Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate WP_086511855.1 BZY95_RS21080 fructose-bisphosphate aldolase
Query= SwissProt::P0A991 (350 letters) >NCBI__GCF_002151265.1:WP_086511855.1 Length = 350 Score = 520 bits (1338), Expect = e-152 Identities = 253/350 (72%), Positives = 299/350 (85%) Query: 1 MTDIAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTG 60 MTDI QLLG DA+ LL HRC P +QL+LPG D+V RV+ D++R PAV+R++Q +++ G Sbjct: 1 MTDITQLLGDDAEYLLDHRCRGFPREQLHLPGPDFVSRVVADSDRSPAVMRSLQAMFDHG 60 Query: 61 RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVS 120 RLAGTGYLS+LPVDQG+EHSAGASFA NP YFDP NIVELAIE GCN VAST GVL++V+ Sbjct: 61 RLAGTGYLSLLPVDQGIEHSAGASFAPNPRYFDPANIVELAIEGGCNGVASTLGVLSAVA 120 Query: 121 RRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIE 180 RRYAHRIP ++KLNHNETLSYP YDQTL+A VEQA +MG VAVGATIYFGS ESRRQI Sbjct: 121 RRYAHRIPMMLKLNHNETLSYPAMYDQTLFAEVEQAHDMGCVAVGATIYFGSPESRRQIM 180 Query: 181 EISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKM 240 EIS AFERAH+LGM TVLWAYLRN AFK +G DYHV+ADLTGQANHLAAT+ ADIVKQK+ Sbjct: 181 EISEAFERAHQLGMATVLWAYLRNPAFKHEGKDYHVAADLTGQANHLAATLKADIVKQKL 240 Query: 241 AENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLS 300 E NGGY+ I +G+T +VY +LTSE+PIDL RYQ+A CYMGRAGLINSGG + G +DL Sbjct: 241 PETNGGYQDIGFGHTHAKVYGELTSEHPIDLARYQVACCYMGRAGLINSGGGSKGHSDLG 300 Query: 301 DAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA 350 +AVRTAVINKRAGGMGLI GRKAF+K M++GV+L++A+QDVYLD +T+A Sbjct: 301 EAVRTAVINKRAGGMGLISGRKAFQKPMSEGVELLHAIQDVYLDQSVTVA 350 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: 426 Number of extensions: 10 Number of successful extensions: 1 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: 350 Length adjustment: 29 Effective length of query: 321 Effective length of database: 321 Effective search space: 103041 Effective search space used: 103041 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 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