Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate WP_013819356.1 METME_RS13795 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::D4GTL3 (345 letters) >NCBI__GCF_000214665.1:WP_013819356.1 Length = 296 Score = 138 bits (347), Expect = 2e-37 Identities = 88/295 (29%), Positives = 142/295 (48%), Gaps = 16/295 (5%) Query: 23 LREMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMTEMVE 82 LR M+ AP +Y + A AE G D + SG+ G PD +T +EM++ Sbjct: 5 LRHMIEQPGIHAAPAVYDCIGALAAERAGFDFIFSSGFGIAASLLGKPDFGYLTASEMID 64 Query: 83 NAKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHIAGKQ 142 AKR+ + +P++AD DTGYG NV R V++ ++ VA + +EDQ PK+CGH GK+ Sbjct: 65 AAKRIAGSVAIPLLADMDTGYGNPLNVIRTVQDVVQSPVAGIILEDQEWPKKCGHFEGKR 124 Query: 143 IVSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVDIVWPE 202 +VS ++ + +AAV A+ V++ARTDA + + RG Y AG D+++ E Sbjct: 125 LVSVDEQVEKIKAAVYARGDSGLVIVARTDARAVEG--LNGAIARGERYLAAGADVLFVE 182 Query: 203 MPNPSREDAVAYAEEIHETHPDLKLAFNYSSSFAWSEEEDPLTFQELGDLGYKYIFITLF 262 P SRE+ A ++ + L+ EL D+GYK + L Sbjct: 183 APQ-SREELAEVARHFQ--------GVPLFANIIEGGKTPNLSVAELDDMGYKLVAFALS 233 Query: 263 GLHSGAHAVYEDFKKLAEQDEEGQFDLEQRYLDHPTESHHELSFVSRYQDIETEF 317 GL S A+ + F L + E + E ++ ++++ ++E F Sbjct: 234 GLFSATQALIDCFNTLKADGSTANINSELSF-----EGFKDVIRMNQHLELENRF 283 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: 267 Number of extensions: 14 Number of successful extensions: 3 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: 296 Length adjustment: 28 Effective length of query: 317 Effective length of database: 268 Effective search space: 84956 Effective search space used: 84956 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