Align Probable 2-methylisocitrate lyase 2; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate AZOBR_RS27820 AZOBR_RS27820 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::Q8NSL2 (307 letters) >FitnessBrowser__azobra:AZOBR_RS27820 Length = 290 Score = 179 bits (453), Expect = 9e-50 Identities = 103/255 (40%), Positives = 147/255 (57%), Gaps = 4/255 (1%) Query: 12 TERRKALRAALAAPEIARMPGAFSPLAARAIQEAGFEGVYVSG-AVVAADLALPDIGLTT 70 T + L+ AL AP + MP F L+AR I++AGF +SG AV A L +PD GL + Sbjct: 2 TTPAQRLKTALEAPGLHLMPCCFDALSARLIEQAGFRVSLMSGFAVSATRLGMPDTGLIS 61 Query: 71 LTEVAHRSRQIARVTD-LPVLVDADTGFGEPMSAARTVSELEDAGVAGCHLEDQVNPKRC 129 E+ + R + + L V+ D DTG+G M+ RTV + AG A +EDQV+PKRC Sbjct: 62 FAEMLDQLRNVCQAAPGLLVIGDGDTGYGNAMNVQRTVRDYARAGAAAVLIEDQVSPKRC 121 Query: 130 GHLDGKEVVGTDIMVRRIAAAVNERRD--EQFVICARTDAAGVEGIDSAIERAKAYADAG 187 GH GK+VVG +I AAV+ R +I ARTDA V G D+A+ER + + + G Sbjct: 122 GHTKGKQVVGRAEARMKIRAAVDAARSGANDILILARTDARAVHGFDAALERCQDFVEEG 181 Query: 188 ADMIFTEALYSPADFEKFRAAVDIPLLANMTEFGKTELLPAQLLEDIGYNAVIYPVTLLR 247 AD+IF EA + + F A +D P +ANM G+T +LP + LE +G+ YP+TL+ Sbjct: 182 ADIIFMEAPHDETEMAAFCAGIDRPAMANMVRGGQTPMLPPRELEALGFKLAAYPLTLMS 241 Query: 248 IAMGQVEQALGDIAN 262 A+ + AL +A+ Sbjct: 242 AAIDAMRAALAAVAD 256 Lambda K H 0.320 0.134 0.382 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: 223 Number of extensions: 16 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: 307 Length of database: 290 Length adjustment: 27 Effective length of query: 280 Effective length of database: 263 Effective search space: 73640 Effective search space used: 73640 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