Align Probable fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Probable fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate WP_012966710.1 FERP_RS11260 fructose-bisphosphate aldolase
Query= curated2:Q9YG90 (272 letters) >NCBI__GCF_000025505.1:WP_012966710.1 Length = 261 Score = 141 bits (356), Expect = 1e-38 Identities = 92/254 (36%), Positives = 142/254 (55%), Gaps = 10/254 (3%) Query: 7 VGKRVRLSRILPDGRSVIFAFDHGIEHGPGEIPEERLDPRLLIREVVEAGVDAIMTTPGI 66 VGKR RL +I + S++ DHGI PE L+ + E ++ DA + G+ Sbjct: 2 VGKRRRLKKIFRNDLSLVVPMDHGITK-----PEAGLEKIDFLLERLDGLADAFVLHKGV 56 Query: 67 ARLTWDIWANRVAMIIKVSGKTSIRPQDDQFLQSAISSVDEVVALGGDGVAATVYWGSQF 126 + + + A+I+ +S TS+ P D ++ ++SV + V LG D V+ + GS+ Sbjct: 57 VKHSKYVEEMESALIVHLSASTSLSP--DPNAKTIVTSVKKAVELGADAVSVHINVGSET 114 Query: 127 EDKMLERWTRIRLRAEKLGLPALQLAYPRGPHIKNRYAVDIVAYGARAAMETGADLIKTY 186 E++ L+ + A++ G+P L ++YPRG + + V+ V + AR A E GAD+IKT Sbjct: 115 EERQLKEVGMVAEEADEYGVPLLVMSYPRGRGVDEK-KVENVMHAARVAYELGADIIKTN 173 Query: 187 YTGSTESFRRVVSAAGGVPVLMSGGARTPSPQEFLHKVYSVMEAGGGGVVVGRNIFQAGD 246 YTGS ESF +VV VPVL++GG + S + FL V + + AG GV GRN+FQA D Sbjct: 174 YTGSAESFSKVVEIV-DVPVLIAGGNK-KSFESFLMDVRNAIRAGAKGVAAGRNVFQAED 231 Query: 247 IRAMVKAIRAIVHE 260 R +V AI++ E Sbjct: 232 PRGVVMAIKSAFKE 245 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: 145 Number of extensions: 7 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: 261 Length adjustment: 25 Effective length of query: 247 Effective length of database: 236 Effective search space: 58292 Effective search space used: 58292 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