Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_037573293.1 BS73_RS16635 class II fructose-bisphosphate aldolase family protein
Query= BRENDA::I3EBM6 (285 letters) >NCBI__GCF_000744815.1:WP_037573293.1 Length = 282 Score = 181 bits (458), Expect = 2e-50 Identities = 111/276 (40%), Positives = 152/276 (55%), Gaps = 7/276 (2%) Query: 1 MPLVSMTEMLNKAKAEGYAVGQFNLNNLEFTQAILLAAEEEKSPVILGVSEGAGRYMGGF 60 M LV ++++KA A G A FN+ LE +AI A + VIL +SE A R+ GG Sbjct: 1 MSLVPTRDLVSKAAAAGRAAAAFNVITLEHAEAITAGASAAGTAVILQISENAVRFHGG- 59 Query: 61 KTVVNMVKGLMEDYK-ITVPVAIHLDHGSSFEKCKEVIDAGFTSVMIDASHHPFEENVEV 119 V + + E + V VA+HLDH + +AGF+S M DA P+ EN+ Sbjct: 60 -RVSPIARAAAEVARGCDVDVALHLDHVTDLRLLHTAAEAGFSSAMFDAGAQPYAENLAA 118 Query: 120 TKKVVEYAHARGVSVEAELGTVGGQED---DVIADGVIYADPKECEELVKRTGIDCLAPA 176 T+ ++AH GV +EAELG VGG+ D A GV DP+E V TG+D LA A Sbjct: 119 TRAAAQWAHGAGVWLEAELGYVGGKPDAPASAHAAGV-RTDPREAAAYVADTGVDALAVA 177 Query: 177 LGSVHGPYKGEPNLGFKEMEEIGRITGVPLVLHGGTGIPTKDIQRAISLGTAKINVNTEN 236 +GS H + L + + + VPLVLHG +G+ +++RA+ G AK+NV T Sbjct: 178 VGSSHAMTERSAALDHELIGRLRDAVPVPLVLHGSSGVGDDELRRAVRAGIAKVNVGTAL 237 Query: 237 QIASAKKVREVLAENPNMYDPRKYLGPARDAIKETV 272 IA + VRE LAE P++ DPR YL P RDA+ ETV Sbjct: 238 NIAFTRAVRETLAEKPDLTDPRGYLAPGRDAMAETV 273 Lambda K H 0.314 0.134 0.379 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: 208 Number of extensions: 7 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: 285 Length of database: 282 Length adjustment: 26 Effective length of query: 259 Effective length of database: 256 Effective search space: 66304 Effective search space used: 66304 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: 42 (21.9 bits) S2: 47 (22.7 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