Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate H281DRAFT_01455 H281DRAFT_01455 beta-glucosidase
Query= CAZy::AAK78365.1 (469 letters) >FitnessBrowser__Burk376:H281DRAFT_01455 Length = 464 Score = 284 bits (727), Expect = 4e-81 Identities = 164/462 (35%), Positives = 244/462 (52%), Gaps = 31/462 (6%) Query: 5 KDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKEDVKL 64 K+F LGAA+ASYQ+EGA +EDG+ S WD F PGK G +G VA DHYHR++ DV + Sbjct: 26 KNFLLGAATASYQIEGAVDEDGRLPSIWDTFCATPGKVLAGDSGAVACDHYHRWESDVDM 85 Query: 65 MAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDMPEV 124 + +GL+ YR S++WPR++ D +G N+KG++FY L+ + GI FVTLYHWD+P+ Sbjct: 86 LVGLGLEGYRLSIAWPRVM-DANGASNRKGLDFYKRLLTRLKEKGITTFVTLYHWDLPQH 144 Query: 125 LEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGITGD 184 LE GGW N++T F YA V W T NE GY +G H PG+ Sbjct: 145 LEDRGGWLNRETAYRFADYADLMSRELAGTVDAWATLNEPWCSAYLGYGNGHHAPGLANG 204 Query: 185 VKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHANQYE 244 + QA H++ AH ++ ++ + GI D E++ AA Sbjct: 205 -RFATQAMHHLLLAHGLALPVLRENDPSSQKGIVANIGRGTPNSDSVEDQRAAQLFEIQH 263 Query: 245 ITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQRVIK 304 W DP+LKG YPE + + G P ++ + +APL DF+G+NYY Sbjct: 264 NAWILDPLLKGAYPEALFE--LWPGTEPLILGGDMQII--SAPL-DFLGINYY------- 311 Query: 305 NHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEKLKEQ 364 RT + GA G + V ++ T+ GWE+ P+ L L + Sbjct: 312 --------FRTNVATDGAHG-------FTEVPLEGVERTQMGWEVYPDGLRDLLIGFSHE 356 Query: 365 YGDI-KIYITENGLGDQDPIIEDEILDMPRIKFIEAHLRAIKEAISRGINLKGYYAWSVI 423 Y ++ +YITENG+ D +I+ + D RI F++ HL A+ EAI G++++GY+ WS++ Sbjct: 357 YSNLPPVYITENGMASDDTVIDGRVNDTQRISFLKRHLAAVDEAIKAGVDIRGYFLWSLM 416 Query: 424 DLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVIEER 465 D W GY++++G ++VD+ R K S + IEER Sbjct: 417 DNFEWAFGYERRFGIVHVDYV-TQKRTTKRSAELVSQFIEER 457 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: 673 Number of extensions: 45 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: 464 Length adjustment: 33 Effective length of query: 436 Effective length of database: 431 Effective search space: 187916 Effective search space used: 187916 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