Align 6-deoxy-5-ketofructose 1-phosphate synthase (EC 2.2.1.11) (characterized)
to candidate WP_011305216.1 MBAR_RS01015 aldolase
Query= BRENDA::Q58980 (310 letters) >NCBI__GCF_000195895.1:WP_011305216.1 Length = 307 Score = 404 bits (1039), Expect = e-117 Identities = 195/303 (64%), Positives = 243/303 (80%), Gaps = 4/303 (1%) Query: 9 LKKRDVKVPLTVPEDRKEEYIKNYLELTKRTGNVMLFAGDQKIEHLNDDFFGEGIAKDDA 68 + K DV VPL VP+ +E Y+ NY+E+T+ TG +MLFAGDQK+EHLNDDF+GEG+ +DD Sbjct: 4 INKEDVIVPLDVPKAMRETYVNNYMEMTRGTGRLMLFAGDQKVEHLNDDFYGEGVPEDDG 63 Query: 69 SPEHLFNIASKGKICGFATQLGLIARYGMDYKKIPYIVKINSKTHLVKT--RDPISRALV 126 PEHLF IAS+ KI FATQLGLI+RYGMDY+ +PY+VK+NSKT+LV T DP S Sbjct: 64 DPEHLFRIASQSKIGVFATQLGLISRYGMDYRDVPYLVKVNSKTNLVGTAQSDPFSNLWY 123 Query: 127 HVKDVVDLKENSGLKILGVGYTIYPGSEYEHIMFEEASRVILEAHKHGLIAIIWSYPRGK 186 V VV+ KENSGLKILGVGYTIY GSE+E M +A++VI +AH+HG+++++W YPRG+ Sbjct: 124 DVDQVVEFKENSGLKILGVGYTIYLGSEFEAEMLVQAAQVIYDAHQHGMLSVLWIYPRGE 183 Query: 187 NVKDEKDPHLIAGAAGVAACLGADFVKVNYPKCD--NPAERFKEAVLAAGRTGVLCAGGK 244 VKDEKDPHLIAGA G+ ACLG DFVKVNYPK + AE FKEA+ AAGRT V+CAGG Sbjct: 184 AVKDEKDPHLIAGATGIGACLGTDFVKVNYPKKEGAKSAESFKEAIKAAGRTKVVCAGGS 243 Query: 245 SIEPEKFLKQIWEQINISGARGNATGRNIHQKPLDAAIRMCNAIYAITIEGKSLEEALKI 304 S E FLK++++QI++SGA+GNATGRNIHQ+PLD A+RMCNA+YAIT+E S E+ALKI Sbjct: 244 SDEAGAFLKKLYDQIHVSGAQGNATGRNIHQRPLDEAVRMCNAVYAITVEDASAEDALKI 303 Query: 305 YYG 307 Y G Sbjct: 304 YKG 306 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: 345 Number of extensions: 13 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: 307 Length adjustment: 27 Effective length of query: 283 Effective length of database: 280 Effective search space: 79240 Effective search space used: 79240 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