Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate N515DRAFT_3391 N515DRAFT_3391 Glycosidase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__Dyella79:N515DRAFT_3391 Length = 526 Score = 219 bits (558), Expect = 2e-61 Identities = 164/538 (30%), Positives = 243/538 (45%), Gaps = 67/538 (12%) Query: 11 GVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYDVSDY 70 GV Y+I+ R++ D+ GDG+GDLNG+T KLDY+ SL V GIWL P SP GYDV+DY Sbjct: 44 GVWYEIFVRAWYDTNGDGIGDLNGVTAKLDYLQSLGVSGIWLMPINPSPTYH-GYDVTDY 102 Query: 71 RDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKADWFVW 130 ++P +G++ DF+ L+ +AH G++V+ID VI+H+SDQHPWF+ + + + W+ W Sbjct: 103 EGINPQYGSMADFEKLVSEAHKRGIEVIIDLVINHSSDQHPWFKSALDPHSQYR-HWYTW 161 Query: 131 ADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLDNMRF 190 A D +S G AW + +Q+YL +F + PD+N+ P R+ + +F Sbjct: 162 AGKDTD----LKAISAVDGPAW--HANGKQHYLGDFTGAMPDLNYDEPAVRREMIAIGKF 215 Query: 191 WLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSRPENL 250 WL G DGFRLD + D + + P N W Sbjct: 216 WLSKGADGFRLDAARHIYDDLKSDNGQP---------AVIRKNAQWWS------------ 254 Query: 251 DFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPHS----- 305 +F + LR + P VGE+ P E A G L+ Sbjct: 255 EFRQGLRQVR---PDVYLVGEVSARQPGELAPYLPALGSVFDFPLAEQLIASAKQEQAGK 311 Query: 306 -ASYLREVIERFQRLAGDAW-PCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRG 363 + L E F AGD + SNHD R ++ G D + + A+L +L G Sbjct: 312 LPALLTESYAAFHAAAGDDYADAPFLSNHDQERVLSQLGGDLH---HMRTAAAMLLTLPG 368 Query: 364 SVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVEPW 423 +Y GEE+G+ P E +++P P G +T +QGG Sbjct: 369 RPYIYYGEEIGM-LGRKPDENLREPMRWQRTPAAPGDSRWKT----YSVKQGG------- 416 Query: 424 LPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDD-LLGFTRQ 482 +++V ++D P++ LN R L+ +R PAL DG L ++ G L+ + R Sbjct: 417 --------DVSVQAERDQPDSLLNLYRTLIHWRVEVPALRDGALRVIATGKPALVAYERA 468 Query: 483 KGDETLLCVFNLTGQEQQTTLPVEVASDLPVAHF----TATRDGSTLTLPAYQAAFMQ 536 D L V NL+G+ L + A AT LTLPAY +Q Sbjct: 469 TADSRALVVHNLSGKPGSFKLDGDSAKAFSAIRLHTVPGATLANGQLTLPAYATVVLQ 526 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: 818 Number of extensions: 58 Number of successful extensions: 4 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: 526 Length adjustment: 35 Effective length of query: 503 Effective length of database: 491 Effective search space: 246973 Effective search space used: 246973 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