Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate SMc03983 SMc03983 fructose-bisphosphate aldolase class I protein
Query= BRENDA::Q8L207 (343 letters) >FitnessBrowser__Smeli:SMc03983 Length = 341 Score = 453 bits (1166), Expect = e-132 Identities = 239/341 (70%), Positives = 273/341 (80%), Gaps = 1/341 (0%) Query: 1 MNERLEDIALTLVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAME 60 M+ERLEDIA+ +V G+G+LAADESTATI KRF+SIG+E TE +RR YREML + +AM Sbjct: 1 MSERLEDIAVAMVANGRGLLAADESTATIKKRFDSIGLESTETSRRDYREMLLRSDDAMR 60 Query: 61 SAISGVILFDETLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGL 120 ISGVIL++ETL QKA+ G L D+IR+AG++PGIKVDTGAKP+A FP ETITEGLDGL Sbjct: 61 EYISGVILYEETLFQKAADGTPLADVIRNAGSIPGIKVDTGAKPMAHFPNETITEGLDGL 120 Query: 121 RERLKDYYTLGARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPE 180 RL Y+ GARFAKWR VIAI + LPT GAI NA ALARYAALCQEA +VPIVEPE Sbjct: 121 AARLARYHEAGARFAKWRGVIAI-SDALPTWGAIRANAHALARYAALCQEAKIVPIVEPE 179 Query: 181 VLMDGPSRQHSITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKDARIASVEE 240 VLMDG HSI R EVT+ VL TVF+EL E RV EGMILKP+MVIDGK AR ASV+E Sbjct: 180 VLMDGAPGDHSIERSEEVTEWVLRTVFEELGELRVRLEGMILKPSMVIDGKKARKASVDE 239 Query: 241 VAEKTVHVLKQTVPAAVPGIAFLSGGQTDEEATAHLSAMNALGALPWKLTFSYGRALQAA 300 VAE+T+ VLK+TVPAAVPGIAFLSGGQ+ EEATAHLSAMNA LPWKLTFSYGRALQ Sbjct: 240 VAERTIKVLKRTVPAAVPGIAFLSGGQSTEEATAHLSAMNAAHDLPWKLTFSYGRALQQE 299 Query: 301 ALKAWAGKNENIVVAQKAFCHRARMNHLAALGQWTKDQEKS 341 AL AW GK+EN+ Q+AF HRA+M LAA G WTKD EK+ Sbjct: 300 ALNAWGGKSENVAAGQRAFAHRAKMCSLAAKGSWTKDFEKA 340 Lambda K H 0.319 0.132 0.378 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: 391 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: 343 Length of database: 341 Length adjustment: 29 Effective length of query: 314 Effective length of database: 312 Effective search space: 97968 Effective search space used: 97968 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 (21.8 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