used: 73602 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