Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate N515DRAFT_4211 N515DRAFT_4211 beta-glucosidase
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_4211 Length = 450 Score = 312 bits (799), Expect = 2e-89 Identities = 177/467 (37%), Positives = 256/467 (54%), Gaps = 32/467 (6%) Query: 10 TYRFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRY 69 +YRFP GF WG+ATSA QIEG+ G G +IW+ + P G ++A D Y RY Sbjct: 4 SYRFPEGFLWGAATSAYQIEGSPLADGAGPSIWER-FAHTPGMMVGGDTGDIACDHYRRY 62 Query: 70 KEDIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYH 129 K+D+ LMK +G + +RFSI+W+R++P+G G VN + + FY ++DELL NGI P L+H Sbjct: 63 KDDVQLMKALGLHGYRFSIAWARVLPEGTGRVNEKGLDFYKRLVDELLENGIAPNATLFH 122 Query: 130 FDMPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHY 189 +DMP A+ GGW NR+ +A YA + F+ RV+ W T NEP V +GGYL+ Sbjct: 123 WDMPAALDDRGGWLNRDSAHWFAEYAEVMFKALDGRVQRWATLNEPWVVTDGGYLHGALA 182 Query: 190 PNVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAH 249 P A A++ M A + A+R A +IG++ N+ P YP SQ D+ A Sbjct: 183 PGHRSKYEAPIAAHNLMRASGAGIQAYR--AHGKHEIGVVFNIEPKYPHSQSADDLAATR 240 Query: 250 IADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPR 309 A N F DPA+ G YP +L E+ E P A+D +L ++ +D +GINYY Sbjct: 241 RAHAYMNEQFADPALLGSYPPELKEIFGE--AWPDFPADDFKLTRQK-VDFVGINYYTRA 297 Query: 310 RVKAKENMPNPDAPFLPERFFDYYAMPGRKMN---PYRGWEIYEKGIYDILINIKENYGN 366 VK N + A P R+ N GWE++E+G+ D L K+ YG+ Sbjct: 298 VVKHDPNQ------------YPLKASPVRQANKTYTETGWEVFEQGLTDTLTWFKDRYGD 345 Query: 367 IECFISENGMGVEGEERFRD----ESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHL 422 I +I+ENG F D E ++ D R ++R+HL+ +H+AIE GVN+KGY+ Sbjct: 346 IPLYITENG------SAFYDPPVAEGEVLDDPLRTGYLRKHLRALHKAIEAGVNLKGYYA 399 Query: 423 WTFMDNWSWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAENNG 469 W+ +DN W+ + R+GL VD KRT K + + + E+NG Sbjct: 400 WSLLDNLEWSLGFSKRFGLYHVDFAT-QKRTPKATAKLYARVIESNG 445 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: 748 Number of extensions: 42 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: 450 Length adjustment: 33 Effective length of query: 437 Effective length of database: 417 Effective search space: 182229 Effective search space used: 182229 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