Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate SMc03160 SMc03160 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__Smeli:SMc03160 Length = 458 Score = 385 bits (990), Expect = e-111 Identities = 209/436 (47%), Positives = 265/436 (60%), Gaps = 17/436 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 F++GVAT+++QIEGA++ DGR SIWDAF+ PG + G+ ACDHY R E+D+ L++ Sbjct: 16 FVFGVATASFQIEGASKADGRKASIWDAFSNMPGRVYGRHNGDVACDHYNRLEQDLDLIK 75 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 SLGV AYRFS+AWPRI+PEG G IN KGL FYDRLVD L A GI F TLYHWDLPLAL Sbjct: 76 SLGVEAYRFSIAWPRIVPEGTGPINEKGLDFYDRLVDGLKARGIKAFATLYHWDLPLALM 135 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 GGW +R TA+A+ YA+ V L DR+ AT NEPWCS +LGH G HAPG RN++A Sbjct: 136 GDGGWTARTTAYAYQRYAKTVIARLGDRLDAVATFNEPWCSVWLGHLYGVHAPGERNMDA 195 Query: 188 ALRAAHHLLLGHGLAVEALRAAGAR-RVGIVLNFAPAY-----GEDPEAVDVADRYHNRY 241 AL A H L HGL V A+R+ VGIV+N Y ED A + A +HN Sbjct: 196 ALAALHFTNLAHGLGVAAIRSERPELPVGIVINAHSVYPGSNSAEDKAAAERAFDFHNGV 255 Query: 242 FLDPILGKGYPE---SPFRDPPPVPILSRDLELVARPLDFLGVNYYAPVRVA--PGTGT- 295 F DPI YPE S + P I D+ +A+PLD+ G+NYY P+RV+ P G Sbjct: 256 FFDPIFKGEYPEDFLSALGERMPA-IEDGDMATIAQPLDWWGLNYYTPMRVSADPAKGAE 314 Query: 296 --LPVRYLPPEGPATAMGWEVYPEGLHHLLKRLGREVPWP-LYVTENGAAYPDLWTGEAV 352 V P T +GWEVY L L++ L P Y+TENGA Y ++ Sbjct: 315 YPATVNAKPVSNVKTDIGWEVYAPALGSLVETLNARYRLPDCYITENGACY-NMGVENGT 373 Query: 353 VEDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQR 412 V+D R+ Y+ H+ +G +RGYF WSLMDNFEWA GY RFG+ +VD+ +Q Sbjct: 374 VDDQPRLDYISDHLAVTADLIAKGYPMRGYFAWSLMDNFEWAEGYRMRFGIVHVDYETQV 433 Query: 413 RIPKRSALWYRERIAR 428 R K+S WY++ R Sbjct: 434 RTIKKSGRWYKDLAER 449 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: 631 Number of extensions: 31 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: 431 Length of database: 458 Length adjustment: 32 Effective length of query: 399 Effective length of database: 426 Effective search space: 169974 Effective search space used: 169974 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