Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate WP_028585272.1 G494_RS0115625 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::D4GTL3 (345 letters) >NCBI__GCF_000429965.1:WP_028585272.1 Length = 290 Score = 139 bits (349), Expect = 1e-37 Identities = 78/236 (33%), Positives = 128/236 (54%), Gaps = 12/236 (5%) Query: 19 KARELREMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMT 78 K + R+++N + + P ++ L G A ++GY + G PD+ +++ T Sbjct: 3 KTTKFRQLINAPEILMLPVVHDGLSILAVAQAGFKATSVAGYGSAGSVLGQPDIGLISST 62 Query: 79 EMVENAKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHI 138 EM+ + ++ LPV+ D DTG+G ++NV R VR+ E+ G AA+ IEDQT PKRCGH+ Sbjct: 63 EMLNHYANLIARVELPVMVDIDTGFGDVNNVIRTVRQVEQMGAAALFIEDQTYPKRCGHM 122 Query: 139 AGKQIVSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVDI 198 GK +V E+ + AA+ A++ D V++ARTDA DE + R +IYA+AG D+ Sbjct: 123 GGKSVVEVEEYLPKLRAALWARKDPDFVIMARTDALAVHG--LDEAIRRAKIYAEAGADM 180 Query: 199 VWPEMPNPSREDAVAYAEEIHETHPDLKLAFNYSSSFAWSEEEDPLTFQELGDLGY 254 V+ E AV EE+ + ++ + +++ + LT EL + GY Sbjct: 181 VFVE--------AVTSVEEMRRVNAEVPVP--SAANMIEGGKTPFLTASELQEAGY 226 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: 226 Number of extensions: 10 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: 290 Length adjustment: 27 Effective length of query: 318 Effective length of database: 263 Effective search space: 83634 Effective search space used: 83634 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