Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate BWI76_RS00545 BWI76_RS00545 putative class-II ketose-bisphosphate aldolase
Query= SwissProt::P13243 (285 letters) >FitnessBrowser__Koxy:BWI76_RS00545 Length = 280 Score = 191 bits (485), Expect = 2e-53 Identities = 104/282 (36%), Positives = 163/282 (57%), Gaps = 6/282 (2%) Query: 1 MPLVSMTEMLNTAKEKGY-AVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGG 59 M L + +L A+E+ + A+G FNL+ +E A +AA++ SP+++ +S G Y+G Sbjct: 1 MSLYNFNAILKIAQERNFKAIGSFNLHCIEMLPAFFKAAQQSHSPLMIQISTGTAEYLG- 59 Query: 60 FKTVVAMVKALMEEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVAT 119 ++ +V V++L E V P +HLDH S + A+ AGFTSVM D SH EEN+ Sbjct: 60 YRLLVDAVRSLAESENV--PTCLHLDHCSDISAIETAMDAGFTSVMYDGSHLDLEENIGN 117 Query: 120 TAKVVELAHFHGVSVEAELGTVGGQEDD--VIAEGVIYADPKECQELVERTGIDCLAPAL 177 T VVE+A ++VE ELG +GG ED V AE + + ++ + VE T +D LA ++ Sbjct: 118 TRIVVEMARPRNITVEGELGAIGGSEDGKAVAAEDICFTTVEDAKRFVEETRVDMLAVSV 177 Query: 178 GSVHGPYKGEPNLGFKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGTAKINVNTENQ 237 G+VHG Y G+ + + ++EI +TG+PLVLHGGTG+ D++++++ G K+NV TE Sbjct: 178 GTVHGLYTGKAQIQHQRLKEISAATGVPLVLHGGTGVSDEDMRQAVTEGINKVNVGTEMN 237 Query: 238 ISSAKAVRETLAAKPDEYDPRKYLGPAREAIKETVIGKMREF 279 + + T RK+L PA A+ +I K+ F Sbjct: 238 VQWVDRCKTTFEKGKVNDSVRKFLIPANNAVTHVLIEKIALF 279 Lambda K H 0.313 0.131 0.367 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: 223 Number of extensions: 9 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: 280 Length adjustment: 26 Effective length of query: 259 Effective length of database: 254 Effective search space: 65786 Effective search space used: 65786 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 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 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