Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate AZOBR_RS25735 AZOBR_RS25735 alpha-amylase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__azobra:AZOBR_RS25735 Length = 537 Score = 426 bits (1094), Expect = e-123 Identities = 219/503 (43%), Positives = 306/503 (60%), Gaps = 18/503 (3%) Query: 1 MQDNMMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPM 60 M D WW+ GVIYQ+YPRSF DS GDGVGDL GI +LD++ +L VD +W+SP + SPM Sbjct: 1 MADGFAWWQSGVIYQVYPRSFQDSNGDGVGDLPGILARLDHLQTLGVDALWVSPIYPSPM 60 Query: 61 LDFGYDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNR 120 DFGYDVSDY V P+FGT+EDF+ LL + H G+K+++D V +H+SD+HPWFQ SR +R Sbjct: 61 ADFGYDVSDYTGVHPLFGTMEDFERLLAELHRRGMKLILDFVPNHSSDRHPWFQASRSSR 120 Query: 121 TNPKADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEA 180 +PK DW++W D PDG PPNNWLS FGG AW +D+ QYY H +L QPD+N+ +P Sbjct: 121 DDPKRDWYIWRDAAPDGGPPNNWLSEFGGGAWEWDAATGQYYYHAYLKEQPDLNWRNPAL 180 Query: 181 RQAQLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEA-NPYTWQR 239 R+A LD +R WLD GVDGFR+D ++ DA+ RDNPP P G E +P Sbjct: 181 REAMLDALRVWLDRGVDGFRVDAIHHLIKDAQFRDNPPNP-------GWREGMSPVRRLI 233 Query: 240 HVYDLSRPENLDFLKDLRALMDEY-PGTTTVGEIGDDNPLER-MAEYTAGGDKLHMAYTF 297 ++ + +PE D + +R + D Y P +GE P+++ MA Y A + + F Sbjct: 234 RLHTVDQPEVHDAIAAMRRVADGYGPDRLLIGEA--YLPIDQLMAYYGADLTGFQLPFNF 291 Query: 298 DLLNMPHSASYLREVIERFQ-RLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLA 356 LL+ P A L +I ++ L WP W NHD R A+R G + +V Sbjct: 292 HLLSTPWEAKALAALIRTYEAALPPGGWPNWVLGNHDRSRVASRLGRGQ-----ARVAAM 346 Query: 357 VLFSLRGSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGG 416 +L +LRG+ LYQG+E+G+ + +P +R+QDP+ K + GRD RTP+PW G +GG Sbjct: 347 LLLTLRGTPTLYQGDEIGMTDVAIPPDRVQDPWEKNIPGLGLGRDPVRTPIPWDGGPRGG 406 Query: 417 FSPVEPWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDL 476 F+ EPWLP+ H + V+ Q DP++ L RALL+ RR+ PAL G V +D+ Sbjct: 407 FTTGEPWLPLGPDHERVNVAAQAADPSSMLALHRALLSLRRAEPALSVGRYEPVSAENDV 466 Query: 477 LGFTRQKGDETLLCVFNLTGQEQ 499 L + R+ G + + NL+ E+ Sbjct: 467 LVYERRHGRDRFRVLLNLSAAER 489 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: 952 Number of extensions: 48 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: 537 Length adjustment: 35 Effective length of query: 503 Effective length of database: 502 Effective search space: 252506 Effective search space used: 252506 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