Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate 209396 DVU0460 predicted phospho-2-dehydro-3-deoxyheptonate aldolase
Query= curated2:Q9V2I6 (281 letters) >MicrobesOnline__882:209396 Length = 266 Score = 174 bits (440), Expect = 2e-48 Identities = 102/275 (37%), Positives = 157/275 (57%), Gaps = 13/275 (4%) Query: 6 NIGIKRRLRRFFRRD-GRALIFAMDHGFEHGPTDFEPVWEHVNPRVIIRKVVRAGVDGVM 64 +IG K R+ R F R GR++I +DHG GP D V+ R + +V G D V+ Sbjct: 2 HIGKKIRMERLFNRTTGRSVIVPLDHGVSVGPID-----GLVDMRDTVNQVAEGGADAVL 56 Query: 65 MLPGMARIAGDDVKPEVGLMIKITSKTNLRPKAEQLMQSQLAFVEDAIKLGADAIAATVY 124 M G+ R + +VGL++ +++ T+L P ++ A VEDAIK GAD ++ V Sbjct: 57 MHKGLVRCGHREGGRDVGLIVHLSASTSLSPLPNA--KTLTATVEDAIKHGADGVSVHVN 114 Query: 125 WGSPQEDAMMRQFAEIVSYAHDLGFPVVQFAYPRGPYIDEKYGRKEDYRVVMYGARAAAE 184 G E M+ + + A+D G P++ Y RGP I ++Y D +VV + AR E Sbjct: 115 LGDETERDMLADLGRVATIANDWGVPLLAMMYARGPRIRDQY----DPQVVAHCARVGVE 170 Query: 185 MGADMIKTYWTGSRETFAKVVDAAAGVPVLLSGGAKAENPLDFLKVVYEVIEAGGSGAVV 244 +GAD++K +TG +TFA VV + VPV+++GG K ++ DFL++V++ + AGGSG V Sbjct: 171 LGADVVKVPYTGDMDTFAHVVQSCC-VPVVIAGGPKLDSTRDFLQMVHDAVRAGGSGLSV 229 Query: 245 GRNIFQRENPEPMIKALIRVIHRNEDPEEAAKAEG 279 GRNIFQ P ++KA+ ++H + D E+A G Sbjct: 230 GRNIFQHARPSQLVKAVRGLVHEDWDVEQAIAIVG 264 Lambda K H 0.321 0.138 0.406 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: 231 Number of extensions: 18 Number of successful extensions: 5 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: 281 Length of database: 266 Length adjustment: 25 Effective length of query: 256 Effective length of database: 241 Effective search space: 61696 Effective search space used: 61696 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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