Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 14469 b0331 2-methylisocitrate lyase (NCBI)
Query= BRENDA::Q05957 (318 letters) >FitnessBrowser__Keio:14469 Length = 296 Score = 168 bits (426), Expect = 1e-46 Identities = 101/269 (37%), Positives = 152/269 (56%), Gaps = 5/269 (1%) Query: 45 GVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVEATRRITAAAPNLCV 104 G +A A + ++ G+ A ++SG V+A LGLPD G+ T +V+ RRIT +L + Sbjct: 24 GTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVC-SLPL 82 Query: 105 VVDGDTG-GGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGKAVVPAEEHALKIA 163 +VD D G G NV R ++ +I AGA G+ +EDQV K+CGH KA+V EE +I Sbjct: 83 LVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIR 142 Query: 164 AAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEAPANVDELKEVSAK 223 AA +A D DF ++ARTDA A GL+ I RA Y EAGA+ F EA + ++ + Sbjct: 143 AAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADA 202 Query: 224 TKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVNIMKILKEKGTTRD 283 + +AN+ E G TPL T +E + + + L+A A RA ++ +L+++GT + Sbjct: 203 VQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKS 262 Query: 284 DLDQMATFSEFNELISLESWYEMESKFKN 312 +D M T +E E I ++Y+ E K N Sbjct: 263 VIDTMQTRNELYESI---NYYQYEEKLDN 288 Lambda K H 0.316 0.131 0.373 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: 181 Number of extensions: 7 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: 318 Length of database: 296 Length adjustment: 27 Effective length of query: 291 Effective length of database: 269 Effective search space: 78279 Effective search space used: 78279 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: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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