Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_008814762.1 M988_RS18375 class II fructose-bisphosphate aldolase
Query= BRENDA::I3EBM6 (285 letters) >NCBI__GCF_001655005.1:WP_008814762.1 Length = 287 Score = 233 bits (595), Expect = 3e-66 Identities = 129/287 (44%), Positives = 175/287 (60%), Gaps = 5/287 (1%) Query: 1 MPLVSMTEMLNKAKAEGYAVGQFNLNNLEFTQAILLAAEEEKSPVILGVSEGAGRYMGGF 60 MP VS M+ +A GYA+G F+ +N E +AILLAA+EE+SPV++ V + MG Sbjct: 1 MPYVSGKTMIQQAWKHGYAIGAFSAHNAETVRAILLAAQEEQSPVMIQVGQKVISVMG-L 59 Query: 61 KTVVNMVKGLMEDYKITVPVAIHLDHGSSFEKCKEVIDAGFTSVMIDASHHPFEENVEVT 120 K + ++ M D ITVPV IHLDH SFE+ + I GF SVM D SH FEENV +T Sbjct: 60 KPMKEIIDAFMHD--ITVPVCIHLDHSRSFEQTMQAIQCGFQSVMFDGSHLSFEENVRIT 117 Query: 121 KKVVEYAHARGVSVEAELGTVGGQEDDVIAD--GVIYADPKECEELVKRTGIDCLAPALG 178 + E AHA + +E E+G +GG EDD+ D + E + T +D LA ++G Sbjct: 118 RAASEVAHALNIGMEGEIGKIGGTEDDISVDEKDALITSCDEALRFSEGTDVDYLAVSIG 177 Query: 179 SVHGPYKGEPNLGFKEMEEIGRITGVPLVLHGGTGIPTKDIQRAISLGTAKINVNTENQI 238 + HG YK EP L F ++EI I P+VLHGG+G+P I++AI+LG AK+NV+TE + Sbjct: 178 TAHGVYKQEPKLAFGRLQEIREIVKKPIVLHGGSGVPDDQIRQAIALGVAKVNVDTELRQ 237 Query: 239 ASAKKVREVLAENPNMYDPRKYLGPARDAIKETVIGKMREFGSSGKA 285 A + + EVL +P Y LG RD +KE VI K+R FGS+GKA Sbjct: 238 AFTQGLCEVLTNDPEEYALAVSLGHGRDVMKEKVIEKIRLFGSNGKA 284 Lambda K H 0.314 0.134 0.379 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: 242 Number of extensions: 10 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: 285 Length of database: 287 Length adjustment: 26 Effective length of query: 259 Effective length of database: 261 Effective search space: 67599 Effective search space used: 67599 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: 42 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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