Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate 350634 BT1106 fructose-bisphosphate aldolase class I (NCBI ptt file)
Query= SwissProt::P0A991 (350 letters) >FitnessBrowser__Btheta:350634 Length = 349 Score = 488 bits (1256), Expect = e-142 Identities = 232/347 (66%), Positives = 288/347 (82%) Query: 4 IAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTGRLA 63 I LLG A+ L H C TI +++PG D +D+V ++++R L ++Q LY GRLA Sbjct: 3 IVDLLGGKAEYYLNHTCKTIDKQLIHIPGPDMIDKVWMNSDRNIRTLESLQALYGHGRLA 62 Query: 64 GTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVSRRY 123 TGY+SILPVDQG+EHSAGASFA NPLYFDP+NI++LAIE GCN VAST+GVL +V+R+Y Sbjct: 63 NTGYVSILPVDQGIEHSAGASFAPNPLYFDPENIIKLAIEGGCNAVASTFGVLGAVARKY 122 Query: 124 AHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIEEIS 183 AH+IPF+VKLNHNE L+YPN+YDQ ++ +V++A+NMGAVAVGATIYFGSE+SRRQI E+S Sbjct: 123 AHKIPFIVKLNHNELLTYPNSYDQVMFGTVKEAWNMGAVAVGATIYFGSEQSRRQIVEVS 182 Query: 184 AAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKMAEN 243 AFE AHELGM T+LW YLRNS+FKKDG DYH +ADLTGQANH+ TI ADIVKQK+ N Sbjct: 183 QAFEYAHELGMATILWCYLRNSSFKKDGTDYHAAADLTGQANHIGVTIKADIVKQKLPSN 242 Query: 244 NGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLSDAV 303 NGG+KAI +G T++ +YS+LT+++PIDL RYQ+AN YMGR GLINSGG + GE+DL DAV Sbjct: 243 NGGFKAIGFGKTNECMYSELTTDHPIDLCRYQVANGYMGRVGLINSGGESHGESDLHDAV 302 Query: 304 RTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA 350 TAV+NKRAGGMGLI GRKAF+K M DG++L+N +QDVYLDS ITIA Sbjct: 303 VTAVVNKRAGGMGLISGRKAFQKPMKDGIQLLNTIQDVYLDSSITIA 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: 447 Number of extensions: 13 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: 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 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