Align β-glucosidase (Bgl1A;PB42H12) (Bgl1A) (EC 3.2.1.21) (characterized)
to candidate 6937232 Sama_1402 Beta-glucosidase (RefSeq)
Query= CAZy::ADD96762.1 (442 letters) >FitnessBrowser__SB2B:6937232 Length = 452 Score = 548 bits (1411), Expect = e-160 Identities = 263/443 (59%), Positives = 323/443 (72%), Gaps = 1/443 (0%) Query: 1 MTKISLPTCSPLLTKEFIYGVATASFQIEGGSAHRLPCIWDTFCDTPGKIADNSNGHVAC 60 ++ +LP S ++ K+F++GVATASFQIEG + HR PCIWDTFCDTPGKIAD SNG VAC Sbjct: 4 LSHFTLPGDSVMMQKDFLFGVATASFQIEGDAEHRQPCIWDTFCDTPGKIADGSNGQVAC 63 Query: 61 DHYNNWKQDIDLIESLGVDAYRLSISWPRVITKSGELNPEGVKFYTDILDELKKRNIKAF 120 DH W+ D+DLI SLGVDAYRLSISW RV+ G +N G+ FY ++LDEL +R I F Sbjct: 64 DHVKLWRDDVDLIASLGVDAYRLSISWGRVLHPDGSVNQRGMDFYINLLDELGRRGINVF 123 Query: 121 VTLYHWDLPQHLEDEGGWLNRETAYAFAHYVDLITLAFGDRVHSYATLNEPFCSAFLGYE 180 VTLYHWDLPQHLED+GGWLNR+TA AFA+Y ++ A G+RV++Y+TLNEPFCSAFLGYE Sbjct: 124 VTLYHWDLPQHLEDKGGWLNRDTAVAFANYAAIVANALGNRVYAYSTLNEPFCSAFLGYE 183 Query: 181 IGIHAPGKVGKQYGRKAAHHLLLAHGLAMTVLKQNSPTTLNGIVLNFTPCYSISEDADDI 240 GIHAPG +Q GR AAH+LLLAHG+AMT +++ +P GIVLNF+P Y + A D Sbjct: 184 AGIHAPGHKSRQQGRTAAHNLLLAHGMAMTEIRREAPEAKAGIVLNFSPAYPYTSSAGDA 243 Query: 241 AATAFADDYLNQWYMKPIMDGTYPAIIEQLPSAHLPDIHDGDMAIISQSIDYLGINFYTR 300 A A +Y N WY+ P+M+G YP II QL P + GDM IIS IDYLGIN+YTR Sbjct: 244 NAARLAHEYHNTWYLMPLMEGRYPDIINQLEPHERPVVEPGDMDIISTPIDYLGINYYTR 303 Query: 301 QFYKAHPTEIYEPIE-PTGPLTDMGWEIYPKSFTELLVTLNNTYTLPPIFITENGAAMPD 359 Y+A +E + P T M WEI P++FT+LL L + LPPI+ITENGAA D Sbjct: 304 NVYRAGGPLGFEEVRIDNVPRTAMDWEICPQAFTDLLTGLAQEFNLPPIYITENGAAEDD 363 Query: 360 SYNNGEINDVDRLDYYNSHLNAVHNATEQGVRIDGYFAWSLMDNFEWAEGYLKRFGIVYV 419 + NG ++D RLDY SHL AVH A E+GV I GYFAWSLMDNFEWAEGY KRFG+VYV Sbjct: 364 APFNGTVHDPMRLDYLQSHLLAVHQAIERGVDIKGYFAWSLMDNFEWAEGYRKRFGLVYV 423 Query: 420 DYSTQQRTIKNSGLAYKALISNR 442 DY TQQR +K+S AY+ +++ R Sbjct: 424 DYGTQQRILKSSAKAYQGMLAIR 446 Lambda K H 0.320 0.137 0.431 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: 663 Number of extensions: 26 Number of successful extensions: 2 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: 442 Length of database: 452 Length adjustment: 33 Effective length of query: 409 Effective length of database: 419 Effective search space: 171371 Effective search space used: 171371 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 (21.8 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