Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_066608734.1 V473_RS17575 DUF3459 domain-containing protein
Query= uniprot:H3K096 (538 letters) >NCBI__GCF_001046645.1:WP_066608734.1 Length = 535 Score = 549 bits (1415), Expect = e-161 Identities = 271/533 (50%), Positives = 349/533 (65%), Gaps = 13/533 (2%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WW+G VIYQIYPRSF DS DG+GDLNGIT++L+++A L D IW+SPFFTSPM DFGYD Sbjct: 12 WWKGAVIYQIYPRSFQDSNHDGIGDLNGITQRLEHIARLGADAIWISPFFTSPMRDFGYD 71 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 ++DY DVDP+FGTL DF AL+ +AH+LGLKV IDQV +HTSD H WF +SR +RT+ KAD Sbjct: 72 IADYCDVDPIFGTLADFDALVARAHALGLKVTIDQVYAHTSDLHDWFAQSRASRTSEKAD 131 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 WFVW DPK DGTPPNNW S+FGG AWT+D+RR QYY+H FL+SQP +N H+P + A LD Sbjct: 132 WFVWVDPKEDGTPPNNWQSVFGGPAWTWDARRGQYYMHQFLSSQPQLNLHNPAVQDALLD 191 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 MRFWLD GVDGFRLD +N HD +LRDNPP P G P + +Q Y S Sbjct: 192 AMRFWLDRGVDGFRLDALNHSMHDPQLRDNPPAP-----DTGKPRTRSFDFQIKTYSQSH 246 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH-S 305 P +DF+K +R L DEY TV E+G D M YTAG L+ AY F+ L + Sbjct: 247 PGVVDFIKRIRTLCDEYGAIFTVAEVGGDLSETEMKAYTAGETHLNSAYGFNFLYADALT 306 Query: 306 ASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGSV 365 + + + ++R+ G WP WA NHD R+ +RW A ED A+ ++ +L +LRG+ Sbjct: 307 PALVADTVDRWPDEPGMGWPSWAFENHDAPRALSRWCAAEDRPAFGRLKAMLLVALRGNA 366 Query: 366 CLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGFSPVEPWL 424 LYQGEELG+ + D+PF+++QDP WP RDG RTP+PW D Q GFS VEPWL Sbjct: 367 ILYQGEELGITQVDIPFDKLQDPEAIANWPLTLSRDGARTPLPWAADAAQAGFSSVEPWL 426 Query: 425 PMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQKG 484 P A HL LAV Q+ DP + LN RA+LA R+++PAL G L ++ D L F R Sbjct: 427 PHGADHLALAVDAQEADPASLLNHTRAMLALRKANPALRHGSLEILVADDQRLLFRRAAD 486 Query: 485 DETLLCVFNLTGQEQQTTLPVEVASDLPVAHFTATRDGSTL-TLPAYQAAFMQ 536 ++LLC+FNL+ + T P E+A P + +G+T LP + A ++ Sbjct: 487 GQSLLCLFNLSA--KPATWPEEIA---PTNKLLSAVNGATPGALPPFGALMIE 534 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: 943 Number of extensions: 43 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: 535 Length adjustment: 35 Effective length of query: 503 Effective length of database: 500 Effective search space: 251500 Effective search space used: 251500 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 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