Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate 3608250 Dshi_1654 Beta-glucosidase (RefSeq)
Query= reanno::Phaeo:GFF770 (444 letters) >FitnessBrowser__Dino:3608250 Length = 435 Score = 657 bits (1696), Expect = 0.0 Identities = 306/434 (70%), Positives = 341/434 (78%), Gaps = 5/434 (1%) Query: 6 RADFPKDFLFGTATSAYQIEGHGFGGAGPTHWDSFAATPGNVVRAEHGQRACDHYHRYAE 65 R +P FLFG ATSAYQIEGHG GGAG THWD F+ATPGNV RAEHG RAC H R E Sbjct: 5 RNTYPDGFLFGVATSAYQIEGHGQGGAGRTHWDDFSATPGNVARAEHGARACGHLDRLEE 64 Query: 66 DLDLAAAAGFDCYRFSTSWARVMPEGRGAPNPEGLDFYDRLTDAILERGLKPCVTLYHWE 125 DLDL A G D YRFSTSWARV+PEGRGAPN EGLDFYDRL D +L RG+KP TLYHWE Sbjct: 65 DLDLIAGLGVDAYRFSTSWARVLPEGRGAPNMEGLDFYDRLVDGLLARGIKPAATLYHWE 124 Query: 126 LPQALADLGGWRNAEIANWFGDYAEVIMGRIGDRMYSAAPINEPWCVGWLSHFLGHHAPG 185 LP ALADLGGWRN +IA+WFGD+ + IM RIGDR++SAAPINEPWCVGWLSHF GHHAPG Sbjct: 125 LPSALADLGGWRNRDIASWFGDFTDTIMDRIGDRVWSAAPINEPWCVGWLSHFQGHHAPG 184 Query: 186 LRDIRATARAMHHVMLAHGTAIQAMRALGMSNLGGVFNLEWATPVDDSEAAQQAAARYDA 245 LRDIRATARAMHH++LAHGTAI MR +GM NLG V N+E+A P+DDS A AA YDA Sbjct: 185 LRDIRATARAMHHILLAHGTAIARMRDMGMRNLGAVVNMEYAQPLDDSPTAMAAAELYDA 244 Query: 246 IYNGFFLGGAFHGRYPDLALEGLEPHLPKGWQDDFATITAPVDWCGLNYYTRKQIAPDAG 305 IYN FFL G FH YP+ L GL PHLP WQDDF TI P+DW GLNYYTRK I P Sbjct: 245 IYNQFFLSGMFHNTYPEPVLAGLAPHLPDRWQDDFDTIATPLDWVGLNYYTRKIIGPGDS 304 Query: 306 PWPQYAEVDGPLPKTQMGWEIYPQGLYDFLTRTARDYTGDLPLIVTENGMANADVVTKGK 365 PWP Y E+DGPLPKTQMGWE++P+GL+ LT +TGDLP+ +TENGMA+A Sbjct: 305 PWPAYREIDGPLPKTQMGWEVFPEGLHALLTMMQARFTGDLPIYITENGMASA-----LP 359 Query: 366 VEDAARITFVDDHLDAVRRAIADGVPVQGYFLWSLLDNYEWALGYEKRFGLVHVDFETLK 425 V DA R+ ++D HL VRRAIADGVPV GYF+WSL+DNYEW+ GYEKRFGLVHVDF+TL Sbjct: 360 VNDADRLAYLDAHLAQVRRAIADGVPVDGYFIWSLMDNYEWSFGYEKRFGLVHVDFDTLV 419 Query: 426 RTPKASYHALRSAL 439 RTPKASY AL SAL Sbjct: 420 RTPKASYRALASAL 433 Lambda K H 0.322 0.138 0.455 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: 37 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: 444 Length of database: 435 Length adjustment: 32 Effective length of query: 412 Effective length of database: 403 Effective search space: 166036 Effective search space used: 166036 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 (21.9 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