Align β-glucosidase (Bgl;Fbgl;FmBGL) (EC 3.2.1.21) (characterized)
to candidate Echvi_2491 Echvi_2491 Beta-glucosidase-related glycosidases
Query= CAZy::AAB66561.1 (726 letters) >FitnessBrowser__Cola:Echvi_2491 Length = 766 Score = 1006 bits (2602), Expect = 0.0 Identities = 489/727 (67%), Positives = 602/727 (82%), Gaps = 5/727 (0%) Query: 1 MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60 MTL+EKIGQLNLP++GDFTTGQA SS+I +KI+ G VGGLFNIK V KI+ VQ+VA+E+S Sbjct: 44 MTLEEKIGQLNLPAAGDFTTGQASSSNIAEKIKAGKVGGLFNIKTVQKIRDVQRVAVEES 103 Query: 61 RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120 RL IP++FGMDVIHGYET FPIPLGL+S+WDM+LI++SAQ+AAKEASADGINWTFSPM D Sbjct: 104 RLGIPLLFGMDVIHGYETIFPIPLGLSSTWDMELIKKSAQLAAKEASADGINWTFSPMTD 163 Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180 +SR+PRWGRVSEGSGEDPYLG++IAKAMV GYQG DLSL +T++ACVKHFALYGAPE GR Sbjct: 164 ISRDPRWGRVSEGSGEDPYLGAQIAKAMVEGYQGDDLSLSHTLMACVKHFALYGAPEAGR 223 Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240 DYNTVDMS RM+NEYFPPYKAAVDAGVG+VM +FNEV+G+PA+ NKWLM +VLR QWGF Sbjct: 224 DYNTVDMSRQRMYNEYFPPYKAAVDAGVGTVMTAFNEVEGIPASANKWLMTEVLRNQWGF 283 Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300 +GF+VTDYT INEM HG+GDL+ VSA AL AGVDMDMVGEGFL+TLK SL EG +TE Q Sbjct: 284 DGFVVTDYTAINEMTAHGIGDLKTVSAKALKAGVDMDMVGEGFLSTLKASLEEGTITETQ 343 Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360 I A RRIL AK+ LGLF+DPYRY D +RA+ E+F+ +R+ +R IAAQS VL+KN+ Q Sbjct: 344 IDEACRRILVAKFKLGLFEDPYRYCDAERAETEIFNAENRQLSREIAAQSFVLMKNEGQV 403 Query: 361 LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETV-KGVNFIYAKGSNV 419 LPLK GT+A+IGP+A+N ENMTGTWSVA R K+++S+ G++ V V I A+G+N+ Sbjct: 404 LPLKKTGTIALIGPMADNAENMTGTWSVAGRFKESISLKQGIQHAVGDQVKIIEARGANI 463 Query: 420 FYDAKMEEKATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAELSGESSSRAN 479 D+ +E + ++FGK RD R +EEL++EA+ A ADV+V A+GE+AE+SGESSSR+ Sbjct: 464 VADSLLESRVSVFGKPTYRDQRPEEELIEEALEAAKAADVIVAAMGESAEMSGESSSRST 523 Query: 480 IEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAGSEAGYAIADV 539 IE+P+ Q+ LL L KTGKP+VMVLF+GRPL + E + +I+N WF GSEAG AIADV Sbjct: 524 IELPENQRRLLKALAKTGKPVVMVLFSGRPLAIQWEAEHIPSILNVWFGGSEAGDAIADV 583 Query: 540 LYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRSNYIDECNTPL 599 L+G+VNPSGKL MTFP++ GQ+P+YYN KNTGRPL + + F+KFRSN++D N PL Sbjct: 584 LFGEVNPSGKLTMTFPQNTGQIPLYYNHKNTGRPLPEGQ----WFQKFRSNFLDVPNAPL 639 Query: 600 FPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQLYIRDMVGSVT 659 FPFGYGLSYT F+Y DI L+ +LSG+ L A++TLTN G++DG EVVQLY+RDMVGS+T Sbjct: 640 FPFGYGLSYTEFDYGDITLSTEKLSGHQTLYATITLTNAGRFDGKEVVQLYVRDMVGSMT 699 Query: 660 RPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIMIGTNSHDVKH 719 RPVKELKGFQKVFLKAGE+K VTF +T EDLKFYN L + +EPGEF+IMIGTNSHDV Sbjct: 700 RPVKELKGFQKVFLKAGETKEVTFELTQEDLKFYNHDLDFVFEPGEFEIMIGTNSHDVSS 759 Query: 720 AKINWNK 726 K+NW + Sbjct: 760 MKVNWEE 766 Lambda K H 0.315 0.133 0.383 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: 1582 Number of extensions: 68 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: 726 Length of database: 766 Length adjustment: 40 Effective length of query: 686 Effective length of database: 726 Effective search space: 498036 Effective search space used: 498036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 55 (25.8 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