Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate AZOBR_RS26030 AZOBR_RS26030 beta-glucosidase
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__azobra:AZOBR_RS26030 Length = 444 Score = 283 bits (723), Expect = 1e-80 Identities = 167/461 (36%), Positives = 246/461 (53%), Gaps = 24/461 (5%) Query: 11 YRFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYK 70 + FP F WG++T+A QIEGA +E G+G +WD + E R G VA D YHR+ Sbjct: 4 FTFPKDFLWGASTAAYQIEGAIHEDGRGPCVWDTF--TEAGRIQDGSSAAVACDHYHRWA 61 Query: 71 EDIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYHF 130 ED ALMK+ G N++RFSI+W R++P G G VN + FY+ ++D LLA+GI P LYH+ Sbjct: 62 EDTALMKDAGFNAYRFSIAWPRILPSGTGAVNAAGLDFYDRLVDGLLADGIRPMACLYHW 121 Query: 131 DMPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYP 190 D+P ++ GGW+ REVV +A YA + DRVK W NEP V GY H P Sbjct: 122 DLPQPLEDRGGWQGREVVGPFADYARIVAARLADRVKDWMMLNEPNVVATHGYGTGEHAP 181 Query: 191 -NVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAH 249 + + ++ +H +A A+ A A +G ++NL P S P DV AA Sbjct: 182 GHKLGETGILRALHHQNLAQGAALRAL-SAEHSGLTLGTVINLQPCRAESDRPQDVAAAA 240 Query: 250 IADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPR 309 D ++NR LD ++G+ P+ + E + ++ LP D E I+ IDLLGINYY Sbjct: 241 RWDAVWNRVALDGVMRGKIPELMAERMKDF-VLP----GDEEAIR-FPIDLLGINYYS-- 292 Query: 310 RVKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYDILINIKENYGNIEC 369 R+ K +P + + D + W + G+YD+L+ + +YGN Sbjct: 293 RMTMKHETGHPFDVWWGDAHCDRWTA--------MAWPVQPDGLYDLLMEFRRDYGNPAV 344 Query: 370 FISENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTFMDNW 429 F++ENG + G +HD R+ F+R+H+ V RA+ +G NVKGY W+ +DN+ Sbjct: 345 FVAENGAAYDD---VVTPDGQVHDAERVAFLRDHVASVGRALADGCNVKGYLCWSLLDNF 401 Query: 430 SWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAENNGF 470 W R+G+V VD + L RT K S + +A++ F Sbjct: 402 EWAFGLSKRFGIVRVDYDT-LVRTPKDSYRFLSEVAKSGQF 441 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: 683 Number of extensions: 48 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