Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate BPHYT_RS29195 BPHYT_RS29195 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__BFirm:BPHYT_RS29195 Length = 470 Score = 402 bits (1033), Expect = e-116 Identities = 217/441 (49%), Positives = 283/441 (64%), Gaps = 20/441 (4%) Query: 6 EKFLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIAL 65 + FL G AT++YQIEGA EDGR PSIWD F+ +PG + G TG ACDHY R++ D+ L Sbjct: 34 KSFLLGAATASYQIEGAVNEDGRLPSIWDTFSAKPGKVLAGDTGAVACDHYHRWQADVDL 93 Query: 66 MQSLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLA 125 + LG+ AYR S+AWPR++ + G N KGL FY RL+ RL GIT F+TLYHWDLP Sbjct: 94 LAGLGLEAYRLSIAWPRVM-DAAGAPNRKGLDFYKRLLARLKEKGITTFVTLYHWDLPQH 152 Query: 126 LEERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNL 185 LE+ GGW +R+TA+ FA+YA+ ++R LA V + TLNEPWCSA+LG+ G HAPGL + Sbjct: 153 LEDCGGWLNRDTAYRFADYADLMSRELAGSVDAWMTLNEPWCSAYLGYGNGHHAPGLADA 212 Query: 186 EAALRAAHHLLLGHGLAVEALRAAG-ARRVGIVLNFAPAYGEDPEAVD-----VADRYHN 239 A +A HHLLL HGLAV LRA A +VGIV N A D + + HN Sbjct: 213 RYATQAMHHLLLAHGLAVPVLRANDPASQVGIVANIGRGTANSESAADQRAAHLFEVQHN 272 Query: 240 RYFLDPILGKGYPESPFRDPPPVP--ILSRDLELVARPLDFLGVNYYAPVRVAPGTGTLP 297 + LDP+L YP+ F P +L D++ +A PLDFLG+NYY VA G Sbjct: 273 AWILDPLLKGSYPQDLFELWPGTEPLVLDGDMQTIAAPLDFLGINYYFRTNVA-SDGAHG 331 Query: 298 VRYLPPEG-PATAMGWEVYPEGLHHLL---KRLGREVPWPLYVTENGAAYPDLWTGEAVV 353 R +P EG T MGWEVYP+GL LL K +P P+Y+TENG A D + V Sbjct: 332 FRDVPLEGVERTQMGWEVYPDGLRDLLTGFKATYANLP-PIYITENGMASDDK-VIDGQV 389 Query: 354 EDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRR 413 ED +R+++L+ H+ A +A + GV++RGYF+WSLMDNFEWAFGY RRFG+ +VD+ +Q+R Sbjct: 390 EDSQRISFLKRHLSAVDQAIKAGVEIRGYFLWSLMDNFEWAFGYERRFGIVHVDYATQKR 449 Query: 414 IPKRSA----LWYRERIARAQ 430 KRSA + +ER AR + Sbjct: 450 TIKRSANLVSKFLKERKARTE 470 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: 600 Number of extensions: 27 Number of successful extensions: 7 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: 470 Length adjustment: 33 Effective length of query: 398 Effective length of database: 437 Effective search space: 173926 Effective search space used: 173926 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