Align β-glucosidase (Bgl;BGL-II) (EC 3.2.1.21) (characterized)
to candidate WP_103233337.1 C1634_RS05580 beta-glucosidase
Query= CAZy::AAG59831.1 (862 letters) >NCBI__GCF_002899945.2:WP_103233337.1 Length = 887 Score = 310 bits (793), Expect = 3e-88 Identities = 260/855 (30%), Positives = 413/855 (48%), Gaps = 128/855 (14%) Query: 40 RLGVPAVKVSDGPNGIRGNHFFMGTPAKCLPSSTALGATWDPEVVEEVGLKLLAPEAKLR 99 RLG+P + + +G+ + A P + AL AT++PE++ +V + A E+KLR Sbjct: 119 RLGIPIIPFDEALHGL------VREGATAFPQAIALAATFNPELMNKVSTAI-AKESKLR 171 Query: 100 AASLVLAPTSNIQRNPLGGRSFESFSEDPYLSGIISASYVNGVQKGGIGATIKHFVGNDK 159 +L P N+ + GR+ E++ EDP+L+ ++ ++V+ + GI T KHF+ N Sbjct: 172 GIRQILTPVVNLASDVRWGRTEETYGEDPFLTSVMGVNFVSSFENQGIITTPKHFLANVG 231 Query: 160 EDDRQGYDSIISERALREIYLLPFMLTQKYAAPWAIMTAYNRVNGVHVAEDPFLLKQVLR 219 E R Y S+R L E +L+PF ++MT+YN ++G + +LL + L+ Sbjct: 232 EGGRDSYPIHWSKRYLEETHLIPFNNAFTNGKSRSVMTSYNLLDGRPSTANHWLLTEKLK 291 Query: 220 NEWKYKGLIMSDW--FGMYSVDH------------GIKAGLD-----------LEMPG-- 252 +W +KG ++SD G +V H I AGLD L +P Sbjct: 292 KDWNFKGFVISDASAVGGANVLHFTAKDYDDASAQAINAGLDVIFQTEYTHYKLFIPPFL 351 Query: 253 ---INKWRTLDLVNRTIQARKLTPRDIKDRARVVLELVKKCAQGAPEILDGDGEERTVEL 309 I+K R D V+R + RA+ L L + +I + ++ Sbjct: 352 DGRISKERIDDAVSRVL------------RAKFELGLFENPYVSVQQIEE-------LKK 392 Query: 310 ESDKLLMRRIASESIVLLKNDNVLPLKPEGGAIKKIAVVGGNAKAQVLSGGGSAALKASY 369 + K L + A+ES VLL+N+N P G +KKI VVG +A L G K Sbjct: 393 LNHKPLAEKTAAESFVLLQNNN--GTLPVPGNVKKILVVGTDALDARLGGYSGPGNKK-- 448 Query: 370 FISPYDGIKAALEPHGVEVTFSEGAR-AYKTLPTLEWDLETETGERGWIGTWHTHESDDS 428 ++ DGIK + +E+ +S+G K T+ + + ++G G + ++ Sbjct: 449 -VNILDGIKNYTKNQDIEIIYSKGIDWNIKDFTTISNEYLSSENKKGLKGIYFSNTDLKG 507 Query: 429 MTALDQPFIAPRLVDETRIFISTSY--------PKGITKRWTMRLKGYLKPREKDTNFEF 480 A ++ DE F T Y P + RWT +L+ N++ Sbjct: 508 DPAFEKQ-------DEQFNFKWTLYSPDPEKLQPDHYSIRWTGKLEA-----PDSGNYQL 555 Query: 481 GLIAAGRAKLWVDGQLVIDNWTRQRRGEAFFGSGSQEETGVYLLKAGKKHEIYVEYCNVR 540 GL KL++DG+LVID W + S S + V +K GKK++I +E+ R Sbjct: 556 GLRGNDGFKLYLDGKLVIDQWEKL--------SYSTKTVHVDFVK-GKKYDITIEFHENR 606 Query: 541 APADGDEDEAIMDSNPGVRLGGAEVANADDLLSEAVKLASEADAVIAVVGLNADWETEGN 600 A+ + + N G+ + EA+ LA AD ++ G++ E E Sbjct: 607 GEANLE-----LIWNYGLH-------DYQKDYKEALHLAQNADYIVVTAGIH---EGEFQ 651 Query: 601 DRRTLALPGRTDELVEKVAKVNSKTVVVTQAGSAI-TLPWLDSVAAVVHAWYLGNATGDA 659 DR +L+LPG + + +V+K+N T VV GSAI T+ W D V A++ WY G G+A Sbjct: 652 DRASLSLPGNQESFIHEVSKLNKPTTVVLVGGSAIKTIAWKDKVGAILDVWYPGEEGGNA 711 Query: 660 IADVLFGKQNPSGKLSLTFPKRLEDVP-SHGHFGSENGKVRYAEDLFVGYKHYHHRNIEP 718 +A LFG +NPSGKL +TFP +P ++ H + G Y+ + EP Sbjct: 712 VAKTLFGVENPSGKLPITFPMEEGQLPLTYNHHPTGRG------------NDYYDLSGEP 759 Query: 719 LFPFGFGLSYTTFSLSNLQLSAPVIDHATSSFSLTATLSITNTGPVTGSEVAQLYVSYPE 778 L+PFGFGLSYTTF +S LQL + + ++ A +++ NTG GSEV QLYV Sbjct: 760 LYPFGFGLSYTTFEISGLQLDKA---KYSENDTIIAKVNVKNTGSKAGSEVVQLYVK-DL 815 Query: 779 TSELTHAPLQLRAFKKVKDLQPGETREVKLELDKYAVSYWNDRYQTWAVENGEYEIKVGN 838 + ++ ++L+ F+K+ +LQPGE++ V +E+ + + N++ + WAVE G Y I VGN Sbjct: 816 LATVSRPVIELKGFQKI-ELQPGESKSVTIEIPIKQLQFLNEKME-WAVEKGIYRIMVGN 873 Query: 839 SSVSKDLTLVQRFVV 853 S SK+L L Q V Sbjct: 874 S--SKNLPLKQNIEV 886 Lambda K H 0.316 0.134 0.399 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: 1833 Number of extensions: 86 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 862 Length of database: 887 Length adjustment: 42 Effective length of query: 820 Effective length of database: 845 Effective search space: 692900 Effective search space used: 692900 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 (21.6 bits) S2: 56 (26.2 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