Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate 3608250 Dshi_1654 Beta-glucosidase (RefSeq)
Query= CAZy::AAK78365.1 (469 letters) >FitnessBrowser__Dino:3608250 Length = 435 Score = 235 bits (599), Expect = 3e-66 Identities = 142/454 (31%), Positives = 229/454 (50%), Gaps = 36/454 (7%) Query: 3 FPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKEDV 62 +P F G A+++YQ+EG + G G ++WD F+ PG +G A H R +ED+ Sbjct: 8 YPDGFLFGVATSAYQIEGH-GQGGAGRTHWDDFSATPGNVARAEHGARACGHLDRLEEDL 66 Query: 63 KLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDMP 122 L+A +G+D+YRFS SW R++P+G G N +G++FY+ L+D L GI P TLYHW++P Sbjct: 67 DLIAGLGVDAYRFSTSWARVLPEGRGAPNMEGLDFYDRLVDGLLARGIKPAATLYHWELP 126 Query: 123 EVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGIT 182 L GGW N+ F + + GDRV NE + G H PG+ Sbjct: 127 SALADLGGWRNRDIASWFGDFTDTIMDRIGDRVWSAAPINEPWCVGWLSHFQGHHAPGLR 186 Query: 183 GDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHANQ 242 D++ +A H++ AH ++ + + +G A +DD AAA + Sbjct: 187 -DIRATARAMHHILLAHGTAIARMRDMGM-RNLGAVVNMEYAQPLDDSPTAMAAAELYDA 244 Query: 243 YEITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQRV 302 ++ + YPE V+ + LPD ++ +T+ A PL D++GLNYY + + Sbjct: 245 IYNQFFLSGMFHNTYPEPVLAGLAPH--LPDRWQDDFDTI--ATPL-DWVGLNYYTRKII 299 Query: 303 IKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEKLK 362 PG++ + YR + T+ GWE+ PE L L ++ Sbjct: 300 -------------------GPGDSPWPA-YREID-GPLPKTQMGWEVFPEGLHALLTMMQ 338 Query: 363 EQY-GDIKIYITENGLGDQDPIIEDEILDMPRIKFIEAHLRAIKEAISRGINLKGYYAWS 421 ++ GD+ IYITENG+ P + D R+ +++AHL ++ AI+ G+ + GY+ WS Sbjct: 339 ARFTGDLPIYITENGMASALP-----VNDADRLAYLDAHLAQVRRAIADGVPVDGYFIWS 393 Query: 422 VIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSF 455 ++D W GY+K++G ++VD L R K S+ Sbjct: 394 LMDNYEWSFGYEKRFGLVHVDF-DTLVRTPKASY 426 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: 628 Number of extensions: 24 Number of successful extensions: 6 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: 435 Length adjustment: 33 Effective length of query: 436 Effective length of database: 402 Effective search space: 175272 Effective search space used: 175272 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