Align β-glucosidase (Bgl;Fbgl;FmBGL) (EC 3.2.1.21) (characterized)
to candidate WP_109739238.1 C1634_RS23580 beta-glucosidase BglX
Query= CAZy::AAB66561.1 (726 letters) >NCBI__GCF_002899945.2:WP_109739238.1 Length = 775 Score = 1140 bits (2948), Expect = 0.0 Identities = 559/727 (76%), Positives = 633/727 (87%), Gaps = 1/727 (0%) Query: 1 MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60 MTLDEKIGQLNLPSSGDFTTG A+SSDIGKK+EQGLVGGLFNIKG KI+AVQKVA+E S Sbjct: 49 MTLDEKIGQLNLPSSGDFTTGLAKSSDIGKKVEQGLVGGLFNIKGAEKIRAVQKVAVENS 108 Query: 61 RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120 RLKIP+IFGMDVIHGYETTFPIPLGLA+SWDM+L+Q+SA++AAKEAS+DGINWTFSPMVD Sbjct: 109 RLKIPLIFGMDVIHGYETTFPIPLGLAASWDMNLVQQSARVAAKEASSDGINWTFSPMVD 168 Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180 +SREPRWGRVSEGSGEDPYLGSEIAK MVYGYQGKDL+ ILACVKHFALYGA E GR Sbjct: 169 ISREPRWGRVSEGSGEDPYLGSEIAKNMVYGYQGKDLANGTNILACVKHFALYGAGESGR 228 Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240 DYNTVDMSH+RMFNEYFPPYKAAVDAGV SVMASFNEVDGVPATG++WL +VLR +W F Sbjct: 229 DYNTVDMSHVRMFNEYFPPYKAAVDAGVASVMASFNEVDGVPATGSRWLQTEVLRNKWNF 288 Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300 GF+VTDYTGINEM+ HGMGDLQQVSALAL AGVDMDMVGEGFLTTLKKSLSEGKVT+ + Sbjct: 289 KGFVVTDYTGINEMVDHGMGDLQQVSALALKAGVDMDMVGEGFLTTLKKSLSEGKVTQAE 348 Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360 I LAA+R+LE+KYDLGLF DPY+Y D K A EV+S +R ARN+AAQSMVL+KN+ Q Sbjct: 349 IDLAAKRVLESKYDLGLFTDPYKYGDAKLAAKEVYSMENRNIARNVAAQSMVLMKNENQV 408 Query: 361 LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETV-KGVNFIYAKGSNV 419 LPLK GTVAVIGPL NN+ NM GTWSVA++ AV++M GL+ + K V F+ AKG+N+ Sbjct: 409 LPLKKSGTVAVIGPLVNNSLNMAGTWSVAAKHDKAVNLMQGLQASYGKEVKFLSAKGANI 468 Query: 420 FYDAKMEEKATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAELSGESSSRAN 479 YDAK+E+ GK +RD+RSKEELLKEAV ANKADV+VLAIGE+AE+SGESSSR Sbjct: 469 DYDAKLEDIYAAHGKKTDRDNRSKEELLKEAVDVANKADVIVLAIGESAEMSGESSSRTE 528 Query: 480 IEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAGSEAGYAIADV 539 I IPQ+Q DLL ELKKTGKPI MVLFTGRPL L + D+I+NAWFAGSEAG AIADV Sbjct: 529 ITIPQSQVDLLNELKKTGKPIAMVLFTGRPLALTNVKDTPDSILNAWFAGSEAGNAIADV 588 Query: 540 LYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRSNYIDECNTPL 599 L+GKVNPSGKLPMTFPRS+GQVPIYYNAKNTGRPLS E +DKCE+++FRSNY+DECNTPL Sbjct: 589 LFGKVNPSGKLPMTFPRSLGQVPIYYNAKNTGRPLSQELTDKCEYQRFRSNYMDECNTPL 648 Query: 600 FPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQLYIRDMVGSVT 659 +PFG+GLSYT F YSDI ++ T GN + ASVT+TN+G YDG EVVQLYIRDMVGS+T Sbjct: 649 YPFGFGLSYTKFGYSDIAVSNTSPKGNQTIQASVTVTNDGNYDGAEVVQLYIRDMVGSIT 708 Query: 660 RPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIMIGTNSHDVKH 719 RPVKELKGFQKVFLK GES+ VTF+ITPE LKFYN LKYDWE G+FD+MIGT+S DVKH Sbjct: 709 RPVKELKGFQKVFLKKGESRKVTFDITPETLKFYNGDLKYDWESGDFDVMIGTSSADVKH 768 Query: 720 AKINWNK 726 +KINW K Sbjct: 769 SKINWTK 775 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: 1734 Number of extensions: 51 Number of successful extensions: 2 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: 775 Length adjustment: 40 Effective length of query: 686 Effective length of database: 735 Effective search space: 504210 Effective search space used: 504210 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 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