Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate AZOBR_RS26030 AZOBR_RS26030 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__azobra:AZOBR_RS26030 Length = 444 Score = 355 bits (911), Expect = e-102 Identities = 204/425 (48%), Positives = 252/425 (59%), Gaps = 20/425 (4%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 FLWG +T+AYQIEGA EDGRGP +WD F G I+DGS+ ACDHY R+ ED ALM+ Sbjct: 10 FLWGASTAAYQIEGAIHEDGRGPCVWDTFTEA-GRIQDGSSAAVACDHYHRWAEDTALMK 68 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 G AYRFS+AWPRILP G G +N GL FYDRLVD LLA GI P LYHWDLP LE Sbjct: 69 DAGFNAYRFSIAWPRILPSGTGAVNAAGLDFYDRLVDGLLADGIRPMACLYHWDLPQPLE 128 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 +RGGW+ RE FA+YA VA LADRV + LNEP A G+ TGEHAPG + E Sbjct: 129 DRGGWQGREVVGPFADYARIVAARLADRVKDWMMLNEPNVVATHGYGTGEHAPGHKLGET 188 Query: 188 A-LRAAHHLLLGHGLAVEALRAA-GARRVGIVLNFAPAYGEDPEAVDVA-----DRYHNR 240 LRA HH L G A+ AL A +G V+N P E DVA D NR Sbjct: 189 GILRALHHQNLAQGAALRALSAEHSGLTLGTVINLQPCRAESDRPQDVAAAARWDAVWNR 248 Query: 241 YFLDPILGKGYPESPFRDPPPVPILSRDLELVARPLDFLGVNYYAPVRVAPGTG-TLPVR 299 LD ++ PE + +L D E + P+D LG+NYY+ + + TG V Sbjct: 249 VALDGVMRGKIPEL-MAERMKDFVLPGDEEAIRFPIDLLGINYYSRMTMKHETGHPFDVW 307 Query: 300 YLPPEGPA-----TAMGWEVYPEGLHHLLKRLGREVPWP-LYVTENGAAYPDLWTGEAVV 353 + G A TAM W V P+GL+ LL R+ P ++V ENGAAY D+ T + V Sbjct: 308 W----GDAHCDRWTAMAWPVQPDGLYDLLMEFRRDYGNPAVFVAENGAAYDDVVTPDGQV 363 Query: 354 EDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRR 413 D ERVA+L HV + RA +G +++GY WSL+DNFEWAFG ++RFG+ VD+ + R Sbjct: 364 HDAERVAFLRDHVASVGRALADGCNVKGYLCWSLLDNFEWAFGLSKRFGIVRVDYDTLVR 423 Query: 414 IPKRS 418 PK S Sbjct: 424 TPKDS 428 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: 597 Number of extensions: 27 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: 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