Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate PP_1389 PP_1389 Oxaloacetate decarboxylase
Query= SwissProt::D4GTL3 (345 letters) >FitnessBrowser__Putida:PP_1389 Length = 291 Score = 93.2 bits (230), Expect = 7e-24 Identities = 58/174 (33%), Positives = 87/174 (50%), Gaps = 4/174 (2%) Query: 24 REMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMTEMVEN 83 RE+L + ++ + AR+A G + + G L PD ++T++E VE Sbjct: 16 RELLASGSCFHTASVFDPMSARIAADLGFEVGILGGSVASLQVLAAPDFALITLSEFVEQ 75 Query: 84 AKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHIAGKQI 143 A R+ LPV+AD D GYG NV R V E E+AGVAA+ IED P + G + Sbjct: 76 ATRIGRVAQLPVLADADHGYGNALNVMRTVIELERAGVAALTIEDTLLPAQFGR-KSTDL 134 Query: 144 VSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVD 197 + E+ + AA++A+ +IART+A S +E + R + Y AG D Sbjct: 135 IPVEEGVGKIRAALEARVDSSLSIIARTNAGVLST---EEIIVRTQSYQKAGAD 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: 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: 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 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