Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate N515DRAFT_4211 N515DRAFT_4211 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__Dyella79:N515DRAFT_4211 Length = 450 Score = 379 bits (974), Expect = e-110 Identities = 202/431 (46%), Positives = 267/431 (61%), Gaps = 16/431 (3%) Query: 6 EKFLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIAL 65 E FLWG ATSAYQIEG+ DG GPSIW+ FA PG + G TG+ ACDHYRRY++D+ L Sbjct: 9 EGFLWGAATSAYQIEGSPLADGAGPSIWERFAHTPGMMVGGDTGDIACDHYRRYKDDVQL 68 Query: 66 MQSLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLA 125 M++LG+ YRFS+AW R+LPEG GR+N KGL FY RLVD LL +GI P TL+HWD+P A Sbjct: 69 MKALGLHGYRFSIAWARVLPEGTGRVNEKGLDFYKRLVDELLENGIAPNATLFHWDMPAA 128 Query: 126 LEERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNL 185 L++RGGW +R++A FAEYAE + +AL RV +ATLNEPW G+ G APG R+ Sbjct: 129 LDDRGGWLNRDSAHWFAEYAEVMFKALDGRVQRWATLNEPWVVTDGGYLHGALAPGHRSK 188 Query: 186 EAALRAAHHLLLGHGLAVEALRAAGARRVGIVLNFAPAYGEDPEAVDV-----ADRYHNR 240 A AAH+L+ G ++A RA G +G+V N P Y A D+ A Y N Sbjct: 189 YEAPIAAHNLMRASGAGIQAYRAHGKHEIGVVFNIEPKYPHSQSADDLAATRRAHAYMNE 248 Query: 241 YFLDPILGKGYP---ESPFRDPPPVPILSRDLELVARPLDFLGVNYYAPVRVAPGTGTLP 297 F DP L YP + F + P + D +L + +DF+G+NYY V P Sbjct: 249 QFADPALLGSYPPELKEIFGEAWP-DFPADDFKLTRQKVDFVGINYYTRAVVKHDPNQYP 307 Query: 298 VRYLP---PEGPATAMGWEVYPEGLHHLLKRL-GREVPWPLYVTENGAAY--PDLWTGEA 351 ++ P T GWEV+ +GL L R PLY+TENG+A+ P + GE Sbjct: 308 LKASPVRQANKTYTETGWEVFEQGLTDTLTWFKDRYGDIPLYITENGSAFYDPPVAEGE- 366 Query: 352 VVEDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQ 411 V++DP R YL H+ A +A E GV+L+GY+ WSL+DN EW+ G+++RFGLY+VDF +Q Sbjct: 367 VLDDPLRTGYLRKHLRALHKAIEAGVNLKGYYAWSLLDNLEWSLGFSKRFGLYHVDFATQ 426 Query: 412 RRIPKRSALWY 422 +R PK +A Y Sbjct: 427 KRTPKATAKLY 437 Lambda K H 0.322 0.140 0.453 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: 677 Number of extensions: 30 Number of successful extensions: 6 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: 431 Length of database: 450 Length adjustment: 32 Effective length of query: 399 Effective length of database: 418 Effective search space: 166782 Effective search space used: 166782 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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