Align Probable fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Probable fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate WP_073037203.1 BUB04_RS04045 hypothetical protein
Query= curated2:Q9YG90 (272 letters) >NCBI__GCF_900129305.1:WP_073037203.1 Length = 263 Score = 124 bits (312), Expect = 2e-33 Identities = 86/264 (32%), Positives = 126/264 (47%), Gaps = 8/264 (3%) Query: 8 GKRVRLSRILP--DGRSVIFAFDHGIEHGPGEIPEERLDPRLLIREVVEAGVDAIMTTPG 65 GKR+RL R DGR V+F DHG+ GP EE ++ V AG D ++ G Sbjct: 3 GKRLRLRRFFSRGDGRLVLFPLDHGVSCGPVAGLEEL---HRVLSYGVRAGADGVVLHKG 59 Query: 66 IARLTWDIWANRVAMIIKVSGKTSIRPQDDQFLQSAISSVDEVVALGGDGVAATVYWGSQ 125 + + + + +S T + P + + SV+E + G DGV+ V G Sbjct: 60 MMACLEKVSGPLPGIFMHLSASTQLGPAFHG--KVLVGSVEEALGRGADGVSVHVNLGDD 117 Query: 126 FEDKMLERWTRIRLRAEKLGLPALQLAYPRGPHIKNRYAVDIVAYGARAAMETGADLIKT 185 E +ML + + G+P L + Y RG H + VA+ AR A E GADLIK Sbjct: 118 AEPQMLRDLGTVGEACFRWGVPLLVMIYVRGAHAPKPVTDEAVAHAARVAGELGADLIKI 177 Query: 186 YYTGSTESFRRVVSAAGGVPVLMSGGARTPSPQEFLHKVYSVMEAGGGGVVVGRNIFQAG 245 E R+ VPV+M+GGA+ L ++ + + AG GV VGRN+FQ Sbjct: 178 PAPKDPEVMERIARCVP-VPVVMAGGAKEADEAVILERIRTGLRAGLAGVAVGRNVFQHR 236 Query: 246 DIRAMVKAIRAIVHEGFDPEKASK 269 D +KAI +VHEG ++A++ Sbjct: 237 DPEGFLKAIVGLVHEGLSAQEAAR 260 Lambda K H 0.320 0.137 0.403 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: 178 Number of extensions: 13 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: 272 Length of database: 263 Length adjustment: 25 Effective length of query: 247 Effective length of database: 238 Effective search space: 58786 Effective search space used: 58786 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: 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