Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_005457249.1 SACCYDRAFT_RS14670 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_000244975.1:WP_005457249.1 Length = 456 Score = 442 bits (1137), Expect = e-128 Identities = 234/443 (52%), Positives = 286/443 (64%), Gaps = 24/443 (5%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 FLWGVAT+A+Q+EG+T DGR PSIWDAF + GA+ G TG+PA DHYRR D+ALM+ Sbjct: 7 FLWGVATAAFQVEGSTTADGRSPSIWDAFCAKEGAVVGGDTGDPATDHYRRMPSDVALMR 66 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 LGVRAYRFS+AWPR+ P+G G +NP GL FY+RLVD LL +GI P+ TLYHWDLP ALE Sbjct: 67 DLGVRAYRFSLAWPRVRPDG-GEVNPAGLDFYERLVDTLLDAGIRPWPTLYHWDLPQALE 125 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 ERGGW SRE A+ FA+YAEAV L DRV + TLNEPWCSAFLG+ +G HAPG A Sbjct: 126 ERGGWTSREVAYRFADYAEAVVDRLGDRVSTWTTLNEPWCSAFLGYGSGRHAPGRTEPRA 185 Query: 188 ALRAAHHLLLGHGLAVEALRA-AGARRVGIVLNFAPAYGEDP------EAVDVADRYHNR 240 A+ AAHHLLL HGL A+RA VG+ LN P DP E D NR Sbjct: 186 AVAAAHHLLLAHGLGTAAVRARVPGAEVGVTLNLFPVNVADPGNAQDLETARRVDGLQNR 245 Query: 241 YFLDPILGKGYPESPFRDPPPV----PILSRDLELVARPLDFLGVNYYAPVRVA--PGTG 294 FLDP+L YPE D P + D ++ +DFLGVNYY + V+ PG Sbjct: 246 LFLDPVLRARYPEDVRADLEPFGFSGVVREGDETVIGAGVDFLGVNYYRDLHVSSVPGEN 305 Query: 295 TLPVR--------YLPPEG-PATAMGWEVYPEGLHHLLKRLGREVP-WPLYVTENGAAYP 344 + P P G P TA GW++ L LL RL E P PLY+TENGAA+P Sbjct: 306 SGPPSEWVGVDHVSFPGRGLPQTASGWDINAGELTGLLLRLHTEYPRLPLYITENGAAFP 365 Query: 345 DLWTGEAVVEDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLY 404 D + ++D +R+A++E H+ AA A ++GVDLRGYF WSL+DNFEWA GY +RFGL Sbjct: 366 DDRQVDGRIDDTDRIAFVEGHLRAAHSAVQQGVDLRGYFYWSLLDNFEWAEGYAKRFGLV 425 Query: 405 YVDFPSQRRIPKRSALWYRERIA 427 +VD+ +QRR PK SA WY +A Sbjct: 426 HVDYDTQRRTPKASAAWYSRVMA 448 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: 684 Number of extensions: 39 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: 456 Length adjustment: 32 Effective length of query: 399 Effective length of database: 424 Effective search space: 169176 Effective search space used: 169176 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 24 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