Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_050750700.1 AMB_RS11280 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_000009985.1:WP_050750700.1 Length = 449 Score = 362 bits (930), Expect = e-104 Identities = 194/431 (45%), Positives = 259/431 (60%), Gaps = 13/431 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 F+WGV+TSA+Q+EGAT+EDGRG SIWD R G + G+ + ACDHY R+ ED+ L++ Sbjct: 15 FVWGVSTSAFQVEGATKEDGRGLSIWDTRCRLQGGVWTGANADVACDHYHRWPEDVGLIK 74 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 LGV AYRFS+AWPR+LP+G+G +N KGL FYDRL+D +L +GITP++ LYHWDLP AL+ Sbjct: 75 DLGVDAYRFSIAWPRLLPKGKGPVNQKGLDFYDRLIDGVLEAGITPWVCLYHWDLPQALD 134 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187 + GGW +R+ A FA+YA A+ DRV FAT NE G+ APG+ + A Sbjct: 135 DLGGWTNRDCAGWFADYAVLAAKRYGDRVKHFATFNEFSVFTMFGYAIDWAAPGVTDRAA 194 Query: 188 ALRAAHHLLLGHGLAVEALR------AAGARRVGIVLNFAPAYGEDPEAVDVADRYHNRY 241 ++A HH+ L HG+ V+ LR + GA ++ E+ A D+ D + N Sbjct: 195 HMKAIHHVNLAHGMGVDVLRDHVKDVSIGAIHNRQIVRPEGGLAENQAAADLLDAHWNGV 254 Query: 242 FLDPILGKGYPESPFRDPPPVPILSRDLELVARPLDFLGVNYYAPV--RVAPGTGTLPVR 299 F DP YPE RD P + + DL + RP D++G+N+Y P+ + P T Sbjct: 255 FCDPQHLGHYPEIMARDVEPY-VQAGDLARICRPTDWMGLNHYGPIYAKADPATTWGYGW 313 Query: 300 YLPPEGP-ATAMGWEVYPEGLHHLLKRLGREVPWPLYVTEN---GAAYPDLWTGEAVVED 355 PPE +GW ++PE L L R P+YVTEN G A D VV+D Sbjct: 314 GAPPESANHPEVGWPIFPEVFKDELLTLTRRYGLPVYVTENGCGGGAGSDTPDENGVVDD 373 Query: 356 PERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRRIP 415 R+AY + +A L A EG D+RGYFVW+L+DNFEW GY RFGLY+VDF SQ+R Sbjct: 374 THRLAYFREYQQAMLDAVAEGADVRGYFVWALLDNFEWGSGYGPRFGLYHVDFDSQKRTL 433 Query: 416 KRSALWYRERI 426 K S WYR+ I Sbjct: 434 KNSGKWYRDMI 444 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: 661 Number of extensions: 27 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: 449 Length adjustment: 32 Effective length of query: 399 Effective length of database: 417 Effective search space: 166383 Effective search space used: 166383 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