Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_094932864.1 CDO52_RS20930 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_002263495.1:WP_094932864.1 Length = 475 Score = 429 bits (1103), Expect = e-125 Identities = 226/453 (49%), Positives = 273/453 (60%), Gaps = 38/453 (8%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 F WG AT+A+QIEGAT+ DGRG SIWD FA PG + G TGEPA +HYRRY ED+AL++ Sbjct: 7 FAWGAATAAFQIEGATRADGRGVSIWDTFAATPGRVLGGDTGEPAANHYRRYAEDVALLR 66 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 SLG+ YRFS+AWPRI P+G G NP GL FYDRLVD LLA+GI P+ TLYHWDLP LE Sbjct: 67 SLGIGNYRFSLAWPRIQPDGTGPGNPAGLDFYDRLVDELLAAGIEPWPTLYHWDLPQPLE 126 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 + GGW +R+TA FAEYA R L DRV + T+NEPW AFLG+ +GEHAPG R + Sbjct: 127 DAGGWPARDTALRFAEYAAIAHRRLGDRVRTWCTINEPWVVAFLGYASGEHAPGRREPAS 186 Query: 188 ALRAAHHLLLGHGLAVEALRAAGAR---------RVGIVLNFAPAYGEDPEAVDV----- 233 AL A HHL+LGHGLA A+R GA VGIVLN P + D+ Sbjct: 187 ALAATHHLMLGHGLAAAAIRGQGATTTGTRPGTPAVGIVLNAQPIRPHEGSVADLDAARR 246 Query: 234 ADRYHNRYFLDPILGKGYPESPFRDPPPVP----ILSRDLELVARPLDFLGVNYYAPVRV 289 D NR FLDP+ YP+ D V + DL +A PLDFLG+NYY+P V Sbjct: 247 VDGVRNRIFLDPLYHGRYPDDVRADLADVSDFAFVRDGDLTTIAAPLDFLGINYYSPASV 306 Query: 290 APGTGTLPVRYLPPEG-------------------PATAMGWEVYPEGLHHLLKRLGREV 330 G + L P G P T WE+ GL LL RL + Sbjct: 307 TGAAGKVDPELLEPAGDGPSRLVGCEDVGVLRGAEPRTDQDWEIDATGLTELLLRLAVDY 366 Query: 331 P-WPLYVTENGAAYPDLWTGEAVVEDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMD 389 P PLYVTENGA+Y D + V DP R +YL+ HV A A G ++GYFVWSL+D Sbjct: 367 PGTPLYVTENGASYRDEVADDGAVHDPRRASYLDQHVRATHAALTAGAPVKGYFVWSLLD 426 Query: 390 NFEWAFGYTRRFGLYYVDFPSQRRIPKRSALWY 422 NFEWA+GY+ RFG+ +VD+ +QRR K S WY Sbjct: 427 NFEWAYGYSERFGIIHVDYDTQRRTVKDSGRWY 459 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: 690 Number of extensions: 38 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: 475 Length adjustment: 33 Effective length of query: 398 Effective length of database: 442 Effective search space: 175916 Effective search space used: 175916 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