Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate CCNA_01980 CCNA_01980 PEP phosphonomutase related enzyme
Query= SwissProt::P77541 (296 letters) >FitnessBrowser__Caulo:CCNA_01980 Length = 255 Score = 83.2 bits (204), Expect = 6e-21 Identities = 72/222 (32%), Positives = 111/222 (50%), Gaps = 21/222 (9%) Query: 9 AFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVL 68 AFRA L E + +A A +R G++A+ + G+A ++G D G T D+V+ Sbjct: 11 AFRA-LHAEGCFVLPNPWDAGGARRLERRGFKALASTSAGMA-WAMGRDD-GQVTRDEVI 67 Query: 69 TDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPN 128 +R + LP+ D + GFG + VA +V I+AG AGL IED G++ Sbjct: 68 AHLRTLCSATELPVNADFENGFGETPAEVAESVTLAIQAGVAGLSIEDWSGSE------- 120 Query: 129 KAIVSKEEMVDRI---RAAVDAKTDPDFVIMARTDAL--AVEGLDAAIERAQAYVEAGAE 183 + E VDR+ RAA+DA + D +++ART+ L +ER AY AGA+ Sbjct: 121 --LYPLEVAVDRLKAARAAIDA-SGQDVILVARTEGYLRGCRDLQPTLERLGAYAAAGAD 177 Query: 184 MLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDEL 225 L+ A+++ A + DAV P N+ +G P T + L Sbjct: 178 CLYAPAVSDPAEIKAIVDAV-APKPVNVLLWG--PEMTVESL 216 Lambda K H 0.319 0.133 0.369 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: 144 Number of extensions: 8 Number of successful extensions: 2 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: 296 Length of database: 255 Length adjustment: 25 Effective length of query: 271 Effective length of database: 230 Effective search space: 62330 Effective search space used: 62330 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: 47 (22.7 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