Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; FBPA; EC 4.1.2.13 (characterized)
to candidate WP_084057834.1 B9A12_RS10395 hypothetical protein
Query= SwissProt::P58315 (263 letters) >NCBI__GCF_900176285.1:WP_084057834.1 Length = 260 Score = 122 bits (307), Expect = 6e-33 Identities = 85/256 (33%), Positives = 127/256 (49%), Gaps = 11/256 (4%) Query: 9 LRIFARRGKS--IILAYDHGIEHGPADFMDNPDSADPEYILRLARDAGFDGVVFQRGIAE 66 LR F RG + ++ DHG+ GP + + ++ +G DGVV +G+ Sbjct: 8 LRRFFWRGDNRLVLFPLDHGVSCGPVSGL-----VELSRVVSYGVRSGADGVVLHKGMLA 62 Query: 67 KY--YDGSVP-LILKLNGKTTLYNGEPVSVANCSVEEAVSLGASAVGYTIYPGSGFEWKM 123 +G +P + L L+ T L V SV EA+ GA V + G E +M Sbjct: 63 CLGEVEGRLPGIFLHLSASTQLGPSFHGKVLVGSVNEALQRGADGVSVHVNLGDDAEPEM 122 Query: 124 FEELARIKRDAVKFDLPLVVWSYPRGGKVVNETAPEIVAYAARIALELGADAMKIKYTGD 183 +L ++ ++ LPL+V Y RG E +A+AAR+A ELGAD +KI D Sbjct: 123 LRDLGKVGEACFRWGLPLLVMIYVRGAHAPKPVTDEAIAHAARVAGELGADVIKIPAPKD 182 Query: 184 PKTFSWAVKVAGKVPVLMSGGPKTKTEEDFLKQVEGVLEAGALGIAVGRNVWQRRDALKF 243 P+ + VPV+M+GG K + E FL++++ L AG G+AVGRNV+Q RD F Sbjct: 183 PEVMDRIARCV-PVPVVMAGGAKERDEAAFLERIQAGLRAGLAGVAVGRNVFQHRDPEGF 241 Query: 244 ARALAELVYGGKKLAE 259 R + LV+G + E Sbjct: 242 LRTIVGLVHGERAARE 257 Lambda K H 0.318 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: 206 Number of extensions: 13 Number of successful extensions: 2 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: 263 Length of database: 260 Length adjustment: 25 Effective length of query: 238 Effective length of database: 235 Effective search space: 55930 Effective search space used: 55930 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 (21.7 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