Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate BPHYT_RS29750 BPHYT_RS29750 phosphoenolpyruvate phosphomutase
Query= curated2:Q9YFM7 (308 letters) >FitnessBrowser__BFirm:BPHYT_RS29750 Length = 581 Score = 112 bits (280), Expect = 2e-29 Identities = 83/281 (29%), Positives = 141/281 (50%), Gaps = 11/281 (3%) Query: 16 LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAMF 75 LR+++ ++ +N A + GF+A++ SG AI+ + D + +++ Sbjct: 17 LRQMLVSNELEFMMEAHNGLSARIVREAGFKAIWGSGLAISAQYGVRDNNEASWTQVVDT 76 Query: 76 TSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA- 134 ++ +P+++D DTG+G NV R VR+LE+ G A + IED+ PK + G+A Sbjct: 77 LEFMADASDLPILLDGDTGYGNFNNVRRLVRKLEQRGIAGVCIEDKQFPKTNSFINGEAQ 136 Query: 135 -LISPEDMVKKIIAAVGARRDA--LIVARTDAR-GVEGFEKAVERAQLYVEAGAD-IIFP 189 L ++ KI A ++ D IVAR +A G ++A+ RA+ Y +AGAD I+ Sbjct: 137 PLADMDEFCGKIKAGKDSQSDENFSIVARVEALIAGWGMDEALRRAEAYRQAGADAILIH 196 Query: 190 EALTSLEEFREFARR--VKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLK 247 L+ +E EFAR + PL+ T++ TP + FREAG VI+ RA+ Sbjct: 197 SKLSRPDEILEFAREWAGRGPLVIVPTKYYSTP---TEVFREAGISTVIWANHLIRAATS 253 Query: 248 ASETVLREIMEKGTQKDILDKLYTRTEFYDLIGYHDYEKRD 288 A + V +EI T ++ D + E + L +Y + + Sbjct: 254 AMQAVAKEIHTSETLVNVEDSIAAVNEIFRLQDADEYSEAE 294 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: 340 Number of extensions: 13 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: 581 Length adjustment: 32 Effective length of query: 276 Effective length of database: 549 Effective search space: 151524 Effective search space used: 151524 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: 50 (23.9 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