Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate SMc03160 SMc03160 beta-glucosidase
Query= CAZy::AAK78365.1 (469 letters) >FitnessBrowser__Smeli:SMc03160 Length = 458 Score = 290 bits (742), Expect = 7e-83 Identities = 164/462 (35%), Positives = 245/462 (53%), Gaps = 24/462 (5%) Query: 2 KFPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKED 61 +FP DF G A+AS+Q+EGA DG+ S WD F+ +PG+ + NGDVA DHY+R ++D Sbjct: 11 RFPGDFVFGVATASFQIEGASKADGRKASIWDAFSNMPGRVYGRHNGDVACDHYNRLEQD 70 Query: 62 VKLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDM 121 + L+ +G+++YRFS++WPRI+P+G G IN+KG++FY+ L+D GI F TLYHWD+ Sbjct: 71 LDLIKSLGVEAYRFSIAWPRIVPEGTGPINEKGLDFYDRLVDGLKARGIKAFATLYHWDL 130 Query: 122 PEVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGI 181 P L GGWT + T A+ +YAK GDR+ TFNE G+L G H PG Sbjct: 131 PLALMGDGGWTARTTAYAYQRYAKTVIARLGDRLDAVATFNEPWCSVWLGHLYGVHAPG- 189 Query: 182 TGDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHAN 241 ++ A H AH V + + +GI + + E+KAAA A Sbjct: 190 ERNMDAALAALHFTNLAHGLGVAAIRSERPELPVGIVINAHSVYPGSNSAEDKAAAERAF 249 Query: 242 QYEITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQR 301 + ++DPI KG+YPE + + ++ +P D ++ T+ A PL D+ GLNYY P R Sbjct: 250 DFHNGVFFDPIFKGEYPEDFLSALGER--MPAIEDGDMATI--AQPL-DWWGLNYYTPMR 304 Query: 302 VIKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEKL 361 V + G + T K T GWE+ +L +E L Sbjct: 305 VSADPAKGAEYPAT-----------------VNAKPVSNVKTDIGWEVYAPALGSLVETL 347 Query: 362 KEQYGDIKIYITENGLGDQDPIIEDEILDMPRIKFIEAHLRAIKEAISRGINLKGYYAWS 421 +Y YITENG + + D PR+ +I HL + I++G ++GY+AWS Sbjct: 348 NARYRLPDCYITENGACYNMGVENGTVDDQPRLDYISDHLAVTADLIAKGYPMRGYFAWS 407 Query: 422 VIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVIE 463 ++D W GY+ ++G ++VD++ + R K S WYK + E Sbjct: 408 LMDNFEWAEGYRMRFGIVHVDYETQV-RTIKKSGRWYKDLAE 448 Lambda K H 0.318 0.138 0.433 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: 684 Number of extensions: 36 Number of successful extensions: 4 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: 469 Length of database: 458 Length adjustment: 33 Effective length of query: 436 Effective length of database: 425 Effective search space: 185300 Effective search space used: 185300 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 (21.7 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