Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate WP_012501688.1 CPAR_RS02230 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Query= curated2:Q9V2I6 (281 letters) >NCBI__GCF_000020505.1:WP_012501688.1 Length = 293 Score = 112 bits (281), Expect = 7e-30 Identities = 84/278 (30%), Positives = 134/278 (48%), Gaps = 41/278 (14%) Query: 8 GIKRRLRRFFRRD-GRALIFAMDHGFEHGPT--------DFEPVWEHVNPRVIIRKVVRA 58 G+K RL R FR D G+ ++FA+DHG+ GPT + P+ +H + ++ R ++R Sbjct: 35 GMKNRLSRIFRPDTGKTVMFAIDHGYFQGPTTGLERPDVNIVPLMKHADAIMLTRGILRT 94 Query: 59 GVDGVMMLPGMARIAGDDVKPEVGLMIKITSKTNLRPKAEQLMQSQLAF-VEDAIKLGAD 117 V + + R +G P + ++L +LA +EDAI++ Sbjct: 95 TVPPSLTKAVVMRCSGG---PSI---------------LKELSDEELAVDIEDAIRMNVA 136 Query: 118 AIAATVYWGSPQEDAMMRQFAEIVSYAHDLGFPVVQF-AYPRGPYIDEKYGRKEDYRVVM 176 I V+ G E + ++V G P + A + D KY R Sbjct: 137 CITLQVFIGGEYETRSIHNMTKLVDMGLRYGIPTMAVTAVGKDMVRDAKYFR-------- 188 Query: 177 YGARAAAEMGADMIKTYWTGSRETFAKVVDAAAGVPVLLSGGAKAENPLDFLKVVYEVIE 236 R AE+GA ++KTY+ E F VV A+ VP++++GG K LD L + Y I+ Sbjct: 189 LATRICAELGAQLVKTYYVP--EDFETVV-ASCPVPIVMAGGKKLPE-LDALTMSYNAIQ 244 Query: 237 AGGSGAVVGRNIFQRENPEPMIKALIRVIHRNEDPEEA 274 G +G +GRNIFQ +NPE M+ A+ +++H +P EA Sbjct: 245 EGAAGVDMGRNIFQSDNPEEMMLAVNKIVHEGYNPNEA 282 Lambda K H 0.321 0.138 0.406 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: 191 Number of extensions: 12 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: 281 Length of database: 293 Length adjustment: 26 Effective length of query: 255 Effective length of database: 267 Effective search space: 68085 Effective search space used: 68085 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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