Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate WP_064573648.1 M988_RS08370 class I fructose-bisphosphate aldolase
Query= SwissProt::P0A991 (350 letters) >NCBI__GCF_001655005.1:WP_064573648.1 Length = 349 Score = 619 bits (1595), Expect = 0.0 Identities = 309/350 (88%), Positives = 329/350 (94%), Gaps = 1/350 (0%) Query: 1 MTDIAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTG 60 MTDIA+LLGK+A++LL+HRC TIPSDQLYLPG D+VDRVMIDNNR P VL MQ LYNTG Sbjct: 1 MTDIAKLLGKEANSLLEHRCTTIPSDQLYLPGADFVDRVMIDNNRSPRVLAAMQNLYNTG 60 Query: 61 RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVS 120 RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAI+AGCNCVASTYGVLA+VS Sbjct: 61 RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIQAGCNCVASTYGVLAAVS 120 Query: 121 RRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIE 180 RRYAH+IPFLVKLNHNETLSYP YDQTLYASVEQAFN+GA AVGATIYFGS ESRRQIE Sbjct: 121 RRYAHKIPFLVKLNHNETLSYPTQYDQTLYASVEQAFNLGAQAVGATIYFGSAESRRQIE 180 Query: 181 EISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKM 240 EISAAFERAHELGMVTVLWAYLRN AF KDGVDYH SADLTGQANHLAATIGADIVKQKM Sbjct: 181 EISAAFERAHELGMVTVLWAYLRNPAFVKDGVDYHSSADLTGQANHLAATIGADIVKQKM 240 Query: 241 AENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLS 300 AENNGGYKA+ +GYTD+RVY+KLTS++PIDLVRYQLANCYMGRAGLINSGGAA GE D+ Sbjct: 241 AENNGGYKAVKFGYTDERVYTKLTSDHPIDLVRYQLANCYMGRAGLINSGGAA-GENDIQ 299 Query: 301 DAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA 350 ++VRTAVINKRAGGMGLILGRKAFKKSM DGV LINAVQDVYLD K+TIA Sbjct: 300 ESVRTAVINKRAGGMGLILGRKAFKKSMKDGVALINAVQDVYLDKKVTIA 349 Lambda K H 0.318 0.134 0.386 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: 506 Number of extensions: 11 Number of successful extensions: 2 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: 350 Length of database: 349 Length adjustment: 29 Effective length of query: 321 Effective length of database: 320 Effective search space: 102720 Effective search space used: 102720 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: 49 (23.5 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