Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate Ga0059261_0725 Ga0059261_0725 Fructose-1,6-bisphosphate aldolase
Query= curated2:B2RLG9 (293 letters) >FitnessBrowser__Korea:Ga0059261_0725 Length = 301 Score = 313 bits (803), Expect = 2e-90 Identities = 163/286 (56%), Positives = 213/286 (74%), Gaps = 3/286 (1%) Query: 8 QMRQAPGFVGALDQSGGSTPKALKAYGIQPDAYQSEEEMFDLIHQMRTRMITSPAFATGK 67 ++ + GF+ ALDQSGGSTPKALK YGI+ DAY +EEMFDLIH MR+R+ITSP+F K Sbjct: 9 KIAEGNGFIAALDQSGGSTPKALKGYGIEEDAYSGDEEMFDLIHAMRSRIITSPSFNGDK 68 Query: 68 IIGVILFERTMRGKIEGMPTADFLWEKRHIVPFLKVDKGLQDEANGVQLMKPFPELGKLC 127 +IG ILFERTM G+++G PT L E R +VPF+K+DKGL+ E NGVQLMKP PEL L Sbjct: 69 VIGAILFERTMDGQVDGEPTPQALIE-RGVVPFIKIDKGLEAEENGVQLMKPMPELDALL 127 Query: 128 EEAVGYHVFGTKMRSVIKQANEQGIRDIVEQQFQWGKEILSHGLVPILEPEVDIHCPEKA 187 A G VFGTK RSV+ AN QGI IV QQF+ G+++L+ GL+PILEPEV+I PE+A Sbjct: 128 ARAKGLGVFGTKERSVVNLANAQGIAAIVAQQFEVGRQVLAAGLMPILEPEVNIKSPERA 187 Query: 188 KAEEILKRELLAQLDKMT--EPVMLKITIPTVDNFYKEIIEHPMMLRVVALSGGYSREQA 245 +A+ IL+ E+L LD MT + VMLK++IP + +++HP +LRVVALSGG+ R +A Sbjct: 188 QADAILRDEILKHLDAMTGDDKVMLKLSIPAQPGLFDALVDHPRVLRVVALSGGFKRPEA 247 Query: 246 NELLSRNHGVIASFSRALVEGLSVQQTDAEFNAMLEASIEDVYQAS 291 L++N G+IASFSRAL+E L TDAEF+A L A+I++++ AS Sbjct: 248 CAELAKNRGMIASFSRALLEDLRHGMTDAEFDASLGAAIDEIHAAS 293 Lambda K H 0.318 0.135 0.384 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: 280 Number of extensions: 11 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: 293 Length of database: 301 Length adjustment: 26 Effective length of query: 267 Effective length of database: 275 Effective search space: 73425 Effective search space used: 73425 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 17 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