Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate GFF770 PGA1_c07840 beta-glucosidase A
Query= CAZy::AAK78365.1 (469 letters) >FitnessBrowser__Phaeo:GFF770 Length = 444 Score = 262 bits (670), Expect = 1e-74 Identities = 155/468 (33%), Positives = 242/468 (51%), Gaps = 35/468 (7%) Query: 3 FPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKEDV 62 FPKDF G A+++YQ+EG G G ++WD F PG +G A DHYHRY ED+ Sbjct: 9 FPKDFLFGTATSAYQIEGH-GFGGAGPTHWDSFAATPGNVVRAEHGQRACDHYHRYAEDL 67 Query: 63 KLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDMP 122 L A G D YRFS SW R++P+G G N +G++FY+ L D L+ G+ P VTLYHW++P Sbjct: 68 DLAAAAGFDCYRFSTSWARVMPEGRGAPNPEGLDFYDRLTDAILERGLKPCVTLYHWELP 127 Query: 123 EVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGIT 182 + L GGW N + + F YA+ GDR+ NE + G H PG+ Sbjct: 128 QALADLGGWRNAEIANWFGDYAEVIMGRIGDRMYSAAPINEPWCVGWLSHFLGHHAPGLR 187 Query: 183 GDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSP--AFSVDDKEENKAAAYHA 240 D++ +A H+V AH ++ + ++ G + VF+ A VDD E + AA Sbjct: 188 -DIRATARAMHHVMLAHGTAI---QAMRALGMSNLGGVFNLEWATPVDDSEAAQQAAARY 243 Query: 241 NQYEITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQ 300 + ++ G+YP+ ++ +E LP ++ T+ AP+ D+ GLNYY + Sbjct: 244 DAIYNGFFLGGAFHGRYPDLALEGLEPH--LPKGWQDDFATI--TAPV-DWCGLNYYTRK 298 Query: 301 RVIKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEK 360 ++ D G P A DG T+ GWEI P+ L L + Sbjct: 299 QIAP--DAGP-----------WPQYAEVDG--------PLPKTQMGWEIYPQGLYDFLTR 337 Query: 361 LKEQY-GDIKIYITENGLGDQDPIIEDEILDMPRIKFIEAHLRAIKEAISRGINLKGYYA 419 Y GD+ + +TENG+ + D + + ++ D RI F++ HL A++ AI+ G+ ++GY+ Sbjct: 338 TARDYTGDLPLIVTENGMANADVVTKGKVEDAARITFVDDHLDAVRRAIADGVPVQGYFL 397 Query: 420 WSVIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVIEERGK 467 WS++D W GY+K++G ++VD + L R K S++ + + K Sbjct: 398 WSLLDNYEWALGYEKRFGLVHVDFE-TLKRTPKASYHALRSALTGASK 444 Lambda K H 0.318 0.138 0.433 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: 638 Number of extensions: 29 Number of successful extensions: 4 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: 469 Length of database: 444 Length adjustment: 33 Effective length of query: 436 Effective length of database: 411 Effective search space: 179196 Effective search space used: 179196 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: 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