Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate N515DRAFT_3393 N515DRAFT_3393 alpha-glucosidase
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__Dyella79:N515DRAFT_3393 Length = 541 Score = 582 bits (1499), Expect = e-170 Identities = 292/536 (54%), Positives = 361/536 (67%), Gaps = 13/536 (2%) Query: 15 ADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKD 74 ++ WWRGAVIYQIYPRSF D++GDG+GDL GIVER+ YIA LGVDAIWI+PFF SPM D Sbjct: 2 SETPWWRGAVIYQIYPRSFLDTDGDGVGDLPGIVERLDYIAGLGVDAIWIAPFFRSPMAD 61 Query: 75 FGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDN 134 FGYDI+DY VDP+FG++ DFD L+ AH GL+VMID VLSHTSDQH WF+ESR+SRDN Sbjct: 62 FGYDIADYRAVDPLFGTIDDFDRLLAKAHALGLKVMIDQVLSHTSDQHEWFKESRASRDN 121 Query: 135 PKADWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQD 194 PKADWYVWADA+ DGTPPNNW+S+FGG W W+ RR QYYLHNFLTSQPDLNFH DVQ Sbjct: 122 PKADWYVWADARDDGTPPNNWMSLFGGVAWQWEPRRGQYYLHNFLTSQPDLNFHHPDVQR 181 Query: 195 ALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLY 254 A+L +FWLD+GVDG RLD INF HD +LRDNPP P R NPY Q H Y Sbjct: 182 AVLDNVQFWLDKGVDGLRLDAINFCFHDRQLRDNPPKPQAMRVGRGFSPDNPYAFQYHYY 241 Query: 255 SKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFLA 314 + QPENL FL + R +++ YP AA+GE+ ++ L + +YT G +HM Y+FE L Sbjct: 242 NNTQPENLAFLEELRGLLDRYPGAAALGEI-SSEDSLATMAEYTTGHR-LHMGYSFELLT 299 Query: 315 QEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDLTPGAQ-------RGMLT 367 + +A + + +++ ++GW CWA SNHDV R +SRW +LT Sbjct: 300 AD-FSAAYIRGTVERLEAQMTEGWPCWAISNHDVERVLSRWGREARGNGDASVRLANLLT 358 Query: 368 LLMC-LRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMS 426 ++C LRGSVC+YQGEEL L EAEV ++ LQDPYGI FWP +KGRDGCRTPM W ++ + Sbjct: 359 AMVCSLRGSVCVYQGEELALTEAEVPYEALQDPYGITFWPNFKGRDGCRTPMPW-DESAN 417 Query: 427 GGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVG 486 GFS PWLPV H LAV+ QE P + LH +R + +R+A P L G I + Sbjct: 418 AGFSSGAPWLPVPAGHRALAVSRQELDPASALHGFRGFMQWRQAQPELRWGAIGFLDTPE 477 Query: 487 DVISFLRKDPEETVFVAINMSDAPGAVDLPPGNWMQIGAELNSGGTSPDGRVHLGP 542 V++F R ETV A N+ AP AV LP +IG + GT DG + L P Sbjct: 478 PVLAFTRTHAGETVLAAFNLGSAPVAVALPLAG-ERIGGHGLAEGTLEDGLLRLPP 532 Lambda K H 0.321 0.138 0.451 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: 1035 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: 541 Length adjustment: 36 Effective length of query: 516 Effective length of database: 505 Effective search space: 260580 Effective search space used: 260580 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