Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate 6937232 Sama_1402 Beta-glucosidase (RefSeq)
Query= CAZy::ABI35984.1 (431 letters) >FitnessBrowser__SB2B:6937232 Length = 452 Score = 368 bits (944), Expect = e-106 Identities = 204/435 (46%), Positives = 277/435 (63%), Gaps = 19/435 (4%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 FL+GVAT+++QIEG + R P IWD F PG I DGS G+ ACDH + + +D+ L+ Sbjct: 20 FLFGVATASFQIEGDAEH--RQPCIWDTFCDTPGKIADGSNGQVACDHVKLWRDDVDLIA 77 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 SLGV AYR S++W R+L G +N +G+ FY L+D L GI F+TLYHWDLP LE Sbjct: 78 SLGVDAYRLSISWGRVLHPD-GSVNQRGMDFYINLLDELGRRGINVFVTLYHWDLPQHLE 136 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 ++GGW +R+TA AFA YA VA AL +RV ++TLNEP+CSAFLG+ G HAPG ++ + Sbjct: 137 DKGGWLNRDTAVAFANYAAIVANALGNRVYAYSTLNEPFCSAFLGYEAGIHAPGHKSRQQ 196 Query: 188 ALRAAHHLLLGHGLAV-EALRAAGARRVGIVLNFAPAY-----GEDPEAVDVADRYHNRY 241 AAH+LLL HG+A+ E R A + GIVLNF+PAY D A +A YHN + Sbjct: 197 GRTAAHNLLLAHGMAMTEIRREAPEAKAGIVLNFSPAYPYTSSAGDANAARLAHEYHNTW 256 Query: 242 FLDPILGKGYPESPFR-DPPPVPILS-RDLELVARPLDFLGVNYYA--PVRVAPGTGTLP 297 +L P++ YP+ + +P P++ D+++++ P+D+LG+NYY R G Sbjct: 257 YLMPLMEGRYPDIINQLEPHERPVVEPGDMDIISTPIDYLGINYYTRNVYRAGGPLGFEE 316 Query: 298 VRYLPPEGPATAMGWEVYPEGLHHLLKRLGRE--VPWPLYVTENGAAYPDLWTGEAVVED 355 VR P TAM WE+ P+ LL L +E +P P+Y+TENGAA D V D Sbjct: 317 VRI--DNVPRTAMDWEICPQAFTDLLTGLAQEFNLP-PIYITENGAAEDDA-PFNGTVHD 372 Query: 356 PERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRRIP 415 P R+ YL++H+ A +A E GVD++GYF WSLMDNFEWA GY +RFGL YVD+ +Q+RI Sbjct: 373 PMRLDYLQSHLLAVHQAIERGVDIKGYFAWSLMDNFEWAEGYRKRFGLVYVDYGTQQRIL 432 Query: 416 KRSALWYRERIARAQ 430 K SA Y+ +A Q Sbjct: 433 KSSAKAYQGMLAIRQ 447 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: 552 Number of extensions: 34 Number of successful extensions: 8 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: 452 Length adjustment: 32 Effective length of query: 399 Effective length of database: 420 Effective search space: 167580 Effective search space used: 167580 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