Align ginsenoside β-glucosidase (Sala_1019) (EC 3.2.1.21) (characterized)
to candidate N515DRAFT_4211 N515DRAFT_4211 beta-glucosidase
Query= CAZy::ABF52736.1 (448 letters) >FitnessBrowser__Dyella79:N515DRAFT_4211 Length = 450 Score = 659 bits (1700), Expect = 0.0 Identities = 308/443 (69%), Positives = 358/443 (80%), Gaps = 2/443 (0%) Query: 6 FPDDFLWGAATAAYQIEGSPLADGAGPSIWQRFSHDPRLMAAKGDTGDIACDHYNRMPAD 65 FP+ FLWGAAT+AYQIEGSPLADGAGPSIW+RF+H P +M GDTGDIACDHY R D Sbjct: 7 FPEGFLWGAATSAYQIEGSPLADGAGPSIWERFAHTPGMMVG-GDTGDIACDHYRRYKDD 65 Query: 66 VALMKELGLQAYRFSVNWGRILPEGTGRVNEPGLDFYERLVDELLRHGIEPLLTLHHWDL 125 V LMK LGL YRFS+ W R+LPEGTGRVNE GLDFY+RLVDELL +GI P TL HWD+ Sbjct: 66 VQLMKALGLHGYRFSIAWARVLPEGTGRVNEKGLDFYKRLVDELLENGIAPNATLFHWDM 125 Query: 126 PAALDDRGGWLNRDSAGWFADYAAIMYRRLDGRVKKWVTLNEPWVITDGGYLHGALAPGH 185 PAALDDRGGWLNRDSA WFA+YA +M++ LDGRV++W TLNEPWV+TDGGYLHGALAPGH Sbjct: 126 PAALDDRGGWLNRDSAHWFAEYAEVMFKALDGRVQRWATLNEPWVVTDGGYLHGALAPGH 185 Query: 186 RNMFEAPIASHNLMRAHGAAVQAYRSEGAHEIGLVVNIEPKYPASDGIEDVAAAARAHAY 245 R+ +EAPIA+HNLMRA GA +QAYR+ G HEIG+V NIEPKYP S +D+AA RAHAY Sbjct: 186 RSKYEAPIAAHNLMRASGAGIQAYRAHGKHEIGVVFNIEPKYPHSQSADDLAATRRAHAY 245 Query: 246 MNRQYLDPALKGSYPAELAEIFGEAWPQWPAEDMRSICQPVDFIGINYYTRNVVQADPNQ 305 MN Q+ DPAL GSYP EL EIFGEAWP +PA+D + Q VDF+GINYYTR VV+ DPNQ Sbjct: 246 MNEQFADPALLGSYPPELKEIFGEAWPDFPADDFKLTRQKVDFVGINYYTRAVVKHDPNQ 305 Query: 306 WPLRASPVRQ-NATHTTTDWEVCPPALTDMLIWFRDTYGNIPVYITENGAAFYDPPTAGP 364 +PL+ASPVRQ N T+T T WEV LTD L WF+D YG+IP+YITENG+AFYDPP A Sbjct: 306 YPLKASPVRQANKTYTETGWEVFEQGLTDTLTWFKDRYGDIPLYITENGSAFYDPPVAEG 365 Query: 365 AGIDDPLRCDYLRTHISAIGDAIRQGVDVRGYMAWSLLDNLEWSLGYSKRFGIVHVDYET 424 +DDPLR YLR H+ A+ AI GV+++GY AWSLLDNLEWSLG+SKRFG+ HVD+ T Sbjct: 366 EVLDDPLRTGYLRKHLRALHKAIEAGVNLKGYYAWSLLDNLEWSLGFSKRFGLYHVDFAT 425 Query: 425 QVRTPKRSARFYSSVIRSNGGNL 447 Q RTPK +A+ Y+ VI SNG L Sbjct: 426 QKRTPKATAKLYARVIESNGAVL 448 Lambda K H 0.320 0.138 0.449 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: 850 Number of extensions: 28 Number of successful extensions: 3 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: 448 Length of database: 450 Length adjustment: 33 Effective length of query: 415 Effective length of database: 417 Effective search space: 173055 Effective search space used: 173055 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 (21.8 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