Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate BPHYT_RS29195 BPHYT_RS29195 beta-glucosidase
Query= CAZy::AAK78365.1 (469 letters) >FitnessBrowser__BFirm:BPHYT_RS29195 Length = 470 Score = 299 bits (765), Expect = 2e-85 Identities = 171/462 (37%), Positives = 249/462 (53%), Gaps = 31/462 (6%) Query: 5 KDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKEDVKL 64 K F LGAA+ASYQ+EGA NEDG+ S WD F+ PGK G G VA DHYHR++ DV L Sbjct: 34 KSFLLGAATASYQIEGAVNEDGRLPSIWDTFSAKPGKVLAGDTGAVACDHYHRWQADVDL 93 Query: 65 MAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDMPEV 124 +A +GL++YR S++WPR++ D G N+KG++FY L+ + GI FVTLYHWD+P+ Sbjct: 94 LAGLGLEAYRLSIAWPRVM-DAAGAPNRKGLDFYKRLLARLKEKGITTFVTLYHWDLPQH 152 Query: 125 LEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGITGD 184 LE GGW N+ T F YA V W+T NE GY +G H PG+ D Sbjct: 153 LEDCGGWLNRDTAYRFADYADLMSRELAGSVDAWMTLNEPWCSAYLGYGNGHHAPGL-AD 211 Query: 185 VKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHANQYE 244 + QA H++ AH +V + ++GI + + ++ AA+ Sbjct: 212 ARYATQAMHHLLLAHGLAVPVLRANDPASQVGIVANIGRGTANSESAADQRAAHLFEVQH 271 Query: 245 ITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQRVIK 304 W DP+LKG YP+ + + G P D ++ T+ AAPL DF+G+NYY Sbjct: 272 NAWILDPLLKGSYPQDLFE--LWPGTEPLVLDGDMQTI--AAPL-DFLGINYY------- 319 Query: 305 NHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEKLKEQ 364 RT S GA G +R V ++ T+ GWE+ P+ L L K Sbjct: 320 --------FRTNVASDGAHG-------FRDVPLEGVERTQMGWEVYPDGLRDLLTGFKAT 364 Query: 365 YGDI-KIYITENGLGDQDPIIEDEILDMPRIKFIEAHLRAIKEAISRGINLKGYYAWSVI 423 Y ++ IYITENG+ D +I+ ++ D RI F++ HL A+ +AI G+ ++GY+ WS++ Sbjct: 365 YANLPPIYITENGMASDDKVIDGQVEDSQRISFLKRHLSAVDQAIKAGVEIRGYFLWSLM 424 Query: 424 DLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVIEER 465 D W GY++++G ++VD+ R K S K ++ER Sbjct: 425 DNFEWAFGYERRFGIVHVDYA-TQKRTIKRSANLVSKFLKER 465 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: 656 Number of extensions: 36 Number of successful extensions: 5 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: 470 Length adjustment: 33 Effective length of query: 436 Effective length of database: 437 Effective search space: 190532 Effective search space used: 190532 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