Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate WP_086510098.1 BZY95_RS11685 DUF3459 domain-containing protein
Query= uniprot:A8LLL3 (552 letters) >NCBI__GCF_002151265.1:WP_086510098.1 Length = 550 Score = 622 bits (1603), Expect = 0.0 Identities = 309/552 (55%), Positives = 371/552 (67%), Gaps = 20/552 (3%) Query: 10 VKSLAADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFT 69 ++ L DPDWWRGAVIYQIYPRSFQDS G GIGDL G+++R+ YIASL VDAIW++PFFT Sbjct: 3 IRQLGGDPDWWRGAVIYQIYPRSFQDSRGAGIGDLQGVIDRLDYIASLNVDAIWLAPFFT 62 Query: 70 SPMKDFGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESR 129 SPMKDFGYD+SDY VDP FG+L DFD L+E AH GLRV ID VLSH+SDQHPWF ESR Sbjct: 63 SPMKDFGYDVSDYRGVDPTFGTLDDFDRLVEAAHARGLRVTIDQVLSHSSDQHPWFAESR 122 Query: 130 SSRDNPKADWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHC 189 SSRDNPKADWYVWADA+ DG+PP NW +IFGGS W WD RRCQYYLHNFL QPDLNFH Sbjct: 123 SSRDNPKADWYVWADARSDGSPPTNWQAIFGGSAWQWDTRRCQYYLHNFLVEQPDLNFHN 182 Query: 190 ADVQDALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPP-EERNSNIAPEVNPYN 248 +V +A+L RFWL+RGVDGFRLD +NF H L+DNPP E + P+ NPY Sbjct: 183 PEVVEAILEEVRFWLERGVDGFRLDAVNFCTH-GPLKDNPPREKIVEGFIGVRPD-NPYA 240 Query: 249 HQRHLYSKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCY 308 QRHLY K QPENL FL + RA+++EYP+ +GEVGD L ++ +YT+G +HMCY Sbjct: 241 FQRHLYDKTQPENLAFLERLRALLDEYPSTTTIGEVGDDD-SLGVMSEYTQGGKRLHMCY 299 Query: 309 AFEFLAQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDLTP--GAQRGML 366 +F L +K T + L +++ DGW CWA NHD+ R +RW++ R L Sbjct: 300 SFNLLT-DKATPADLLAPLTEMEARIGDGWPCWAVGNHDITRVATRWNVASDMAKLRLYL 358 Query: 367 TLLMCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMS 426 L+ RGS+CLYQGEELGL EAE+ F+ L DP GI FWP YKGRDGCRTPM W +D + Sbjct: 359 AFLLTQRGSICLYQGEELGLTEAELTFEQLVDPAGITFWPSYKGRDGCRTPMPWVADALH 418 Query: 427 GGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVG 486 GGF+ PWLPV HL LAV QE P +LL+ YR L FRR PALVKGDI + G Sbjct: 419 GGFTTATPWLPVPEAHLALAVDRQERDPGSLLNAYRDFLLFRRNQPALVKGDIHYHPLQG 478 Query: 487 DVISFLRKDPEETVFVAINMSDAP-------------GAVDLPPGNWMQIGAELNSGGTS 533 DVI F R ++ + VA+N ++ P GA L G W EL + G + Sbjct: 479 DVICFERLHGDDRLLVALNFANDPCTLSAPLDARPLAGAPSLVNGRWTAERLELPAFGIA 538 Query: 534 PDGRVHLGPWQP 545 PWQP Sbjct: 539 IARCPSDLPWQP 550 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: 1090 Number of extensions: 39 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: 550 Length adjustment: 36 Effective length of query: 516 Effective length of database: 514 Effective search space: 265224 Effective search space used: 265224 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: 53 (25.0 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