Align β-glucosidase (BglM1;Mmwyl1_4295) (cold-active) (EC 3.2.1.21) (characterized)
to candidate H281DRAFT_01455 H281DRAFT_01455 beta-glucosidase
Query= CAZy::ABR73190.1 (447 letters) >FitnessBrowser__Burk376:H281DRAFT_01455 Length = 464 Score = 518 bits (1335), Expect = e-151 Identities = 249/444 (56%), Positives = 314/444 (70%), Gaps = 2/444 (0%) Query: 4 TLPSHSKMLTSDFIFGVATASFQIEGATTADNRLPSIWDTFCATPGKVKGMDNGEIACDH 63 T + S + +F+ G ATAS+QIEGA D RLPSIWDTFCATPGKV D+G +ACDH Sbjct: 16 TPAADSALWRKNFLLGAATASYQIEGAVDEDGRLPSIWDTFCATPGKVLAGDSGAVACDH 75 Query: 64 YHLWEQDIQLIKDLGVDAYRLSIAWPRVMDKKGEANQAGLDFYRNLLKKLKAEGLTVFAT 123 YH WE D+ ++ LG++ YRLSIAWPRVMD G +N+ GLDFY+ LL +LK +G+T F T Sbjct: 76 YHRWESDVDMLVGLGLEGYRLSIAWPRVMDANGASNRKGLDFYKRLLTRLKEKGITTFVT 135 Query: 124 LYHWDLPQHLEDKGGWLNRETAYQFKNYADLVTKELAEWVDSWATFNEPFCAAILGYELG 183 LYHWDLPQHLED+GGWLNRETAY+F +YADL+++ELA VD+WAT NEP+C+A LGY G Sbjct: 136 LYHWDLPQHLEDRGGWLNRETAYRFADYADLMSRELAGTVDAWATLNEPWCSAYLGYGNG 195 Query: 184 IHAPGLSKPAFGRQAAHHILLAHGLALPVIRKNAPKSQVGIVLNMNRSYAASEKTEDQFA 243 HAPGL+ F QA HH+LLAHGLALPV+R+N P SQ GIV N+ R S+ EDQ A Sbjct: 196 HHAPGLANGRFATQAMHHLLLAHGLALPVLRENDPSSQKGIVANIGRGTPNSDSVEDQRA 255 Query: 244 CLMRETLDNQFFIEPLMKGQYPQLLKTVAPQYLPTILPGDMDIISQPIDFLGMNFYTCNH 303 + E N + ++PL+KG YP+ L + P P IL GDM IIS P+DFLG+N+Y + Sbjct: 256 AQLFEIQHNAWILDPLLKGAYPEALFELWPGTEPLILGGDMQIISAPLDFLGINYYFRTN 315 Query: 304 NAYDADDMFKNVQNSQTVEYTDIGWEIAPHAFTELLVNLHKQYS-LPPIYITENGAACAD 362 A D F V + VE T +GWE+ P +LL+ +YS LPP+YITENG A D Sbjct: 316 VATDGAHGFTEVP-LEGVERTQMGWEVYPDGLRDLLIGFSHEYSNLPPVYITENGMASDD 374 Query: 363 QIIDGEINDEQRVRYLDGHINAVNQAIESGVDIRGYFAWSLMDNFEWAEGYSKRFGLTYV 422 +IDG +ND QR+ +L H+ AV++AI++GVDIRGYF WSLMDNFEWA GY +RFG+ +V Sbjct: 375 TVIDGRVNDTQRISFLKRHLAAVDEAIKAGVDIRGYFLWSLMDNFEWAFGYERRFGIVHV 434 Query: 423 DYQTQERTIKRSGHAYQTLLSSRK 446 DY TQ+RT KRS + RK Sbjct: 435 DYVTQKRTTKRSAELVSQFIEERK 458 Lambda K H 0.320 0.136 0.422 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: 670 Number of extensions: 36 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: 447 Length of database: 464 Length adjustment: 33 Effective length of query: 414 Effective length of database: 431 Effective search space: 178434 Effective search space used: 178434 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 (21.8 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