Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_011382666.1 AMB_RS01115 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_000009985.1:WP_011382666.1 Length = 453 Score = 350 bits (898), Expect = e-101 Identities = 190/430 (44%), Positives = 257/430 (59%), Gaps = 14/430 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 F WG +T+AYQIEGA DGRG +IWD F G I DGS+ + ACDHY RY EDIALM+ Sbjct: 21 FFWGASTAAYQIEGAYDTDGRGMTIWDKFTA-DGKIMDGSSAKVACDHYHRYPEDIALMK 79 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 + G AYRFS+AWPRI+P G G IN KGL FYDRLVD++L +GI P LYHWDLP LE Sbjct: 80 AAGFNAYRFSLAWPRIIPAGTGAINAKGLDFYDRLVDKILEAGIKPMACLYHWDLPQPLE 139 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLR-NLE 186 ++GGW+ R+ FAEYA + L DRV + LNEP A +G+ GEHAPG + + Sbjct: 140 DKGGWQGRDIVGPFAEYARIATKRLGDRVKDWYMLNEPNVVAIIGYGIGEHAPGYKLGED 199 Query: 187 AALRAAHHLLLGHGLAVEALRAAGARRV-GIVLNFAPAYGEDPEAVDVA-----DRYHNR 240 L+A HH L G A+ A+RA + V G V+N P +D + + A D NR Sbjct: 200 GILKALHHQNLAQGTALRAIRAEHSDAVLGTVINLQPCRSQDDDPKNRAAAIRWDAVWNR 259 Query: 241 YFLDPILGKGYPESPFRDPPPVPILSRDLELVARPLDFLGVNYYAPVRVAPGTGTLPVRY 300 LD ++ P+ + + D+E + P+D LG+NYY+ + + G P Sbjct: 260 VPLDGVMRGAIPDVLAEKMAHI-VKPGDMETIKFPIDMLGINYYSRMTMKHEEGH-PFDV 317 Query: 301 LPPEGPA---TAMGWEVYPEGLHHLLKRLGREVPWP-LYVTENGAAYPDLWTGEAVVEDP 356 + TAM W V P+GL+ LL+ P +++ ENGAAY D+ T + V D Sbjct: 318 FWGDAHCDRWTAMAWPVQPDGLYDLLREFKELYGNPAVFIAENGAAYDDVVTPDGQVHDA 377 Query: 357 ERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRRIPK 416 ERVA++ HV RA ++G +++GY VWSL+DNFEWA+G ++RFG+ VD+ + +R PK Sbjct: 378 ERVAFIRDHVSEVARAVKDGCNVKGYLVWSLLDNFEWAYGLSKRFGIVRVDYETLKRTPK 437 Query: 417 RSALWYRERI 426 S W+ E I Sbjct: 438 DSYKWFAEVI 447 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: 616 Number of extensions: 32 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: 431 Length of database: 453 Length adjustment: 32 Effective length of query: 399 Effective length of database: 421 Effective search space: 167979 Effective search space used: 167979 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