Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_011841073.1 RSPH17029_RS07690 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_000015985.1:WP_011841073.1 Length = 440 Score = 389 bits (999), Expect = e-112 Identities = 209/422 (49%), Positives = 270/422 (63%), Gaps = 14/422 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 FL+GVATSAYQIEG G G + WD FA PG + G G ACDHY R+EED+ L++ Sbjct: 12 FLFGVATSAYQIEGHGA-GGAGRTHWDDFAATPGNVAHGEDGRRACDHYHRWEEDLDLVR 70 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 G +YRFS +W R++PEGRG +N +GL FYDRLVD +LA G+ P LTLYHW+LP AL+ Sbjct: 71 DAGFDSYRFSASWARVMPEGRGTVNAEGLDFYDRLVDGMLARGLKPALTLYHWELPSALQ 130 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 + GGWR+R+ A FA++AE + + DRV A +NEPWC A+L H+ G HAPGLR++ A Sbjct: 131 DLGGWRNRDIAGWFADFAEVLLGRIGDRVWSTAPVNEPWCVAWLSHFLGHHAPGLRDIRA 190 Query: 188 ALRAAHHLLLGHGLAVEALRAAGARRVGIVLNFAPAYGED-PEAVDVADRYH----NRYF 242 A RA HH+LL HG AVEA R G +G V NF A D EA A R H NR+F Sbjct: 191 AARAMHHVLLAHGAAVEAARGLGVGNLGAVCNFEHAIPADGSEASAAATRRHDALINRWF 250 Query: 243 LDPILGKGYPESPFRD-PPPVPI-LSRDLELVARPLDFLGVNYYAPVRVAPGTGTLP-VR 299 + + + YPE P +P +D + +A+PLD+ G+NYY VA G P + Sbjct: 251 VSALFNRQYPEEALDGIAPHLPSGWEKDRDRIAQPLDWFGINYYTRKLVAAAPGPWPGLS 310 Query: 300 YLPPEGPATAMGWEVYPEGLHHLLKRL--GREVPWPLYVTENGAAYPD-LWTGEAVVEDP 356 + P T +GWE++PEGL +L R+ G PL VTENG A D + GE V+DP Sbjct: 311 EVEGPLPRTRIGWEIHPEGLSDILLRIHEGYTRGLPLIVTENGMAAADRVQAGE--VQDP 368 Query: 357 ERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRRIPK 416 +R+AYLE H+ A A +GV +RGY VWSL+DNFEWAFGY +RFGL +VDF + +R PK Sbjct: 369 DRIAYLEGHLAAVRTALAQGVPVRGYHVWSLLDNFEWAFGYDQRFGLVHVDFQNLQRTPK 428 Query: 417 RS 418 S Sbjct: 429 AS 430 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: 660 Number of extensions: 36 Number of successful extensions: 7 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: 440 Length adjustment: 32 Effective length of query: 399 Effective length of database: 408 Effective search space: 162792 Effective search space used: 162792 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 24 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