Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_017598012.1 D471_RS0107340 beta-glucosidase
Query= CAZy::ABI35984.1 (431 letters) >NCBI__GCF_000341125.1:WP_017598012.1 Length = 439 Score = 435 bits (1118), Expect = e-126 Identities = 239/434 (55%), Positives = 279/434 (64%), Gaps = 16/434 (3%) Query: 8 FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67 FLWGVA+SA Q+EGA EDGR PSIWD F RRPGA+RDG + ACDHY R+ ED+ L+ Sbjct: 5 FLWGVASSALQVEGALTEDGRTPSIWDDFHRRPGAVRDGHSPAEACDHYHRWAEDVELLG 64 Query: 68 SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127 LGV AYRFSV+WPR++P GRG +N G+AFYDRLVD LL GI P TL+HWDLP+ LE Sbjct: 65 RLGVNAYRFSVSWPRVVPRGRGPVNKSGVAFYDRLVDALLERGIEPVPTLFHWDLPVELE 124 Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPG-LRNLE 186 E GGW +RETA AFAEYA A A AL DRV + TLNEP GH G HAPG + ++ Sbjct: 125 EAGGWSARETAHAFAEYAAATADALGDRVRRWITLNEPVVHMAYGHAFGIHAPGRVLDVP 184 Query: 187 AALRAAHHLLLGHGLAVEALRAAGARRVGIVLNFAPA-----YGEDPEAVDVADRYHNRY 241 L AHH LL HGLA LR+ G + + N++P D A D D HNR Sbjct: 185 DVLAVAHHQLLAHGLAARELRSRGLEAL-LTNNYSPVEPASDSPADRAAADAYDALHNRL 243 Query: 242 FLDPILGKGYPESPFRDPPPVP-ILSRDLELVARPLDFLGVNYYAPVRV-APGTGT-LPV 298 F DP+L YP+ VP DLEL+A +D LGVNYY P R+ AP G+ LP Sbjct: 244 FTDPVLFGAYPDLSAFGAGEVPGAREGDLELIAGSVDGLGVNYYNPSRIAAPAEGSGLPF 303 Query: 299 RYLPPEG-PATAMGWEVYPEGLHHLL----KRLGREVPWPLYVTENGAAYPDLWTGEAVV 353 + G P TA GW V PEGL LL +R G +P PLYVTENG + D T E V Sbjct: 304 DFAEVTGAPTTAFGWPVAPEGLERLLLLLGERYGDALP-PLYVTENGCSQTDAVTPEGRV 362 Query: 354 EDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRR 413 DPER+AYLE HV A RARE G D+RGYFVW+L DNFEWA GY +RFGL YVD +QRR Sbjct: 363 HDPERIAYLEGHVAAVDRARERGADVRGYFVWTLTDNFEWAEGYHQRFGLVYVDHTTQRR 422 Query: 414 IPKRSALWYRERIA 427 +PK S WYR IA Sbjct: 423 VPKDSFDWYRGLIA 436 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: 686 Number of extensions: 36 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: 439 Length adjustment: 32 Effective length of query: 399 Effective length of database: 407 Effective search space: 162393 Effective search space used: 162393 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