Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_007665535.1 BN137_RS16150 alpha-glucosidase
Query= uniprot:H3K096 (538 letters) >NCBI__GCF_000319285.1:WP_007665535.1 Length = 558 Score = 338 bits (868), Expect = 2e-97 Identities = 199/524 (37%), Positives = 286/524 (54%), Gaps = 52/524 (9%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WW+ YQIYPRSF DS GDG+GDLNGI +KLDY+ L +D IW+ P + SP D GYD Sbjct: 12 WWKEATAYQIYPRSFKDSNGDGIGDLNGIIDKLDYLKDLGIDLIWICPMYPSPNDDNGYD 71 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 +SDY+ + FGT+ DF LLE H G+++++D V++HTSD+HPWF ESR +R NPK D Sbjct: 72 ISDYQGIMAEFGTMADFDRLLEGVHQRGMRLILDLVVNHTSDEHPWFLESRASRDNPKRD 131 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 W++W D K +G PNNW SIF GSAW D+ QY++H F + QPD+N+ + E R A D Sbjct: 132 WYIWRDGK-NGAEPNNWESIFSGSAWKHDAATGQYFMHLFSSRQPDLNWENHEMRAAVYD 190 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 MR+WLD G+DGFR+D + + L D P P+ PY V L+ Sbjct: 191 MMRWWLDKGIDGFRIDAIAHMKKEPTLSDVP-----------NPDKLPYA-PSMVAHLNY 238 Query: 247 PENLDFLKDL-RALMDEYPGTTTVGEIG--DDNPLERMAEYTAGGDKLHMAYTFDLLNM- 302 LD++ D+ R + D Y TVGE+ D + E G +L+M + F+ + + Sbjct: 239 DGLLDYVDDICRNVFDHY-DIVTVGEMNGLDADHAEEWVGENRG--RLNMVFQFEHVRLW 295 Query: 303 -PHSA-----SYLREVIERFQR-LAGDAWPCWATSNHDVVRSATRWGADEDPH--AYPKV 353 P + + LR++ +Q+ L G W NHDV R +RWG D + H Sbjct: 296 EPQAGLRPTPAVLRKIFTAWQQALEGKGWNALYVENHDVTRIVSRWG-DTERHWRESATC 354 Query: 354 MLAVLFSLRGSVCLYQGEELGLPEADVPFERIQD-----PYGK--------------VLW 394 + A+ F ++G+ +YQG+E+G+ + F ++D + K V + Sbjct: 355 IAAMYFLMQGTPFIYQGQEIGM--TNTRFASLEDFDDVSAHNKARDLREQGMSEAEIVAF 412 Query: 395 PEFKGRDGCRTPMPWTDGEQGGFSPVEPWLPMEARHLELAVSRQQDDPNATLNTVRALLA 454 GRD RTPM W GFS EPWL + + + V QQ DP++ LN R ++ Sbjct: 413 LTRTGRDNSRTPMQWDASPYAGFSTHEPWLKVNPNYEMINVESQQHDPHSVLNFYRQMIH 472 Query: 455 FRRSHPALFDGDL-SLVDVGDDLLGFTRQKGDETLLCVFNLTGQ 497 R+ PAL G SL+D + + + R GDE L+ + NL+G+ Sbjct: 473 LRKREPALIYGRYESLLDDHEQIYAYGRVLGDERLVVLCNLSGK 516 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: 898 Number of extensions: 53 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 538 Length of database: 558 Length adjustment: 36 Effective length of query: 502 Effective length of database: 522 Effective search space: 262044 Effective search space used: 262044 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: 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