Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate AZOBR_RS16895 AZOBR_RS16895 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__azobra:AZOBR_RS16895 Length = 482 Score = 392 bits (1006), Expect = e-113 Identities = 211/435 (48%), Positives = 270/435 (62%), Gaps = 13/435 (2%) Query: 6 EKFLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIAL 65 +KF+WG +TS+YQIEGA GRGPS+WD F+ G + +G TG+ ACDHY RY ED+ L Sbjct: 42 DKFVWGASTSSYQIEGAVTAGGRGPSVWDTFSHSFGKVANGDTGDVACDHYNRYAEDVDL 101 Query: 66 MQSLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLA 125 M G+ AYRFSVAWPR+ P G G N +GL FYDRL D LLA GI P+ LYHWDLP A Sbjct: 102 MAKAGMNAYRFSVAWPRVQPTGTGPANAEGLDFYDRLTDALLAKGIAPWPCLYHWDLPQA 161 Query: 126 LEERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNL 185 L++RGGW +R+ A F +YA+ VA + DR + LNEP A GH G HAPG+ Sbjct: 162 LQDRGGWTNRDIAGWFTDYAQLVAARIGDRAKHWTMLNEPSVHAIFGHGLGGHAPGMTGK 221 Query: 186 EAALRAAHHLLLGHGLAVEALRAAGARR---VGIVLNFAPAY---GEDPE--AVDVADRY 237 +A HH L G+A++ALRAAG + +G VL+ P + G D A + D Sbjct: 222 GNYFKAIHHQNLAQGMALKALRAAGGAKGWQLGTVLSLQPVWPVGGLDANYAASLMWDAV 281 Query: 238 HNRYFLDPILGKGYPESPFRDPPPVPILSRDLELVARPLDFLGVNYYAPVRVAPG-TGTL 296 NR LDP+L YPE RD + + DLE + +P+DFLG+NYY+ + P G Sbjct: 282 WNRACLDPLLRGEYPEL-LRDGFAPLVKAGDLEAIRQPIDFLGINYYSRMHQQPDPAGLF 340 Query: 297 PVRY-LPPEG-PATAMGWEVYPEGLHHLLKRLGREV-PWPLYVTENGAAYPDLWTGEAVV 353 Y PPEG P T MGW V P+G+ +L L +E P+YV ENGAAYP+ + V Sbjct: 341 GTGYGSPPEGTPTTGMGWPVEPDGIAEILIELKQEYGNPPVYVMENGAAYPEQTGPKGFV 400 Query: 354 EDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRR 413 +D +R++YL H+ A +A EEGVDLRG+FVWSL+DNFEWA GY RRFGL VD + R Sbjct: 401 QDNDRISYLRRHILAGHQALEEGVDLRGWFVWSLLDNFEWAEGYQRRFGLIEVDRQTLER 460 Query: 414 IPKRSALWYRERIAR 428 PK S WY + I + Sbjct: 461 RPKASYHWYADVIRK 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: 700 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: 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