Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_041742016.1 CALKRO_RS12150 alpha-glucosidase
Query= CAZy::CAA54266.1 (587 letters) >NCBI__GCF_000166775.1:WP_041742016.1 Length = 555 Score = 745 bits (1923), Expect = 0.0 Identities = 353/567 (62%), Positives = 432/567 (76%), Gaps = 12/567 (2%) Query: 17 IRRAWWKEAVVYQIYPRSFMDSNGDGIGDLRGILSKLDYLKLLGVDVLWLNPIYDSPNDD 76 + + WWKEAVVYQIYPRSF DSNGDGIGDL GI+ KLDYL+ LGVDV+WLNPIY SPN D Sbjct: 1 MHKKWWKEAVVYQIYPRSFYDSNGDGIGDLPGIIEKLDYLQELGVDVIWLNPIYKSPNAD 60 Query: 77 MGYDIRDYYKIMEEFGTMEDFEELLREVHARGMKLVMDLVANHTSDEHPWFIESRSSRDN 136 GYDI DYY IM+EFGTMEDF+ LL E H RG+K+VMDLV NHTSDEH WF+ESR S+DN Sbjct: 61 NGYDISDYYDIMDEFGTMEDFDRLLNEAHKRGIKIVMDLVVNHTSDEHKWFLESRKSKDN 120 Query: 137 PYRDWYIWRDPKDGREPNNWLSYFSGSAWEYDERTGQYYLHLFSRRQPDLNWENPKVREA 196 PYRD+Y WR K+G PNNW S+FSG AW+YDE TG+YYLHLF+ +QPDLNW NP+VR+ Sbjct: 121 PYRDFYFWRPGKNGGPPNNWTSFFSGPAWKYDELTGEYYLHLFAVKQPDLNWNNPQVRQE 180 Query: 197 IFEMMRFWLDKGIDGFRMDVINAIAKAEGLPDAPARPGERYAWGGQYFLNQPKVHEYLRE 256 I++MM++WLDKGIDGFRMDVIN I+K EGLPD P + G +Y+ N P+VHEYL+E Sbjct: 181 IYKMMKWWLDKGIDGFRMDVINLISKVEGLPDDPDE-NQGGLIGFKYYANGPRVHEYLQE 239 Query: 257 MYDKVLSHYDIMTVGETGGVTTKDALLFAGEDRRELNMVFQFEHMDIDATDGDKWRPRPW 316 M +VLS YDIMTVGET VT + A L+ DR ELNM+F FEHMD+D + G KW +PW Sbjct: 240 MNREVLSKYDIMTVGETPFVTPEIAKLYVEYDRNELNMIFHFEHMDMDCS-GSKWNIKPW 298 Query: 317 RLTELKTIMTRWQNDLYGKAWNSLYWTNHDQPRAVSRFGNDGPYRVESAKMLATVLHMMQ 376 +LT+LK IM +W L K WNSLY NHDQPR VSRFGND YRVESAK+LAT+LH Q Sbjct: 299 KLTDLKKIMFKWYLALKDKGWNSLYLNNHDQPRMVSRFGNDKEYRVESAKLLATLLHTWQ 358 Query: 377 GTPYIYQGEEIGMTNCPFDSIDEYRDVEIHNLWRHRVMEGGQDPAEVLRVIQLKGRDNAR 436 GTPYIYQGEEIGMTNC F+S DE+RD+E N W + + G+ E+L ++ + RD+AR Sbjct: 359 GTPYIYQGEEIGMTNCKFESFDEFRDIETLN-WYKEMKKLGKSDEELLEILNKRSRDHAR 417 Query: 437 TPMQWDDSPNAGFTTGTPWIKVNPNYREINVKQALADPNSIFHYYRRLIQLRKQHPIVVY 496 TPMQWDDS NAGFT GTPWIKVNPNY+EINVK+AL D NS+F+YY++LI+LRK+HP++VY Sbjct: 418 TPMQWDDSKNAGFTKGTPWIKVNPNYKEINVKKALEDKNSVFYYYKKLIELRKKHPVIVY 477 Query: 497 GKYDLILPDHEEIWAYTRTLGDERWLIVANFFGGTPEFELPPEVRCEGAELVIANYPVDD 556 G ++ D E+I+AYTR+ DER L+V NF EF P E+ + EL+I+NY +DD Sbjct: 478 GDVQMLYEDDEKIFAYTRSYEDERLLVVMNFSEEESEFLAPNEIFTQKPELLISNYEIDD 537 Query: 557 SEAGGPAAAGAPHRFRLRPYECRVYRL 583 + + L+PYE RVY++ Sbjct: 538 N---------IQEKIVLKPYESRVYKI 555 Lambda K H 0.320 0.139 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: 1347 Number of extensions: 72 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: 587 Length of database: 555 Length adjustment: 36 Effective length of query: 551 Effective length of database: 519 Effective search space: 285969 Effective search space used: 285969 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