Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate N515DRAFT_4211 N515DRAFT_4211 beta-glucosidase
Query= CAZy::AAK78365.1 (469 letters) >FitnessBrowser__Dyella79:N515DRAFT_4211 Length = 450 Score = 331 bits (849), Expect = 3e-95 Identities = 182/467 (38%), Positives = 256/467 (54%), Gaps = 29/467 (6%) Query: 2 KFPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKED 61 +FP+ F GAA+++YQ+EG+ DG G S W+ F PG G GD+A DHY RYK+D Sbjct: 6 RFPEGFLWGAATSAYQIEGSPLADGAGPSIWERFAHTPGMMVGGDTGDIACDHYRRYKDD 65 Query: 62 VKLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDM 121 V+LM +GL YRFS++W R++P+G G +N+KG++FY L+DE L+ GI P TL+HWDM Sbjct: 66 VQLMKALGLHGYRFSIAWARVLPEGTGRVNEKGLDFYKRLVDELLENGIAPNATLFHWDM 125 Query: 122 PEVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGI 181 P L+ GGW N+ + F +YA+ F+A RV+RW T NE V GYL GA PG Sbjct: 126 PAALDDRGGWLNRDSAHWFAEYAEVMFKALDGRVQRWATLNEPWVVTDGGYLHGALAPGH 185 Query: 182 TGDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHAN 241 + A HN+ A + Y+ ++ EIG+ P + ++ AA A+ Sbjct: 186 RSKYEAPI-AAHNLMRASGAGIQAYRAHGKH-EIGVVFNIEPKYPHSQSADDLAATRRAH 243 Query: 242 QYEITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQR 301 Y + DP L G YP + K+ F W D + + DF+G+NYY R Sbjct: 244 AYMNEQFADPALLGSYPPEL-----KEIFGEAWPDFPADDFKLTRQKVDFVGINYY--TR 296 Query: 302 VIKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEKL 361 + HD + P AS V+ +KTYT+ GWE+ + L L Sbjct: 297 AVVKHDPNQ-----------YPLKAS------PVRQANKTYTETGWEVFEQGLTDTLTWF 339 Query: 362 KEQYGDIKIYITENGLGDQD-PIIEDEILDMP-RIKFIEAHLRAIKEAISRGINLKGYYA 419 K++YGDI +YITENG D P+ E E+LD P R ++ HLRA+ +AI G+NLKGYYA Sbjct: 340 KDRYGDIPLYITENGSAFYDPPVAEGEVLDDPLRTGYLRKHLRALHKAIEAGVNLKGYYA 399 Query: 420 WSVIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVIEERG 466 WS++D L W G+ K++G +VD R K + Y +VIE G Sbjct: 400 WSLLDNLEWSLGFSKRFGLYHVDFA-TQKRTPKATAKLYARVIESNG 445 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: 767 Number of extensions: 38 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: 450 Length adjustment: 33 Effective length of query: 436 Effective length of database: 417 Effective search space: 181812 Effective search space used: 181812 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