Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate AZOBR_RS27785 AZOBR_RS27785 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= curated2:Q9YFM7 (308 letters) >FitnessBrowser__azobra:AZOBR_RS27785 Length = 292 Score = 214 bits (546), Expect = 1e-60 Identities = 119/281 (42%), Positives = 166/281 (59%), Gaps = 6/281 (2%) Query: 16 LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSG-AAITGSLAMPDLGLITLSELAM 74 L++ + + ++ APGV++ A +A+ MGF+ LY++G + L +PD GL T S++ Sbjct: 10 LKQRLSQPGLISAPGVFDMISAKVADGMGFDTLYMTGYGTVASHLGLPDAGLATFSDMVG 69 Query: 75 FTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA 134 I R P++ D DTG+G +NV+ T+R E AGAAAIQ+EDQ PKKCGH G+ Sbjct: 70 RVRAIARGTSTPLVADGDTGYGGLLNVDFTIRGYEEAGAAAIQLEDQEFPKKCGHTPGRR 129 Query: 135 LISPEDMVKKIIAAVGARR--DALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEAL 192 +I DMV+KI A AR D LI+ARTDAR G ++A+ RA Y EAGADIIF E+ Sbjct: 130 VIPMADMVRKIRVACEARSSSDFLIIARTDARTTLGLDEALRRADAYAEAGADIIFVESP 189 Query: 193 TSLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETV 252 S E R + PL+ANM E G+TP +T Q GY+I IFP T F A A + Sbjct: 190 ESEAEMERICRTIGKPLIANMVEGGRTPVMTGAQLESLGYRIAIFPATGFLAMAAALRSA 249 Query: 253 LREIMEKGTQKDILDKLYTRTEFYDLIGYH---DYEKRDAE 290 EI+ KG+ + +LY +F L+G+ ++EKR E Sbjct: 250 YGEILAKGSSAEYRGELYPFPDFTRLMGFERVWEFEKRHPE 290 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: 274 Number of extensions: 7 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: 292 Length adjustment: 27 Effective length of query: 281 Effective length of database: 265 Effective search space: 74465 Effective search space used: 74465 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