Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_018232328.1 THITHI_RS0106810 fructose-bisphosphate aldolase class I
Query= BRENDA::Q8L207 (343 letters) >NCBI__GCF_000378965.1:WP_018232328.1 Length = 340 Score = 355 bits (911), Expect = e-103 Identities = 196/339 (57%), Positives = 235/339 (69%), Gaps = 7/339 (2%) Query: 5 LEDIALTLVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAMESAIS 64 L IA +V GKGILA DES TI KRF+S+ VE TE+NRRAYRE+L T E IS Sbjct: 6 LASIAQAMVAPGKGILAIDESLGTIRKRFDSVHVESTEENRRAYRELLITVPGGGEY-IS 64 Query: 65 GVILFDETLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGLRERL 124 G+ILFDET+RQ G ++ D G +PGIKVD GAK LA P E +TEGLDGLRERL Sbjct: 65 GMILFDETIRQHTRDGVPFVQVLADQGILPGIKVDAGAKDLAGHPGEKVTEGLDGLRERL 124 Query: 125 KDYYTLGARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPEVLMD 184 +Y LGA+FAKWR VI I + +P+ G I NA ALARYAALCQEAGLVPIVEPE LMD Sbjct: 125 AEYAQLGAKFAKWRTVITI-GEGIPSSGCIEANAHALARYAALCQEAGLVPIVEPETLMD 183 Query: 185 GPSRQHSITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKDA-RIASVEEVAE 243 G ++I RC+EVT++ L TVF EL RV+ E ILK NMV+ GK A VE+VA+ Sbjct: 184 G---DNTIERCYEVTELTLRTVFSELHRQRVVTEHTILKVNMVVPGKKCPDQAGVEQVAD 240 Query: 244 KTVHVLKQTVPAAVPGIAFLSGGQTDEEATAHLSAMN-ALGALPWKLTFSYGRALQAAAL 302 TV LK VPAA+PG+ FLSGGQ+ +AT HL AMN LPW L+FSYGRALQ +L Sbjct: 241 LTVRCLKNCVPAALPGVVFLSGGQSARDATVHLDAMNRKYPDLPWPLSFSYGRALQEPSL 300 Query: 303 KAWAGKNENIVVAQKAFCHRARMNHLAALGQWTKDQEKS 341 KAWAG+ EN+ AQ A HR + N LAALG++ + E++ Sbjct: 301 KAWAGRPENVEAAQAALLHREKCNSLAALGRYDESLEEA 339 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: 362 Number of extensions: 22 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: 340 Length adjustment: 29 Effective length of query: 314 Effective length of database: 311 Effective search space: 97654 Effective search space used: 97654 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