Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate H281DRAFT_02776 H281DRAFT_02776 maltose alpha-D-glucosyltransferase/ alpha-amylase
Query= curated2:Q9Z3R8 (551 letters) >FitnessBrowser__Burk376:H281DRAFT_02776 Length = 554 Score = 233 bits (595), Expect = 1e-65 Identities = 165/518 (31%), Positives = 239/518 (46%), Gaps = 48/518 (9%) Query: 17 WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76 W++ A++Y + +F D NGDG+GD QG+ RL ++ GLG IW+ PF SP RD GYD Sbjct: 6 WYKNAIVYCLSVGTFMDANGDGVGDFQGLLRRLDYLQGLGVTTIWLMPFQPSPGRDNGYD 65 Query: 77 VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNAKAD 136 +S+Y +VDP +GTL DF GLRVMIDLV++HTSD+HPWF E+RS + D Sbjct: 66 ISDYYNVDPKYGTLGDFSEFTHACRERGLRVMIDLVVNHTSDQHPWFREARSDPDSQYRD 125 Query: 137 WYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQVQEALLA 196 WYVW+D +P S W +D ++Y H F QPDLN NP V+ LL Sbjct: 126 WYVWSDKQPPNAKDGVVFPGVQKSTWTFDKQAKRWYFHRFYEFQPDLNTANPYVRAELLK 185 Query: 197 VERFWLERGVDGFRLDTINF---------------YFHDRELRDNPALVPERRNASTAPA 241 + FW++ GV GFR+D + F Y RE R+ L + +A Sbjct: 186 IMGFWIQLGVSGFRMDAVPFVIATKGPKVREPVEQYDMLREFRE--FLQWRQGDAIILAE 243 Query: 242 VNPYNYQEHIYDKNRPENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTSGGDK 301 N + Y + E L+ + F+ + F A+ A G+ ++ L + Sbjct: 244 ANVLPDTDLEYFGDEGERLQMMFNFQLNQNTFYAL-ATGDTAPLKKALTATRPRPATAQW 302 Query: 302 VHMCYAFEFLAPDRLTPQRVAEVLRDFHRAAPEGWACWAFSNHDVVRHVSRWADGVTDHD 361 + L RLTP++ V F APE + R R A + Sbjct: 303 GVFLRNHDELDLGRLTPEQREAVFAAF---APE--PDMQLYERGIRR---RLAPMLAGDR 354 Query: 362 AHAKLLASLLMSLRGTVCIYQGEELALAEAELDYEDLQDPYGIQFWPDFKGRDGCRTPMV 421 +L SL+++L GT G+E+ + +DL+ P R+ RTPM Sbjct: 355 RRLELAYSLMLTLPGTPVFRYGDEIGMG------DDLRLP----------ERECARTPMQ 398 Query: 422 WESLPDGGFSS-ATPWLPI----SQSHIPRAVAVQEGDPASVLHHYRRFLAFRKANPALA 476 W + P+GGF+ A P + + VA Q DP S L+ R + R+ P ++ Sbjct: 399 WSTEPEGGFTKHAKPPCRVITGGAYGFERVNVASQRRDPNSFLNWMERMIRMRREVPEIS 458 Query: 477 KGEIEFVET-RGSLLGFLRSHGNEKVFCLFNMSDEAAT 513 G+ + + T R +L N V CL N EA T Sbjct: 459 WGDFDVLRTSRSDVLALRFDWRNNSVLCLHNFGAEACT 496 Lambda K H 0.321 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: 928 Number of extensions: 56 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 554 Length adjustment: 36 Effective length of query: 515 Effective length of database: 518 Effective search space: 266770 Effective search space used: 266770 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: 53 (25.0 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