Align amb0219 (EC 3.2.1.21) (characterized)
to candidate AZOBR_RS16895 AZOBR_RS16895 beta-glucosidase
Query= CAZy::BAE49023.1 (453 letters) >FitnessBrowser__azobra:AZOBR_RS16895 Length = 482 Score = 478 bits (1231), Expect = e-139 Identities = 233/453 (51%), Positives = 307/453 (67%), Gaps = 6/453 (1%) Query: 1 MTVAKAAQSAPQGA-RQFPKDFFWGASTAAYQIEGAYDTDGRGMTIWDKFTAD-GKIMDG 58 +T +AA + P FP F WGAST++YQIEGA GRG ++WD F+ GK+ +G Sbjct: 23 LTTRRAAVAQPSEVLAAFPDKFVWGASTSSYQIEGAVTAGGRGPSVWDTFSHSFGKVANG 82 Query: 59 SSAKVACDHYHRYPEDIALMKAAGFNAYRFSLAWPRIIPAGTGAINAKGLDFYDRLVDKI 118 + VACDHY+RY ED+ LM AG NAYRFS+AWPR+ P GTG NA+GLDFYDRL D + Sbjct: 83 DTGDVACDHYNRYAEDVDLMAKAGMNAYRFSVAWPRVQPTGTGPANAEGLDFYDRLTDAL 142 Query: 119 LEAGIKPMACLYHWDLPQPLEDKGGWQGRDIVGPFAEYARIATKRLGDRVKDWYMLNEPN 178 L GI P CLYHWDLPQ L+D+GGW RDI G F +YA++ R+GDR K W MLNEP+ Sbjct: 143 LAKGIAPWPCLYHWDLPQALQDRGGWTNRDIAGWFTDYAQLVAARIGDRAKHWTMLNEPS 202 Query: 179 VVAIIGYGIGEHAPGYKLGEDGILKALHHQNLAQGTALRAIRAEHSDA--VLGTVINLQP 236 V AI G+G+G HAPG G+ KA+HHQNLAQG AL+A+RA LGTV++LQP Sbjct: 203 VHAIFGHGLGGHAPG-MTGKGNYFKAIHHQNLAQGMALKALRAAGGAKGWQLGTVLSLQP 261 Query: 237 CRSQDDDPKNRAAAIRWDAVWNRVPLDGVMRGAIPDVLAEKMAHIVKPGDMETIKFPIDM 296 N AA++ WDAVWNR LD ++RG P++L + A +VK GD+E I+ PID Sbjct: 262 VWPVGGLDANYAASLMWDAVWNRACLDPLLRGEYPELLRDGFAPLVKAGDLEAIRQPIDF 321 Query: 297 LGINYYSRMTMKHEEGHPFDVFWGD-AHCDRWTAMAWPVQPDGLYDLLREFKELYGNPAV 355 LGINYYSRM + + F +G T M WPV+PDG+ ++L E K+ YGNP V Sbjct: 322 LGINYYSRMHQQPDPAGLFGTGYGSPPEGTPTTGMGWPVEPDGIAEILIELKQEYGNPPV 381 Query: 356 FIAENGAAYDDVVTPDGQVHDAERVAFIRDHVSEVARAVKDGCNVKGYLVWSLLDNFEWA 415 ++ ENGAAY + P G V D +R++++R H+ +A+++G +++G+ VWSLLDNFEWA Sbjct: 382 YVMENGAAYPEQTGPKGFVQDNDRISYLRRHILAGHQALEEGVDLRGWFVWSLLDNFEWA 441 Query: 416 YGLSKRFGIVRVDYETLKRTPKDSYKWFAEVIR 448 G +RFG++ VD +TL+R PK SY W+A+VIR Sbjct: 442 EGYQRRFGLIEVDRQTLERRPKASYHWYADVIR 474 Lambda K H 0.321 0.139 0.447 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: 790 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: 453 Length of database: 482 Length adjustment: 33 Effective length of query: 420 Effective length of database: 449 Effective search space: 188580 Effective search space used: 188580 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 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