Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate WP_086508306.1 BZY95_RS01855 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::D4GTL3 (345 letters) >NCBI__GCF_002151265.1:WP_086508306.1 Length = 291 Score = 147 bits (371), Expect = 3e-40 Identities = 76/183 (41%), Positives = 111/183 (60%), Gaps = 2/183 (1%) Query: 20 ARELREMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMTE 79 A +L+ L+ + V APG+Y AL A LA G D Y+SG S Q G PD+ +V+++E Sbjct: 5 ASDLKARLHAPEIVVAPGVYDALSASLAAEAGFDTVYLSGASIAYTQLGRPDIGLVSVSE 64 Query: 80 MVENAKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHIA 139 + + + E T L V+ DCDTG+G NV R+VR E+AG A+ +EDQT PKRCGH+ Sbjct: 65 VNDVMSHIRERTELSVVVDCDTGFGNAMNVMRSVRMLERAGANAIQLEDQTYPKRCGHLR 124 Query: 140 GKQIVSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVDIV 199 GK +V + + +AA+DA+ S+ T++I RTDA +ER Y +AGVD++ Sbjct: 125 GKTLVPEGEMVGKLKAALDARASDATLIIGRTDAVAVEG--TARAIERAHAYREAGVDML 182 Query: 200 WPE 202 + E Sbjct: 183 FIE 185 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: 219 Number of extensions: 4 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: 291 Length adjustment: 27 Effective length of query: 318 Effective length of database: 264 Effective search space: 83952 Effective search space used: 83952 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 10 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