Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_011189689.1 DP_RS12390 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_000025945.1:WP_011189689.1 Length = 486 Score = 325 bits (834), Expect = 1e-93 Identities = 185/449 (41%), Positives = 260/449 (57%), Gaps = 38/449 (8%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 F WG+AT++YQIEG+ + DG+G SIWD +A PG +++ TG+ A DHY+RY+ED+ +M+ Sbjct: 36 FCWGLATASYQIEGSPKVDGKGMSIWDTYAHIPGKMKNNDTGDVAIDHYQRYKEDVQIMK 95 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 +G YRFS+AW RI P G G NPKGL FY+RLVD LL +GI PF TLYHWDLP AL+ Sbjct: 96 EMGATGYRFSIAWSRIFPSGTGLANPKGLDFYNRLVDELLNAGIQPFATLYHWDLPQALQ 155 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTG----------- 176 ++GGW+SRETA FA+YA +A L+DRV F TLNE +GH G Sbjct: 156 DKGGWQSRETAECFAQYAGYMAEKLSDRVKNFFTLNEFQNIVDMGH-RGVDMVVQGKPVH 214 Query: 177 -EHAPGLR-NLEAALRAAHHLLLGHGLAVEALRAAGARRV----------GIVLNFAPAY 224 E APGL+ + +A + AHH +L HGL+V+A+RA G + G+ + +P Sbjct: 215 IELAPGLKLDNQALNQVAHHTVLAHGLSVQAIRAMGKKGTKVGPAEVMFCGVPIMDSP-- 272 Query: 225 GEDPEAVDVADRYHNRYFLDPIL-GK---GYPESPFRDPPPVPILSRDLELVARPLDFLG 280 E +A ++A R N FLD +L GK Y + +D P DL+ + P+DF+G Sbjct: 273 -EHVKAAELATRRLNARFLDVMLTGKYSDAYLQEAGKDAP--KFTEEDLQAIGSPVDFVG 329 Query: 281 VNYYAP---VRVAPGTGTLPVRYLPPEGPATAMGWEVYPEGLHHLLKRLGREV--PWPLY 335 +N Y P V + + P + W + + + RL + P +Y Sbjct: 330 INVYIPKMYVMASEDESGYKEVPMSVSHPKMSSPWHTFAPEVLYWAPRLTHSIWKPKAIY 389 Query: 336 VTENGAAYPDLWTGEAVVEDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAF 395 +TENG A D + + + D +RV YL + RA EGV ++G FVWS DN EW+ Sbjct: 390 ITENGCAASDEISADGNIYDTDRVMYLRNAMGQLQRASAEGVPIKGNFVWSAFDNLEWSG 449 Query: 396 GYTRRFGLYYVDFPSQRRIPKRSALWYRE 424 G+ RFGL +V+F +Q+R PK SA W++E Sbjct: 450 GFGTRFGLVHVNFKTQKRTPKLSAKWFKE 478 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: 561 Number of extensions: 30 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: 486 Length adjustment: 33 Effective length of query: 398 Effective length of database: 453 Effective search space: 180294 Effective search space used: 180294 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