Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate N515DRAFT_3391 N515DRAFT_3391 Glycosidase
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__Dyella79:N515DRAFT_3391 Length = 526 Score = 204 bits (518), Expect = 9e-57 Identities = 165/540 (30%), Positives = 240/540 (44%), Gaps = 70/540 (12%) Query: 5 AQLDPAQVLAADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWI 64 A P + P V Y+I+ R++ D+NGDGIGDL G+T +L ++ SLGV IW+ Sbjct: 26 ADSTPPVATSTAPKTQGSGVWYEIFVRAWYDTNGDGIGDLNGVTAKLDYLQSLGVSGIWL 85 Query: 65 SPFFTSPMKDFGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAW 124 P SP GYDV+DY ++P +GS+++F++LV+ AH+ G+ V+IDLV++H+SDQH W Sbjct: 86 MPINPSPTYH-GYDVTDYEGINPQYGSMADFEKLVSEAHKRGIEVIIDLVINHSSDQHPW 144 Query: 125 FGESRQSRDNARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPD 184 F + R WY WA D +S G AW +Q+YL +F + PD Sbjct: 145 FKSALDPHSQYR-HWYTWAGKDTD----LKAISAVDGPAWH--ANGKQHYLGDFTGAMPD 197 Query: 185 LNFHSPAVQDALLDVTRFWLERGVDGFRLDTINFYYHD--------AELRSNPALPPEQR 236 LN+ PAV+ ++ + +FWL +G DGFRLD Y D A +R N E R Sbjct: 198 LNYDEPAVRREMIAIGKFWLSKGADGFRLDAARHIYDDLKSDNGQPAVIRKNAQWWSEFR 257 Query: 237 NATIAPSVNPYNHQEHLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGS 296 V P + S QP LA P A+G V D +++ S Sbjct: 258 QG--LRQVRPDVYLVGEVSARQPGELA------------PYLPALGSVFDFPLAEQLIAS 303 Query: 297 YTAANTGVHMCYAFELLAKDVLTASRLAEVFAEVDRVAANGWACWAF-SNHDVIRHSSRW 355 G + L E +A A + +A F SNHD R S+ Sbjct: 304 AKQEQAG--------------KLPALLTESYAAFHAAAGDDYADAPFLSNHDQERVLSQL 349 Query: 356 GLNPAAQRLFTTMMMCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCR 415 G + R M++ L G IY GEE+G+ K + R Sbjct: 350 GGDLHHMRTAAAMLLTLPGRPYIYYGEEIGMLGR-------------------KPDENLR 390 Query: 416 TPMVWEPSNGSGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALA 475 PM W+ + + G S K + + ++SV ++ PD++L+ YR I R PAL Sbjct: 391 EPMRWQRTPAAPGDSRWKTY--SVKQGGDVSVQAERDQPDSLLNLYRTLIHWRVEVPALR 448 Query: 476 VGTHDQLRAEGNVAF--FTRQDRDEVIFCAFNLGDIPAEITLPEGTWRKPDTDIALADLP 533 G ++ A G A + R D NL P L +G K + I L +P Sbjct: 449 DGAL-RVIATGKPALVAYERATADSRALVVHNLSGKPGSFKL-DGDSAKAFSAIRLHTVP 506 Lambda K H 0.321 0.137 0.444 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: 875 Number of extensions: 45 Number of successful extensions: 5 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: 552 Length of database: 526 Length adjustment: 35 Effective length of query: 517 Effective length of database: 491 Effective search space: 253847 Effective search space used: 253847 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 (21.9 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