Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_040660580.1 ON16_RS06835 alpha-amylase
Query= BRENDA::P21517 (604 letters) >NCBI__GCF_000307265.1:WP_040660580.1 Length = 623 Score = 218 bits (554), Expect = 8e-61 Identities = 176/569 (30%), Positives = 249/569 (43%), Gaps = 94/569 (16%) Query: 82 KLLWHDRQRW-------------FTPQGFSRMPPARLEQFAVDVPDIGPQWAADQIFYQI 128 +LLW+ + W + GF PA + D P+W + I YQI Sbjct: 82 ELLWYHFRFWREDGSGCDLDGSGYRSDGF----PADWQLTVYDDSHPTPRWFGEGITYQI 137 Query: 129 FPDRFAR-SLPREAEQDHVYYHHAAGQEIILRDWDEPVTAQAGGSTFYGGDLDGISEKLP 187 FPDRF R S+P A H ++ DW T F+GG L GI+ +L Sbjct: 138 FPDRFCRLSVPDPAGMVGDRMVHENWEDT--PDWRPDETGAVRNRDFFGGSLQGIASRLA 195 Query: 188 YLKKLGVTALYLNPVFKAPSVHKYDTEDYRHVDPQFGGDGALLRLRHNTQQLGMRLVLDG 247 L++L VT LYL PVF++ S H+Y+T DY +DP G + L + G+R++LDG Sbjct: 196 ELEQLHVTTLYLCPVFESASNHRYNTADYTKIDPMLGTEEDFRFLCAQAETHGIRVILDG 255 Query: 248 VFNHSGDSHAWFDRHN-RGTGGACHNPESPWRDWYSF---SDDGTALDWLGYASLPKLDY 303 VFNH+G + +F+ T GA + +SP+ +WY+F DD A W G +LP ++ Sbjct: 256 VFNHTGSNSVYFNAEGFYPTVGAAQSQDSPYFNWYTFHPWPDDYEA--WWGIRTLPAVNE 313 Query: 304 QSESLVNEIYRGEDSIVRHWLKAPWNMDGWRLDVVHMLGEAGGARNNMQHVAGITEAAKE 363 S S I GE+S++R WL+A GWRLDV L + + +A + A Sbjct: 314 SSASYGAFIADGENSVIRRWLRA--GASGWRLDVADELPD--------EFLARLRSAVDT 363 Query: 364 TQPEAYIVGEHFGDA---------RQWLQADVEDAAMNYRGFTFPLWGFLANTDISYDPQ 414 +P + ++GE + D R++L MNY T L +L Q Sbjct: 364 AKPGSILLGEVWEDGSNKIAYSKRRKYLLGSETHGLMNYPFRTAAL-AYL---------Q 413 Query: 415 QIDAQTCMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFKTLLG----------------- 457 DA + + M+ R N L +HDTAR T+LG Sbjct: 414 GGDACSFVQAMETIRENYPPPAFYSAMNFLGTHDTARILTVLGAPTVPESKAERADFLLS 473 Query: 458 -----RDIARLPLAVVWLFTWPGVPCIYYGDEVGLDGKNDPFCRKPFPWQVEKQDTALFA 512 +A L +A L+ +PG P IYYGDE G++G DPF R +PW K+D AL A Sbjct: 474 PNQRTEGLALLRVAAALLYAFPGSPMIYYGDEAGMEGWEDPFNRGTYPW--GKEDQALRA 531 Query: 513 LYQRMIALRKKSQALRHGGCQVLYAEDNVVVFVRVLNQQRVLVAINRGEACEVVLPASPF 572 Y R+ LR +LR G + LYA + + F R + N G P Sbjct: 532 FYVRLGQLRHSRVSLRRGDIRYLYAAGSGLAFSRSWEDETTTAVFNAGR--------EPL 583 Query: 573 LNAVQWQCKEGHGQLT-------DGILAL 594 V W LT DG+L L Sbjct: 584 TMEVPWVFSAARDFLTGRAFSPVDGVLKL 612 Lambda K H 0.322 0.138 0.451 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: 1199 Number of extensions: 79 Number of successful extensions: 7 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: 604 Length of database: 623 Length adjustment: 37 Effective length of query: 567 Effective length of database: 586 Effective search space: 332262 Effective search space used: 332262 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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