Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate BPHYT_RS25670 BPHYT_RS25670 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::D4GTL3 (345 letters) >FitnessBrowser__BFirm:BPHYT_RS25670 Length = 292 Score = 145 bits (365), Expect = 2e-39 Identities = 70/191 (36%), Positives = 106/191 (55%), Gaps = 2/191 (1%) Query: 19 KARELREMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMT 78 K + L+ + V APG++ + A++A+ G + YM+G+ TV G PD + T T Sbjct: 8 KRQALKARFARNEIVTAPGIFDMISAKIADSMGFECLYMTGFGTVASYLGLPDAGLATYT 67 Query: 79 EMVENAKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHI 138 +MV TN P+I D DTGYGG+ NV VR YE+AG A + +EDQ PK+CGH Sbjct: 68 DMVNRVAAFCGGTNTPMICDADTGYGGLLNVAHTVRGYEQAGAAGIQLEDQEFPKKCGHT 127 Query: 139 AGKQIVSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVDI 198 G++++ + + + A +++ D ++ARTDA S DE + RG YA AG D+ Sbjct: 128 PGRRVIPVDDMVRKIKVAAESRSDRDFQIVARTDARTSLG--LDEALRRGEAYAKAGADV 185 Query: 199 VWPEMPNPSRE 209 ++ E P E Sbjct: 186 LFIESPESIEE 196 Lambda K H 0.315 0.132 0.384 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: 244 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: 345 Length of database: 292 Length adjustment: 27 Effective length of query: 318 Effective length of database: 265 Effective search space: 84270 Effective search space used: 84270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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