Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_057687359.1 ABB28_RS15935 fructose-bisphosphate aldolase class I
Query= BRENDA::Q8L207 (343 letters) >NCBI__GCF_001431535.1:WP_057687359.1 Length = 334 Score = 362 bits (930), Expect = e-105 Identities = 196/335 (58%), Positives = 235/335 (70%), Gaps = 9/335 (2%) Query: 3 ERLEDIALTLVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAMESA 62 E+L + A +V GKGI+A DEST TI KRF S+GVE TE+NRRAYRE+L T + E Sbjct: 4 EQLAETAQAMVAPGKGIIAIDESTGTIAKRFASVGVENTEENRRAYRELLLTTPKLNEH- 62 Query: 63 ISGVILFDETLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGLRE 122 ISG ILFDET+RQ G + D G +PGIKVD GA PLA P E +TEGLDGLRE Sbjct: 63 ISGAILFDETIRQSTKDGVPFAKYMSDNGMIPGIKVDKGAHPLAGCPGELVTEGLDGLRE 122 Query: 123 RLKDYYTLGARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPEVL 182 RL++YY LGARFAKWRAVI I +++P+ I NA ALARYAALCQE GLVP+VEPEV+ Sbjct: 123 RLQEYYKLGARFAKWRAVINI-GESIPSGTCIESNAHALARYAALCQECGLVPMVEPEVI 181 Query: 183 MDGPSRQHSITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKDA-RIASVEEV 241 MDG H I C+EVT+ L ++F L++ VL EG ILK +MVI GKD A EEV Sbjct: 182 MDG---DHDIETCYEVTEATLRSLFDALYQQNVLLEGTILKASMVISGKDCEEQADAEEV 238 Query: 242 AEKTVHVLKQTVPAAVPGIAFLSGGQTDEEATAHLSAMNALGALPWKLTFSYGRALQAAA 301 AE TV LK TVPA +PG+ FLSGGQ+DE++T HL+AMN +G LPW L+FSYGRA+Q AA Sbjct: 239 AESTVMCLKSTVPAILPGVVFLSGGQSDEQSTEHLNAMNQMGNLPWPLSFSYGRAMQQAA 298 Query: 302 LKAWAGKNE--NIVVAQKAFCHRARMNHLAALGQW 334 L W GK+ N AQK RA+ N AALG+W Sbjct: 299 LALW-GKDTKGNYAAAQKTVYERAKENGQAALGKW 332 Lambda K H 0.319 0.132 0.378 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: 338 Number of extensions: 14 Number of successful extensions: 6 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: 343 Length of database: 334 Length adjustment: 28 Effective length of query: 315 Effective length of database: 306 Effective search space: 96390 Effective search space used: 96390 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 (21.8 bits) S2: 49 (23.5 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