Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate GFF770 PGA1_c07840 beta-glucosidase A
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__Phaeo:GFF770 Length = 444 Score = 366 bits (939), Expect = e-106 Identities = 191/422 (45%), Positives = 258/422 (61%), Gaps = 14/422 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 FL+G ATSAYQIEG G GP+ WD+FA PG + G+ ACDHY RY ED+ L Sbjct: 13 FLFGTATSAYQIEGHGF-GGAGPTHWDSFAATPGNVVRAEHGQRACDHYHRYAEDLDLAA 71 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 + G YRFS +W R++PEGRG NP+GL FYDRL D +L G+ P +TLYHW+LP AL Sbjct: 72 AAGFDCYRFSTSWARVMPEGRGAPNPEGLDFYDRLTDAILERGLKPCVTLYHWELPQALA 131 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 + GGWR+ E A F +YAE + + DR+ A +NEPWC +L H+ G HAPGLR++ A Sbjct: 132 DLGGWRNAEIANWFGDYAEVIMGRIGDRMYSAAPINEPWCVGWLSHFLGHHAPGLRDIRA 191 Query: 188 ALRAAHHLLLGHGLAVEALRAAGARRVGIVLNFAPAYG-EDPEAVDVA----DRYHNRYF 242 RA HH++L HG A++A+RA G +G V N A +D EA A D +N +F Sbjct: 192 TARAMHHVMLAHGTAIQAMRALGMSNLGGVFNLEWATPVDDSEAAQQAAARYDAIYNGFF 251 Query: 243 LDPILGKGYPESPFR--DPPPVPILSRDLELVARPLDFLGVNYYAPVRVAPGTGTLPVRY 300 L YP+ +P D + P+D+ G+NYY ++AP G P +Y Sbjct: 252 LGGAFHGRYPDLALEGLEPHLPKGWQDDFATITAPVDWCGLNYYTRKQIAPDAGPWP-QY 310 Query: 301 LPPEG--PATAMGWEVYPEGLHHLLKRLGREV--PWPLYVTENGAAYPDLWTGEAVVEDP 356 +G P T MGWE+YP+GL+ L R R+ PL VTENG A D+ T + VED Sbjct: 311 AEVDGPLPKTQMGWEIYPQGLYDFLTRTARDYTGDLPLIVTENGMANADVVT-KGKVEDA 369 Query: 357 ERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRRIPK 416 R+ +++ H++A RA +GV ++GYF+WSL+DN+EWA GY +RFGL +VDF + +R PK Sbjct: 370 ARITFVDDHLDAVRRAIADGVPVQGYFLWSLLDNYEWALGYEKRFGLVHVDFETLKRTPK 429 Query: 417 RS 418 S Sbjct: 430 AS 431 Lambda K H 0.322 0.140 0.453 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: 632 Number of extensions: 40 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: 431 Length of database: 444 Length adjustment: 32 Effective length of query: 399 Effective length of database: 412 Effective search space: 164388 Effective search space used: 164388 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