Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate GFF770 PGA1_c07840 beta-glucosidase A
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__Phaeo:GFF770 Length = 444 Score = 256 bits (654), Expect = 1e-72 Identities = 160/452 (35%), Positives = 232/452 (51%), Gaps = 24/452 (5%) Query: 13 FPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYKED 72 FP F +G+ATSA QIEG GG G WD + P + + A D YHRY ED Sbjct: 9 FPKDFLFGTATSAYQIEGHGF-GGAGPTHWDS-FAATPGNVVRAEHGQRACDHYHRYAED 66 Query: 73 IALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYHFDM 132 + L G + +RFS SW+R++P+G G NPE + FY+ + D +L G++P V LYH+++ Sbjct: 67 LDLAAAAGFDCYRFSTSWARVMPEGRGAPNPEGLDFYDRLTDAILERGLKPCVTLYHWEL 126 Query: 133 PLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYPNV 192 P A+ +GGW N E+ + + YA + GDR+ + NEP + H P + Sbjct: 127 PQALADLGGWRNAEIANWFGDYAEVIMGRIGDRMYSAAPINEPWCVGWLSHFLGHHAPGL 186 Query: 193 VDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAHIAD 252 D R + +H M+AH A+ A R A+ +G + NL + P A +AA D Sbjct: 187 RDIRATARAMHHVMLAHGTAIQAMR--ALGMSNLGGVFNLEWATPVDDSEAAQQAAARYD 244 Query: 253 LLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPRRVK 312 ++N FL A G YP +E L+ + LP +D I +D G+NYY +++ Sbjct: 245 AIYNGFFLGGAFHGRYPDLALEGLEPH--LPKGWQDDFATITA-PVDWCGLNYYTRKQIA 301 Query: 313 AKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYDILINIKENY-GNIECFI 371 PDA P+ Y + G GWEIY +G+YD L +Y G++ + Sbjct: 302 -------PDAGPWPQ----YAEVDGPLPKTQMGWEIYPQGLYDFLTRTARDYTGDLPLIV 350 Query: 372 SENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTFMDNWSW 431 +ENGM G + D RI F+ +HL V RAI +GV V+GY LW+ +DN+ W Sbjct: 351 TENGMANADVV----TKGKVEDAARITFVDDHLDAVRRAIADGVPVQGYFLWSLLDNYEW 406 Query: 432 TNAYKNRYGLVAVDLENGLKRTIKKSGYWFKS 463 Y+ R+GLV VD E LKRT K S + +S Sbjct: 407 ALGYEKRFGLVHVDFET-LKRTPKASYHALRS 437 Lambda K H 0.321 0.140 0.446 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: 664 Number of extensions: 40 Number of successful extensions: 6 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: 470 Length of database: 444 Length adjustment: 33 Effective length of query: 437 Effective length of database: 411 Effective search space: 179607 Effective search space used: 179607 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