Align Probable fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Probable fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate WP_012675743.1 PERMA_RS08670 fructose-bisphosphate aldolase
Query= curated2:Q9YG90 (272 letters) >NCBI__GCF_000021565.1:WP_012675743.1 Length = 266 Score = 149 bits (375), Expect = 8e-41 Identities = 94/270 (34%), Positives = 151/270 (55%), Gaps = 13/270 (4%) Query: 7 VGKRVRLSRIL--PDGRSVIFAFDHGIEHGPGEIPEERLDPRLLIREVVEAGVDAIMTTP 64 +GKRVRL RI+ G++VI DHG+ GP + ++ + + ++ E G +AI+ Sbjct: 3 IGKRVRLERIMNRDTGKTVIVPMDHGVSSGP---MKGIINIKDTVEKIAEGGANAIILHK 59 Query: 65 GIARLTWDIWANRVAMIIKVSGKT--SIRPQDDQFLQSAISSVDEVVALGGDGVAATVYW 122 G+ V +I+ +S T SIR D + + +V+E + LG DGV+ V Sbjct: 60 GMVEQGHRGKGKDVGLIVHMSASTDLSIRKND----KVLVCTVEEAIKLGADGVSIHVNI 115 Query: 123 GSQFEDKMLERWTRIRLRAEKLGLPALQLAYPRGPHIKNRYAVDIVAYGARAAMETGADL 182 G++ E +ML+ + + + +P + + Y RGP +KN + D VA+ AR E GAD+ Sbjct: 116 GAEDEKQMLKDFGAVSKACIEWQMPLVAMIYYRGPEVKNPFDPDAVAHIARIGAELGADI 175 Query: 183 IKTYYTGSTESFRRVVSAAGGVPVLMSGGARTPSPQEFLHKVY-SVMEAGGGGVVVGRNI 241 +K YTG E+FR+VV VPV+++GG + S +E L +Y +V+ AG G+ VGRNI Sbjct: 176 VKVPYTGDPETFRKVVEGC-PVPVVIAGGPKVSSDKELLQMIYDAVVVAGCAGLSVGRNI 234 Query: 242 FQAGDIRAMVKAIRAIVHEGFDPEKASKLL 271 FQ ++ + + IVHEG ++A K+L Sbjct: 235 FQHDNVSKITYVLSKIVHEGITVDEALKIL 264 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: 160 Number of extensions: 7 Number of successful extensions: 4 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: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 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