Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_057507037.1 ABB28_RS02135 alpha-glucosidase
Query= uniprot:H3K096 (538 letters) >NCBI__GCF_001431535.1:WP_057507037.1 Length = 538 Score = 647 bits (1668), Expect = 0.0 Identities = 300/529 (56%), Positives = 382/529 (72%), Gaps = 4/529 (0%) Query: 4 NMMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDF 63 N WWRG VIYQIYPRSFLD+ GDGVGDL GI ++LDY+A+L VD IW+SPFF SPM DF Sbjct: 3 NTPWWRGAVIYQIYPRSFLDANGDGVGDLPGIIDRLDYIAALGVDAIWISPFFRSPMADF 62 Query: 64 GYDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNP 123 GYD++DYRDVDP+FG L+DF LL KAH+LGLKVMIDQV+SHTS +H WF+ESRQ+RTNP Sbjct: 63 GYDIADYRDVDPLFGNLDDFDRLLAKAHALGLKVMIDQVLSHTSIEHDWFRESRQDRTNP 122 Query: 124 KADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQA 183 KADW+VWADP+ DGT PNNW+S+FGG AW ++ RR+QY+LHNFL QPD+NFH+P ++A Sbjct: 123 KADWYVWADPREDGTAPNNWMSLFGGVAWQWEPRREQYFLHNFLADQPDLNFHNPAVQKA 182 Query: 184 QLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYD 243 LDN+RFWLD GVDGFRLD +NF FHD +LRDNPP P + G NPY +Q H ++ Sbjct: 183 TLDNVRFWLDRGVDGFRLDAINFCFHDRQLRDNPPKPADKRVGRGFSPDNPYAYQYHYFN 242 Query: 244 LSRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMP 303 ++PENL FL++LRAL+D+YPG ++GEI ++ L AEYT +LHM Y+F+LL Sbjct: 243 NTQPENLPFLEELRALLDQYPGAVSLGEISSEDSLATTAEYTT-AKRLHMGYSFELLVDD 301 Query: 304 HSASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRG 363 +SA+Y+R+ + R + + WPCWA SNHDV R+ TRWG ++++A+L SLRG Sbjct: 302 YSAAYIRDTVSRLETAMIEGWPCWAISNHDVERAVTRWGGHPADPRLARMLVAMLCSLRG 361 Query: 364 SVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVEPW 423 S+CLYQGEELGL EADVPFE +QDPYG WP FKGRDGCRTP+PW D GF+ EPW Sbjct: 362 SICLYQGEELGLGEADVPFEALQDPYGITFWPNFKGRDGCRTPLPWIDAPLAGFTTGEPW 421 Query: 424 LPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQK 483 LP+ A H AV+ Q+ P++ L R LA+RR+ P L GD+ +D + +L F R Sbjct: 422 LPIPADHQSRAVAVQEAQPDSVLLAFRRFLAWRRTQPVLLHGDIRFLDSAEPVLLFERTL 481 Query: 484 GDETLLCVFNLTGQEQQTTLPVEV--ASDLPVAHFTATRDGSTLTLPAY 530 GDE +L FNL+ + LP A D+P + DG+ L LPA+ Sbjct: 482 GDEVMLLAFNLSSLPGRQLLPEGAWQAMDVP-GPDAGSVDGTELALPAH 529 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: 1041 Number of extensions: 54 Number of successful extensions: 2 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: 538 Length adjustment: 35 Effective length of query: 503 Effective length of database: 503 Effective search space: 253009 Effective search space used: 253009 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 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