Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate Pf1N1B4_5858 carboxyphosphonoenolpyruvate phosphonomutase, putative
Query= SwissProt::D4GTL3 (345 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5858 Length = 289 Score = 91.3 bits (225), Expect = 3e-23 Identities = 55/177 (31%), Positives = 86/177 (48%), Gaps = 4/177 (2%) Query: 21 RELREMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMTEM 80 R R++ + ++ + AR+A G + + G L G PD ++T++E Sbjct: 11 RNFRQLFASNACYHTASVFDPMSARIAADLGFEVGILGGSVASLQVLGAPDFALITLSEF 70 Query: 81 VENAKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHIAG 140 E A R+ LPVIAD D GYG NV R + E E+AGVAA+ IED P + G Sbjct: 71 AEQATRIGRVAQLPVIADADHGYGNALNVMRTIVELERAGVAALTIEDTLLPAQFGR-KS 129 Query: 141 KQIVSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVD 197 +++ + + AA++A+ + +IART+A E + R + Y AG D Sbjct: 130 TDLITVAEGVGKIRAALEARVDSEMAIIARTNA---GILPVQEIISRTKQYQQAGAD 183 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: 240 Number of extensions: 11 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: 289 Length adjustment: 27 Effective length of query: 318 Effective length of database: 262 Effective search space: 83316 Effective search space used: 83316 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