Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate WP_011382666.1 AMB_RS01115 beta-glucosidase
Query= CAZy::AAK78365.1 (469 letters) >NCBI__GCF_000009985.1:WP_011382666.1 Length = 453 Score = 293 bits (749), Expect = 1e-83 Identities = 166/468 (35%), Positives = 249/468 (53%), Gaps = 43/468 (9%) Query: 2 KFPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKED 61 +FPKDFF GA++A+YQ+EGA++ DG+G++ WD FT GK +G++ VA DHYHRY ED Sbjct: 16 QFPKDFFWGASTAAYQIEGAYDTDGRGMTIWDKFTA-DGKIMDGSSAKVACDHYHRYPED 74 Query: 62 VKLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDM 121 + LM G ++YRFS++WPRIIP G G IN KG++FY+ L+D+ L+ GI P LYHWD+ Sbjct: 75 IALMKAAGFNAYRFSLAWPRIIPAGTGAINAKGLDFYDRLVDKILEAGIKPMACLYHWDL 134 Query: 122 PEVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGI 181 P+ LE GGW + V F +YA+ + GDRVK W NE V GY G H PG Sbjct: 135 PQPLEDKGGWQGRDIVGPFAEYARIATKRLGDRVKDWYMLNEPNVVAIIGYGIGEHAPGY 194 Query: 182 TGDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHAN 241 +A H+ A ++ + +G P S DD +N+AAA Sbjct: 195 KLGEDGILKALHHQNLAQGTALRAIRAEHSDAVLGTVINLQPCRSQDDDPKNRAAAI--- 251 Query: 242 QYEITWY---YDPILKGKYPEYV---IKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLN 295 +++ W D +++G P+ + + +I K G ++ T++ P+ D +G+N Sbjct: 252 RWDAVWNRVPLDGVMRGAIPDVLAEKMAHIVKPG--------DMETIK--FPI-DMLGIN 300 Query: 296 YYQPQRVIKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLI 355 YY R+ H+ G FD F+ D +T W + P+ L Sbjct: 301 YY--SRMTMKHEEGH----------------PFDVFWGDAHCD--RWTAMAWPVQPDGLY 340 Query: 356 LGLEKLKEQYGDIKIYITENGLGDQDPIIED-EILDMPRIKFIEAHLRAIKEAISRGINL 414 L + KE YG+ ++I ENG D + D ++ D R+ FI H+ + A+ G N+ Sbjct: 341 DLLREFKELYGNPAVFIAENGAAYDDVVTPDGQVHDAERVAFIRDHVSEVARAVKDGCNV 400 Query: 415 KGYYAWSVIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVI 462 KGY WS++D W G K++G + VD++ L R K S+ W+ +VI Sbjct: 401 KGYLVWSLLDNFEWAYGLSKRFGIVRVDYE-TLKRTPKDSYKWFAEVI 447 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: 651 Number of extensions: 28 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: 453 Length adjustment: 33 Effective length of query: 436 Effective length of database: 420 Effective search space: 183120 Effective search space used: 183120 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