Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate RR42_RS22175 RR42_RS22175 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::Q8EJW1 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS22175 Length = 288 Score = 207 bits (527), Expect = 2e-58 Identities = 115/257 (44%), Positives = 157/257 (61%), Gaps = 6/257 (2%) Query: 13 LANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGMTSMNDVLIDAGR 72 L + L + G +A+ AL+A Q GF+ALYLSGA VA G D+G+T+ + + GR Sbjct: 10 LCQPRVLLVPGVYDAFSALVAAQAGFEALYLSGAAVAYTQLGRSDVGLTTATETVDIVGR 69 Query: 73 ITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKRCGHRPNKAVVST 132 IT LPL+VD DTG+G A N+ RT++ E+ G A + +EDQ KRCGH NK VV+ Sbjct: 70 ITDRVDLPLIVDADTGYGNALNVIRTVRTLERAGAAMIQLEDQTFPKRCGHLDNKRVVTP 129 Query: 133 EEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGADMIFAEAL-TEL 191 EM ++KAA+DAR +I+ARTDAVA+EGL+A IERA+AY+A G D +F EAL TE Sbjct: 130 AEMCGKLKAALDARASSRTLILARTDAVAIEGLDAAIERAEAYVACGVDALFIEALRTEQ 189 Query: 192 DQYR---HFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRAANQAALKV 248 D R HF +V P+LANM E G+T + + ELA G +V++P G R + Sbjct: 190 DMARVCAHFAGRV--PLLANMVEGGKTPVQSAAELAGRGFRIVIFPGGVVRFIGAQMKRY 247 Query: 249 MQALMNDGHQRNVLDTM 265 +L+ G + D M Sbjct: 248 YSSLLEHGTTAPMRDAM 264 Lambda K H 0.319 0.132 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: 228 Number of extensions: 6 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: 292 Length of database: 288 Length adjustment: 26 Effective length of query: 266 Effective length of database: 262 Effective search space: 69692 Effective search space used: 69692 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