Align 6-deoxy-5-ketofructose 1-phosphate synthase (EC 2.2.1.11) (characterized)
to candidate WP_067073672.1 MCUHO_RS04020 aldolase
Query= BRENDA::Q58980 (310 letters) >NCBI__GCF_001602375.1:WP_067073672.1 Length = 306 Score = 373 bits (957), Expect = e-108 Identities = 181/301 (60%), Positives = 233/301 (77%), Gaps = 4/301 (1%) Query: 13 DVKVPLTVPEDRKEEYIKNYLELTKRTGNVMLFAGDQKIEHLNDDFFGEGIAKDDASPEH 72 D+++PL VP + +E Y +NY ++T TG +MLFAGDQK+EHLNDDF+GEGI DDA PEH Sbjct: 6 DIRIPLDVPSEEQERYRENYRKITHGTGRLMLFAGDQKVEHLNDDFYGEGIHPDDADPEH 65 Query: 73 LFNIASKGKICGFATQLGLIARYGMDYKKIPYIVKINSKTHLVKT--RDPISRALVHVKD 130 LF IA + +I FATQLG+IARYG DY+ +PY+VK+NSKTHLVKT RDP+S L V+ Sbjct: 66 LFRIADRARIGVFATQLGMIARYGEDYRDVPYLVKLNSKTHLVKTAQRDPLSSELHLVRQ 125 Query: 131 VVDLKENSGLKILGVGYTIYPGSEYEHIMFEEASRVILEAHKHGLIAIIWSYPRGKNVKD 190 VVDL++ +GL ILGVGYTIY GSEYE +M +A++++ AH +GLI ++W YPRGK VKD Sbjct: 126 VVDLRDRTGLAILGVGYTIYLGSEYEPMMLFQAAQIVNNAHANGLITVLWMYPRGKAVKD 185 Query: 191 EKDPHLIAGAAGVAACLGADFVKVNYPKCDN--PAERFKEAVLAAGRTGVLCAGGKSIEP 248 E+DPHLIAGAAGVAA LG+DFVKVN PK + A +EAV A GRTGV+CAGG + Sbjct: 186 ERDPHLIAGAAGVAATLGSDFVKVNPPKAGDRIDAALLREAVAAGGRTGVVCAGGSHADA 245 Query: 249 EKFLKQIWEQINISGARGNATGRNIHQKPLDAAIRMCNAIYAITIEGKSLEEALKIYYGD 308 +FL+Q+ +QI++ G GNATGRNIHQ+PLD A+R CNAI AIT++ ++EA+ IY G Sbjct: 246 PEFLQQLHDQIHVGGTLGNATGRNIHQRPLDEAVRFCNAISAITLDDAGVDEAVGIYEGG 305 Query: 309 R 309 + Sbjct: 306 K 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: 336 Number of extensions: 14 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: 306 Length adjustment: 27 Effective length of query: 283 Effective length of database: 279 Effective search space: 78957 Effective search space used: 78957 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 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