Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 16203 b2096 tagatose-bisphosphate aldolase 1 (VIMSS)
Query= BRENDA::Q5HE75 (286 letters) >FitnessBrowser__Keio:16203 Length = 284 Score = 221 bits (564), Expect = 1e-62 Identities = 121/287 (42%), Positives = 176/287 (61%), Gaps = 5/287 (1%) Query: 1 MPLVSMKEMLIDAKENGYAVGQYNINNLEFTQAILEASQEENAPVILGVSEGAARYMSGF 60 M +VS K+ML +A+ GYAV +NI+NLE Q ++E + +APVI+ + G + +G Sbjct: 1 MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTH-AGT 59 Query: 61 YTIVKMVEGLMHDLNITIPVAIHLDHGSSFEKCKEAIDAGFTSVMIDASHSPFEENVATT 120 ++ +V + + P+AIHLDH + F+ + + +G SVMIDASH PF +N++ Sbjct: 60 ENLLALVSAMAKQYHH--PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLPFAQNISRV 117 Query: 121 KKVVEYAHEKGVSVEAELGTVGGQEDDVVAD--GIIYADPKECQELVEKTGIDALAPALG 178 K+VV++ H VSVEAELG +GGQEDDV + +Y +P + +E E TGID+LA A+G Sbjct: 118 KEVVDFCHRFDVSVEAELGQLGGQEDDVQVNEADALYTNPAQAREFAEATGIDSLAVAIG 177 Query: 179 SVHGPYKGEPKLGFKEMEEIGLSTGLPLVLHGGTGIPTKDIQKAIPFGTAKINVNTENQI 238 + HG Y P L F +E I LPLVLHG +G+ TKDIQ+ I G KINV TE + Sbjct: 178 TAHGMYASAPALDFSRLENIRQWVNLPLVLHGASGLSTKDIQQTIKLGICKINVATELKN 237 Query: 239 ASAKAVRDVLNNDKEVYDPRKYLGPAREAIKETVKGKIKEFGTSNRA 285 A ++A+++ L E DPR YL A+ A+++ V I + G RA Sbjct: 238 AFSQALKNYLTEHPEATDPRDYLQSAKSAMRDVVSKVIADCGCEGRA 284 Lambda K H 0.312 0.133 0.370 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: 234 Number of extensions: 9 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: 286 Length of database: 284 Length adjustment: 26 Effective length of query: 260 Effective length of database: 258 Effective search space: 67080 Effective search space used: 67080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 47 (22.7 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