Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate WP_086511658.1 BZY95_RS20055 methylisocitrate lyase
Query= SwissProt::D4GTL3 (345 letters) >NCBI__GCF_002151265.1:WP_086511658.1 Length = 301 Score = 151 bits (382), Expect = 2e-41 Identities = 90/249 (36%), Positives = 138/249 (55%), Gaps = 14/249 (5%) Query: 37 GMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMTEMVENAKRMVEATNLPVI 96 G +A A +AE GH A Y+SG FG PDL M +M ++V++A R+ AT+LP++ Sbjct: 24 GTINAYTAMMAERVGHQAIYLSGGGVANASFGLPDLGMTSMNDVVQDAHRICGATDLPLL 83 Query: 97 ADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHIAGKQIVSREKAKARFEAA 156 D DTG+GG N+ R V+E ++AGVAAVH+EDQ KRCGH K+IVS+++ R +AA Sbjct: 84 VDIDTGWGGAFNIARTVKEMQRAGVAAVHLEDQVAQKRCGHRPNKEIVSKQEMVDRIKAA 143 Query: 157 VDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVDIVWPEMPNPSREDAVAYAE 216 DA+ D +IARTDA+ D +ER +AG D ++ E + + +D A+ E Sbjct: 144 ADARIDPDFYLIARTDAFQKEG--LDAAIERANACIEAGADAIFAEAVH-TLDDYRAFCE 200 Query: 217 EIHETHPDLKLAFNYSSSFAWSEEEDPL-TFQELGDLGYKYIFITLFGLHSGAHAVYEDF 275 + D + N + A PL T QELG++G + + L + A + + Sbjct: 201 RV-----DAPILANITEFGA-----TPLFTQQELGEVGCRMVLYPLSAFRAMNAAALKVY 250 Query: 276 KKLAEQDEE 284 + + E+ + Sbjct: 251 RSIHEKGHQ 259 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: 258 Number of extensions: 16 Number of successful extensions: 1 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: 301 Length adjustment: 28 Effective length of query: 317 Effective length of database: 273 Effective search space: 86541 Effective search space used: 86541 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