Align 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate BWI76_RS07295 BWI76_RS07295 6-phospho-beta-glucosidase
Query= CAZy::BAD77499.1 (478 letters) >FitnessBrowser__Koxy:BWI76_RS07295 Length = 474 Score = 435 bits (1118), Expect = e-126 Identities = 224/475 (47%), Positives = 303/475 (63%), Gaps = 24/475 (5%) Query: 9 FPPGFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYKEDV 68 FP GFLWGA+++AYQVEGAWNEDGKG SV D+ + PG + +A DHYHR +EDV Sbjct: 9 FPDGFLWGASTSAYQVEGAWNEDGKGPSVVDMLSHPPGTA----DFRIASDHYHRVEEDV 64 Query: 69 ALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRTHGIEPIVTLYHWDVP 128 ALMA+MGLKAYRFSV+WSRV PDG+G VN GL FY RLI+ L HGI PIVTLYH+D+P Sbjct: 65 ALMAQMGLKAYRFSVAWSRVIPDGDGPVNPTGLAFYHRLIDALTRHGITPIVTLYHFDLP 124 Query: 129 QALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISLGYRLGLHPPGV 188 AL + G W +R+ + F RYA LF F +V W+T+NEQN I LHP + Sbjct: 125 WAL-ELKGGWLNRKTGEAFVRYARLLFSEFAAKVPLWLTINEQNTMI-------LHPGAI 176 Query: 189 --------KDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPENV 240 D K +Y+ NH LA A++ P +IGP+ + MY +PE+ Sbjct: 177 GVPADRELPDKKALYQQNHHMMLAQAQIFALCHREFPGLRIGPAINTTSMYAESCKPEDA 236 Query: 241 LAFENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQEAKPDFMGVNY 300 +A N E + ++DV A G Y AW Y++ +GL P + P D +LQ+ +PDF+ +NY Sbjct: 237 IAAHNWETLRCWSFLDVAAHGRYNALAWAYMQDRGLAPELQPEDALILQQGRPDFIAINY 296 Query: 301 YQTTTVEHNPPDGVSEGVMNTTGKKGTSTSSGIPGLFKTVRNPYVDTTNWDWAIDPVGLR 360 Y T T+ + DG V G + G G+++ NP+V T + W +DPVGLR Sbjct: 297 YSTATIAASRGDGGD--VAPRAGDQ--QIMLGEEGVYRPAENPWVGKTPYGWVVDPVGLR 352 Query: 361 IGLRRIANRYRLPILITENGLGEFDTLEPDDIVNDDYRIDYLRRHIQEIQRAITDGVDVL 420 + LR++ RY LPILI+ENG+G D L PD VNDDYRI +L+ HI++++ AI DGV+++ Sbjct: 353 LTLRKVCERYGLPILISENGMGAPDKLAPDGTVNDDYRIAFLQAHIEQMRLAIADGVELM 412 Query: 421 GYCVWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIATNG 475 GYC W+ D++S GY KRYGF+YV+R ++ K L+RI+K+SF+WY+ VIA NG Sbjct: 413 GYCPWAAIDVVSTHQGYAKRYGFIYVDRGEDDLKSLQRIRKRSFWWYKDVIAQNG 467 Lambda K H 0.320 0.139 0.448 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: 861 Number of extensions: 42 Number of successful extensions: 5 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: 478 Length of database: 474 Length adjustment: 33 Effective length of query: 445 Effective length of database: 441 Effective search space: 196245 Effective search space used: 196245 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