Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate AZOBR_RS10395 AZOBR_RS10395 fructose-bisphosphate aldolase
Query= SwissProt::P0A991 (350 letters) >FitnessBrowser__azobra:AZOBR_RS10395 Length = 309 Score = 169 bits (428), Expect = 9e-47 Identities = 105/297 (35%), Positives = 154/297 (51%), Gaps = 11/297 (3%) Query: 47 PAVLRNMQTLYNTGRLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGC 106 P V N+ + G+L GTG L ILPVDQG EH SFA N +DP +LAI+AGC Sbjct: 19 PGVKANLARILMEGKLGGTGKLVILPVDQGFEHGPARSFAPNEPGYDPHYHYQLAIDAGC 78 Query: 107 NCVASTYGVLASVSRRYAHRIPFLVKLNHNETLS-YPNTYDQTLYASVEQAFNMGAVAVG 165 N A+ G L + + +A IP ++K+N +LS DQ + ASV+ A +G A+G Sbjct: 79 NAYAAPLGSLEAGASTFAGSIPLILKMNSANSLSRQKEDADQAVTASVQDALRLGCSAIG 138 Query: 166 ATIYFGSEESRRQIEEISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQAN 225 TIY GS+ Q EEI + A +G+ TVLW+Y R K+G ++ D+ G A Sbjct: 139 FTIYPGSDAMYDQYEEIRELSKEAKSVGLPTVLWSYPRGGTISKEG---ELAIDVIGYAA 195 Query: 226 HLAATIGADIVKQKMAENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAG 285 H+AA +GA I+K K+ + Y + D VR+ + + GR Sbjct: 196 HMAALLGAHIIKVKLPSAHLEQAEAKKVYES----KNIPIATQADRVRHIMQCAFNGRRI 251 Query: 286 LINSGGAAGGETDLSDAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVY 342 ++ SGGA GE + + R + GG G I+GR AF++ D +KL++ + +Y Sbjct: 252 VVFSGGATKGEDAVFEDARAI---RDGGGNGSIIGRNAFQRPREDALKLLDRIMKIY 305 Lambda K H 0.318 0.134 0.386 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: 261 Number of extensions: 10 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: 350 Length of database: 309 Length adjustment: 28 Effective length of query: 322 Effective length of database: 281 Effective search space: 90482 Effective search space used: 90482 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: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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