Align 6-deoxy-5-ketofructose 1-phosphate synthase (EC 2.2.1.11) (characterized)
to candidate WP_014450335.1 LFE_RS11210 aldolase
Query= BRENDA::Q58980 (310 letters) >NCBI__GCF_000284315.1:WP_014450335.1 Length = 305 Score = 313 bits (802), Expect = 3e-90 Identities = 154/299 (51%), Positives = 207/299 (69%), Gaps = 8/299 (2%) Query: 14 VKVPLTVPEDR-KEEYIKNYLELTKRTGNVMLFAGDQKIEHLNDDFFGEGIAKDDASPEH 72 + +PL VP + Y +NY +TK TG + L AGDQK+EHLNDDF G +A DD+SPEH Sbjct: 4 LSIPLDVPRGAARRRYEENYRLMTKETGRLFLMAGDQKVEHLNDDFVGAAVAADDSSPEH 63 Query: 73 LFNIASKGKICGFATQLGLIARYGMDYKKIPYIVKINSKTHLVK--TRDPISRALVHVKD 130 LF IA + FA Q+GLIARYGMDY+ IPY++K+NSKTHLVK +DP+S Sbjct: 64 LFKIAQSAPVGCFAGQMGLIARYGMDYRDIPYLIKLNSKTHLVKKDQKDPVSLQWQETSQ 123 Query: 131 VVDLKENSGLKILGVGYTIYPGSEYEHIMFEEASRVILEAHKHGLIAIIWSYPRGKNVKD 190 V ++G++++ +GYT+YPGSEYE M EASR+I EAH+ GL+ ++W YPRG++V + Sbjct: 124 VEQFVRHAGVRVVALGYTLYPGSEYEPAMLSEASRLIFEAHQMGLVFVLWVYPRGRSVGN 183 Query: 191 EKDPHLIAGAAGVAACLGADFVKVNYPKCDNPAER----FKEAVLAAGRTGVLCAGGKSI 246 E D HLIAG AGV ACLGADF+K+N P D + +EAV AAGR+ V+CAGG Sbjct: 184 ENDAHLIAGGAGVGACLGADFIKIN-PPVDPSGQMDGMLLREAVAAAGRSQVVCAGGAET 242 Query: 247 EPEKFLKQIWEQINISGARGNATGRNIHQKPLDAAIRMCNAIYAITIEGKSLEEALKIY 305 FLK++++QI++ G G ATGRN+HQ+ + AIR C AI+AI + +S+EEAL +Y Sbjct: 243 TVPSFLKRLYDQIHLGGTSGCATGRNVHQRSFEEAIRFCRAIHAIAVLDQSVEEALALY 301 Lambda K H 0.319 0.139 0.408 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: 304 Number of extensions: 15 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: 310 Length of database: 305 Length adjustment: 27 Effective length of query: 283 Effective length of database: 278 Effective search space: 78674 Effective search space used: 78674 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: 48 (23.1 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