Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_005455834.1 SACCYDRAFT_RS09900 ketose-bisphosphate aldolase
Query= BRENDA::I3EBM6 (285 letters) >NCBI__GCF_000244975.1:WP_005455834.1 Length = 278 Score = 188 bits (478), Expect = 1e-52 Identities = 114/273 (41%), Positives = 150/273 (54%), Gaps = 4/273 (1%) Query: 1 MPLVSMTEMLNKAKAEGYAVGQFNLNNLEFTQAILLAAEEEKSPVILGVSEGAGRYMGGF 60 MPLV+ L +A E + FN+ LE ++ AAE ++L +S+ A RY G Sbjct: 1 MPLVTPHAALRRAHTERRGLAAFNVIQLEHAESYATAAEAAGRTIVLQISQNAVRYHGAL 60 Query: 61 KTVVNMVKGLMEDYKITVPVAIHLDHGSSFEKCKEVIDAGFTSVMIDASHHPFEENVEVT 120 + V + E T P+ +HLDH +E +D GFTSVM DAS P+E+NV T Sbjct: 61 TPLAKAVIAVAE--ASTAPLVLHLDHADDRTLVREALDLGFTSVMFDASALPYEDNVANT 118 Query: 121 KKVVEYAHARGVSVEAELGTVGGQEDDVIADGVIYADPKECEELVKRTGIDCLAPALGSV 180 +VV AHA GV+VEAELG VGG+ D V A GV DPKE V+ TG+D LA A+GS Sbjct: 119 AEVVAEAHAVGVTVEAELGEVGGK-DGVHAPGV-RTDPKEAVAFVRDTGVDSLAVAVGSS 176 Query: 181 HGPYKGEPNLGFKEMEEIGRITGVPLVLHGGTGIPTKDIQRAISLGTAKINVNTENQIAS 240 H + +L + E+ VPLVLHG +G+P + + A+ G KIN+ T A Sbjct: 177 HAMTERTASLDLDRITELREALDVPLVLHGSSGVPDETLTAAVRAGMTKINIATHLNHAF 236 Query: 241 AKKVREVLAENPNMYDPRKYLGPARDAIKETVI 273 VR LAE P + DPRKYLG R A+ VI Sbjct: 237 TDAVRAYLAERPEVVDPRKYLGAGRAAMTAEVI 269 Lambda K H 0.314 0.134 0.379 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: 212 Number of extensions: 11 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: 285 Length of database: 278 Length adjustment: 26 Effective length of query: 259 Effective length of database: 252 Effective search space: 65268 Effective search space used: 65268 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: 42 (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