Align 6-P-β-glucosidase 2 (AscB;b2716) (EC 3.2.1.86) (characterized)
to candidate BWI76_RS22295 BWI76_RS22295 6-phospho-beta-glucosidase
Query= CAZy::AAA69226.1 (476 letters) >FitnessBrowser__Koxy:BWI76_RS22295 Length = 474 Score = 878 bits (2269), Expect = 0.0 Identities = 416/473 (87%), Positives = 445/473 (94%) Query: 3 MSVFPESFLWGGALAANQSEGAFREGDKGLTTVDMIPHGEHRMAVKLGLEKRFQLRDDEF 62 M+ FP+ FLWGGALAANQSEGA+ EG KG TTVDMIPHG HR+AVKLG EKRF RDDEF Sbjct: 1 MATFPQGFLWGGALAANQSEGAWLEGGKGPTTVDMIPHGAHRLAVKLGQEKRFAPRDDEF 60 Query: 63 YPSHEATDFYHRYKEDIALMAEMGFKVFRTSIAWSRLFPQGDEITPNQQGIAFYRSVFEE 122 YPSHEA DFYHRYKEDIALMAEMGF VFRTSIAWSRLFP+GDE PN +GIAFYRS+FEE Sbjct: 61 YPSHEAIDFYHRYKEDIALMAEMGFSVFRTSIAWSRLFPKGDEQEPNPEGIAFYRSLFEE 120 Query: 123 CKKYGIEPLVTLCHFDVPMHLVTEYGSWRNRKLVEFFSRYARTCFEAFDGLVKYWLTFNE 182 CKK+ IEPLVTLCHFDVPMHLVTEYGSWRNRK+VEFF+RYARTCFEAFDGLVKYWLTFNE Sbjct: 121 CKKHNIEPLVTLCHFDVPMHLVTEYGSWRNRKMVEFFTRYARTCFEAFDGLVKYWLTFNE 180 Query: 183 INIMLHSPFSGAGLVFEEGENQDQVKYQAAHHQLVASALATKIAHEVNPQNQVGCMLAGG 242 INIMLHSPFSGAGLVFEEGENQ+QVKYQAAHH+LVASALATKIAHEVNPQNQVGCMLAGG Sbjct: 181 INIMLHSPFSGAGLVFEEGENQEQVKYQAAHHELVASALATKIAHEVNPQNQVGCMLAGG 240 Query: 243 NFYPYSCKPEDVWAALEKDRENLFFIDVQARGTYPAYSARVFREKGVTINKAPGDDEILK 302 NFYPYSCKPEDVW ALEKDRENLFFIDVQARG YP ++ARVFREKGVTI K GDDEIL+ Sbjct: 241 NFYPYSCKPEDVWMALEKDRENLFFIDVQARGAYPVWAARVFREKGVTIAKEAGDDEILR 300 Query: 303 NTVDFVSFSYYASRCASAEMNANNSSAANVVKSLRNPYLQVSDWGWGIDPLGLRITMNMM 362 +TVDFVSFSYYASRCASAEMNA N+SAAN+VKSL+NPY++ S+WGWGIDPLGLRITMNMM Sbjct: 301 HTVDFVSFSYYASRCASAEMNAGNTSAANIVKSLKNPYIKASEWGWGIDPLGLRITMNMM 360 Query: 363 YDRYQKPLFLVENGLGAKDEFAANGEINDDYRISYLREHIRAMGEAIADGIPLMGYTTWG 422 YDRYQKPLFLVENGLGA+DE ANGEINDDYRISYLREHI+AMG+AI DGIP+MGYT+WG Sbjct: 361 YDRYQKPLFLVENGLGARDEIDANGEINDDYRISYLREHIQAMGDAIEDGIPVMGYTSWG 420 Query: 423 CIDLVSASTGEMSKRYGFVFVDRDDAGNGTLTRTRKKSFWWYKKVIASNGEDL 475 CIDLVSASTGEMSKRYGFV+VDRDDAG+GTL R RKKSFWWYKKVIASNGEDL Sbjct: 421 CIDLVSASTGEMSKRYGFVYVDRDDAGHGTLARRRKKSFWWYKKVIASNGEDL 473 Lambda K H 0.321 0.136 0.423 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: 918 Number of extensions: 30 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: 476 Length of database: 474 Length adjustment: 33 Effective length of query: 443 Effective length of database: 441 Effective search space: 195363 Effective search space used: 195363 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: 51 (24.3 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