Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate CCNA_02220 CCNA_02220 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__Caulo:CCNA_02220 Length = 482 Score = 352 bits (902), Expect = e-101 Identities = 192/436 (44%), Positives = 256/436 (58%), Gaps = 17/436 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 F+WGVAT+A+Q EG+ DGRGPSIWD F R PG +++G T A D YRRY++D+ L+ Sbjct: 45 FVWGVATAAFQTEGSQTADGRGPSIWDVFERVPGHVKNGDTAADATDSYRRYQDDVDLIA 104 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 + AYRFS++W RILP G G +N GL Y RLVD LLA GITP+ TL+HWDLP L+ Sbjct: 105 GASLSAYRFSMSWSRILPTGAGAVNAAGLDHYSRLVDALLAKGITPYATLFHWDLPQGLQ 164 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 ++GGW +R+TA A+YA AV L DR+ + LNE GH G+HAPGL++ Sbjct: 165 DKGGWANRDTAQRLADYARAVVERLGDRLKNYIILNEAAVHTVFGHVLGDHAPGLKDAAL 224 Query: 188 ALRAAHHLLLGHGLAVEALRAAGA-RRVGIVLNFAPAYGE-------DPEAVDVADRYHN 239 HH+ LG GLA++ALRAA + VG + P + A D D N Sbjct: 225 LGPVTHHMNLGQGLAIQALRAARSDLSVGTTMALQPCRPAGGPLAFWNRLASDGLDEIWN 284 Query: 240 RYFLDPILGKGYPESPFRDPPPVPILSRDLELVARPLDFLGVNYYAPVRV---APGTGTL 296 +LDP+ YP++ +P + DL+ +P+DFLGVNYYAP V + Sbjct: 285 LAWLDPLFKGTYPKA-MEEPLKGVVRDGDLKTTRQPVDFLGVNYYAPAYVRLDLSAPSKI 343 Query: 297 PVRYLPPEGPATAMGWEVYPEGLHHLLKRLGREVPWP-LYVTENGAAYPDLWTGEAVVED 355 P A G + P GL +L R+ RE P + VTENG + P +G A+++D Sbjct: 344 AAAAAPNSAEQDAFGRHIDPSGLFEVLDRVRREYGAPKMLVTENGCSDP-FSSGPAILDD 402 Query: 356 PERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRRIP 415 R+ YL H+EA L ARE G D+RGYF W+L+DNFEW GYT +FG+ ++ S RRIP Sbjct: 403 TFRIKYLRRHLEAVLAAREAGCDVRGYFEWTLIDNFEWDLGYTSKFGITTMEAASGRRIP 462 Query: 416 KRSALWYRERIARAQT 431 K S W++ A AQT Sbjct: 463 KASYGWFK---ALAQT 475 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: 649 Number of extensions: 33 Number of successful extensions: 3 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: 482 Length adjustment: 33 Effective length of query: 398 Effective length of database: 449 Effective search space: 178702 Effective search space used: 178702 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