Align α-glucosidase (AglA) (EC 3.2.1.20) (characterized)
to candidate WP_076480784.1 BW971_RS14260 DUF3459 domain-containing protein
Query= CAZy::AAA57313.1 (544 letters) >NCBI__GCF_900156495.1:WP_076480784.1 Length = 538 Score = 587 bits (1513), Expect = e-172 Identities = 293/528 (55%), Positives = 364/528 (68%), Gaps = 13/528 (2%) Query: 19 WWRHAVIYQIYVRSFADSNGDGEGDLNGIRERLPALVSLGVDAIWLTPFYVSPLADGGYD 78 WW+ A+ YQIY RSFAD NGDG GDL G+ E+L L LG+DA+WL+P SP+AD GYD Sbjct: 17 WWQDAIFYQIYPRSFADGNGDGVGDLRGVAEKLGYLELLGIDALWLSPVMRSPMADHGYD 76 Query: 79 VADYRDVDPRFGTLADFDALLATAHDLGLRVIIDIVPNHTSSAHRWFRDALAAGPGSPER 138 V+D RD+DP FG+LA DALL AH+ G++V +D+VPNHTS H WF +AL + PGSPER Sbjct: 77 VSDPRDIDPLFGSLAAMDALLVAAHERGMKVTMDLVPNHTSDQHPWFVEALNSAPGSPER 136 Query: 139 DRYVFRPGRGENGELPPNNWQSIFGGPAWTRVTEPDGTPGEWYLHLFDVEQPDLNWENPE 198 RY+FR GRG++GELPPNNW S+FGGPAW RVTE DG+PG+WYLHLF EQPDLNWENPE Sbjct: 137 ARYIFRDGRGDHGELPPNNWPSVFGGPAWHRVTEADGSPGQWYLHLFAPEQPDLNWENPE 196 Query: 199 VRAEFADILRFWLDRGVDGFRIDVAHGMIKDPALPDIAEGQKADMLDGHTRLPYFDQDGV 258 V + LRFWLDRGVDGFRIDVAHGM+K LPD+ + + +L P F+ GV Sbjct: 197 VFEDLEKTLRFWLDRGVDGFRIDVAHGMVKPSDLPDM-DVSEVQLLVNRDGDPRFNNPGV 255 Query: 259 HEIYREWRAIVDSYPGERALVAEAWVENAERVARYLRPDELHQAFNFEYLTADWDAATLR 318 H I+R R ++D YP E V E WVE+ + A YLRPDELH FNF + +DA +R Sbjct: 256 HAIHRRIRTVMDEYP-EAMTVGELWVESNDAFAEYLRPDELHLGFNFRLVKTAFDAVEIR 314 Query: 319 AVVDRSLAANNAVGAPTTWVLSNHDVTRHVTRFGGG---AQGLARARAALLLMLALPGSV 375 ++ S+ A + VG TW LSNHDV R VTR+ G GL RA+A +L+ LALPG+ Sbjct: 315 EAIEESINAVDLVGGTPTWTLSNHDVEREVTRYADGVGPGAGLERAKAMILVELALPGTS 374 Query: 376 YLYQGEELGLPEVTDLPEEALQDPTWKRSGYTERGRDGCRVPLPWEGDEPPFGFGCSAER 435 ++Y G ELGLP V DLP+E LQDPTW+RSG+TERGRDGCRVPLPWEG+ PPFGF + R Sbjct: 375 FVYNGAELGLPNV-DLPDEVLQDPTWERSGHTERGRDGCRVPLPWEGNRPPFGFSTN-PR 432 Query: 436 SWLPVPAEWRSLTREVQERDPDSTLSLYKKALRLRRELLLPAEDALHWADAPQNVLAFRR 495 +WLP+P EW T E Q + STLSLY++A+ +R+ + + W AP+ LAFRR Sbjct: 433 TWLPIPPEWADRTAEGQLENVHSTLSLYREAIEMRKTRPEFSGRGVEWYGAPEGCLAFRR 492 Query: 496 EPGF-TCAVNFGADPVTLPFEGEVVLSSGPVEQDGTHLVLPGDTAVWL 542 G CA+N PV P GE++L S P+ QDG L + A WL Sbjct: 493 SEGHAVCALNTTDTPVGFP-PGELLLCSAPL-QDGK---LAPNAAAWL 535 Lambda K H 0.320 0.139 0.448 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: 1261 Number of extensions: 72 Number of successful extensions: 7 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: 544 Length of database: 538 Length adjustment: 35 Effective length of query: 509 Effective length of database: 503 Effective search space: 256027 Effective search space used: 256027 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