Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate N515DRAFT_3393 N515DRAFT_3393 alpha-glucosidase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__Dyella79:N515DRAFT_3393 Length = 541 Score = 630 bits (1624), Expect = 0.0 Identities = 300/539 (55%), Positives = 375/539 (69%), Gaps = 10/539 (1%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WWRG VIYQIYPRSFLD+ GDGVGDL GI E+LDY+A L VD IW++PFF SPM DFGYD Sbjct: 6 WWRGAVIYQIYPRSFLDTDGDGVGDLPGIVERLDYIAGLGVDAIWIAPFFRSPMADFGYD 65 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 ++DYR VDP+FGT++DF LL KAH+LGLKVMIDQV+SHTSDQH WF+ESR +R NPKAD Sbjct: 66 IADYRAVDPLFGTIDDFDRLLAKAHALGLKVMIDQVLSHTSDQHEWFKESRASRDNPKAD 125 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 W+VWAD + DGTPPNNW+S+FGG AW ++ RR QYYLHNFLTSQPD+NFHHP+ ++A LD Sbjct: 126 WYVWADARDDGTPPNNWMSLFGGVAWQWEPRRGQYYLHNFLTSQPDLNFHHPDVQRAVLD 185 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 N++FWLD GVDG RLD +NF FHD +LRDNPP P+ G NPY +Q H Y+ ++ Sbjct: 186 NVQFWLDKGVDGLRLDAINFCFHDRQLRDNPPKPQAMRVGRGFSPDNPYAFQYHYYNNTQ 245 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPHSA 306 PENL FL++LR L+D YPG +GEI ++ L MAEYT G +LHM Y+F+LL SA Sbjct: 246 PENLAFLEELRGLLDRYPGAAALGEISSEDSLATMAEYTT-GHRLHMGYSFELLTADFSA 304 Query: 307 SYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLF-----SL 361 +Y+R +ER + + WPCWA SNHDV R +RWG + + V LA L SL Sbjct: 305 AYIRGTVERLEAQMTEGWPCWAISNHDVERVLSRWGREARGNGDASVRLANLLTAMVCSL 364 Query: 362 RGSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVE 421 RGSVC+YQGEEL L EA+VP+E +QDPYG WP FKGRDGCRTPMPW + GFS Sbjct: 365 RGSVCVYQGEELALTEAEVPYEALQDPYGITFWPNFKGRDGCRTPMPWDESANAGFSSGA 424 Query: 422 PWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTR 481 PWLP+ A H LAVSRQ+ DP + L+ R + +R++ P L G + +D + +L FTR Sbjct: 425 PWLPVPAGHRALAVSRQELDPASALHGFRGFMQWRQAQPELRWGAIGFLDTPEPVLAFTR 484 Query: 482 QKGDETLLCVFNLTGQEQQTTLPVEVASDLPVAHFTA--TRDGSTLTLPAYQAAFMQVA 538 ET+L FNL LP +A + H A T + L LP + F +++ Sbjct: 485 THAGETVLAAFNLGSAPVAVALP--LAGERIGGHGLAEGTLEDGLLRLPPHGLLFARLS 541 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: 1019 Number of extensions: 56 Number of successful extensions: 3 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: 541 Length adjustment: 35 Effective length of query: 503 Effective length of database: 506 Effective search space: 254518 Effective search space used: 254518 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