Align beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate WP_066329731.1 BLR17_RS09380 family 1 glycosylhydrolase
Query= BRENDA::A4XIG7 (453 letters) >NCBI__GCF_900100165.1:WP_066329731.1 Length = 465 Score = 331 bits (848), Expect = 3e-95 Identities = 191/465 (41%), Positives = 268/465 (57%), Gaps = 32/465 (6%) Query: 5 KGFLWGAATASYQIEGAWNEDGKGESIWDRFTHQK--RNILYGHN--GDVACDHYHRFE- 59 K FLWG A+A+YQ+EGA+ DGKGES WD T++ + G G+VA + Y R + Sbjct: 13 KPFLWGVASAAYQVEGAYQADGKGESKWDFLTNKVGVTQFIIGQKQTGNVAINMYDRTQY 72 Query: 60 -EDVSLMKELGLKAYRFSIAWTRIFPDGFGTVNQKGLEFYDRLINKLVENGIEPVVTLYH 118 +D+ LMKELG+ +YRFS+ W+RI PDG G VN+K L YD LI+ L GIEPVVTLYH Sbjct: 73 LKDIQLMKELGVNSYRFSLDWSRIIPDGIGAVNEKALAHYDVLIDDLKAAGIEPVVTLYH 132 Query: 119 WDLPQKLQDIGGWANPEIVNYYFDYAMLVINRYKDKVKKWITFNEPYCIAFLGYF----H 174 +D P L GGW NPE++N+Y +YA +V RY KVK +ITFNEPY F+ F Sbjct: 133 FDYPFALVQKGGWGNPEMINWYKNYAQIVFKRYGKKVKHFITFNEPYIEFFVAEFLMNME 192 Query: 175 GIHAPGIKDFKVAMDVVHSLMLSHFKVVKAVKENNIDVEVGITLNLTPVYLQTERLGYKV 234 P + F M H +++ +V+K + N+ ++G+T N +P Sbjct: 193 QSKEPAVTRFARGMMKAHRELVASAEVIKMYHKMNLGGKIGMTFNFSPCSPLDPN----- 247 Query: 235 SEIEREMVSLSSQLDNQLFLDPVLKGSYPQKLLDYLVQKD-----LLDSQKALSMQQEVK 289 + + + +L +L N +FLD KG+YP++++D + D D K L+ + Sbjct: 248 NPKDVQASALQEKLLNTVFLDGYFKGTYPKEVVDLFTKYDPAFQPAADDMKILAANK--- 304 Query: 290 ENFIFPDFLGINYYTRAVRLYDENSSWIFPIRW-EHPAGEYTEMGWEVFPQGLFDLLIWI 348 PDFLGIN+Y A+ YD + F ++W + + V P+ L+ L+ I Sbjct: 305 -----PDFLGINFYAPALVKYDPSEP--FEMKWMDINTDKIKSHNGPVRPEELYKFLVKI 357 Query: 349 KESYPQIPIYITENGAAY-NDIVTEDGKVHDSKRIEYLKQHFEAARKAIENGVDLRGYFV 407 K+ Y I ITENGA + + + V D R +Y+K+H EA KA + GV + GYF Sbjct: 358 KKEYNNPEIMITENGAGFEGEDIKATPIVKDPLRADYIKRHVEAVDKAKKEGVKMIGYFP 417 Query: 408 WSLMDNFEWAMGYTKRFGIIYVDYETQKRIKKDSFYFYQQYIKEN 452 WS DNFEW GYTKRFG+IYVD+ETQ+RI K SFY YQ+ IK++ Sbjct: 418 WSGWDNFEWVFGYTKRFGLIYVDFETQERIPKQSFYEYQKIIKQH 462 Lambda K H 0.322 0.140 0.439 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: 705 Number of extensions: 38 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: 453 Length of database: 465 Length adjustment: 33 Effective length of query: 420 Effective length of database: 432 Effective search space: 181440 Effective search space used: 181440 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 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