Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate BWI76_RS02960 BWI76_RS02960 glucohydrolase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__Koxy:BWI76_RS02960 Length = 551 Score = 310 bits (795), Expect = 7e-89 Identities = 187/530 (35%), Positives = 276/530 (52%), Gaps = 59/530 (11%) Query: 6 MWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGY 65 +WW+ GVIYQIYP+SF D+ G G GDL G+T +LDY+ L VD IWL+PF+ SP +D GY Sbjct: 6 LWWQNGVIYQIYPKSFQDTTGTGTGDLRGVTSRLDYLQKLGVDAIWLTPFYVSPQVDNGY 65 Query: 66 DVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKA 125 DV++Y +DP +GTL+DF L+ +AH+ G+++++D V++HTS +H WF+E+ N+ +P Sbjct: 66 DVANYTAIDPTYGTLDDFDELVAQAHARGIRIVLDMVLNHTSTEHAWFREA-LNKESPYR 124 Query: 126 DWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQL 185 +++W D +P TPPNNW S FGG+AW + + +QYYLH F Q D+N+ +P R Sbjct: 125 QFYIWRDGEPT-TPPNNWRSKFGGNAWQWHAESEQYYLHLFAVEQADLNWENPAVRAELK 183 Query: 186 DNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLS 245 FW D GVDG RLD VN D P G+ + YT Sbjct: 184 KVCEFWADRGVDGLRLDVVNLISKDQTF---PSDTDGDGRRF-------YT--------D 225 Query: 246 RPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTA-GGDKLHMAYTFDLLNMPH 304 P +FL+++ + G TVGE+ L +Y A G +L M + F L + + Sbjct: 226 GPRAHEFLQEMSRDVFTPRGLMTVGEM-SSTTLAHCQQYAALDGGELSMTFNFHHLKVDY 284 Query: 305 SAS-----------YLREVIERFQR-LAGDAWPCWATSNHDVVRSATRWGADEDPHAYP- 351 L+ + +Q+ + AW NHD R +R+G DE + P Sbjct: 285 PGGEKWTLARPDFVALKSLFRHWQQGMHNRAWNALFWCNHDQPRIVSRFG-DEGEYRVPA 343 Query: 352 -KVMLAVLFSLRGSVCLYQGEELGLPEADVPFERI-------------------QDPYGK 391 K++ VL ++G+ +YQGEE+G+ + F RI QDP Sbjct: 344 AKMLAMVLHGMQGTPYIYQGEEIGM--TNPHFMRITDYRDVESHNMFIERAAQGQDPDEL 401 Query: 392 VLWPEFKGRDGCRTPMPWTDGEQGGFSPVEPWLPMEARHLELAVSRQQDDPNATLNTVRA 451 + K RD RTPM W + + GGFS EPW+ + + E+ Q DP + T + Sbjct: 402 LAILASKSRDNSRTPMQWNNADHGGFSAGEPWIALCDNYREINAEAAQADPESVFYTYQQ 461 Query: 452 LLAFRRSHPALFDGDL-SLVDVGDDLLGFTRQKGDETLLCVFNLTGQEQQ 500 L+A R+S P L GD L+ L + RQ +TL+ V NL+ + Q+ Sbjct: 462 LIALRKSAPVLTWGDYQDLLPEHPSLWCYRRQWQGQTLVVVANLSREFQR 511 Lambda K H 0.320 0.138 0.443 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: 965 Number of extensions: 57 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: 538 Length of database: 551 Length adjustment: 35 Effective length of query: 503 Effective length of database: 516 Effective search space: 259548 Effective search space used: 259548 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: 52 (24.6 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