Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 6937506 Sama_1662 alpha amylase, catalytic region (RefSeq)
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__SB2B:6937506 Length = 544 Score = 640 bits (1651), Expect = 0.0 Identities = 293/503 (58%), Positives = 363/503 (72%), Gaps = 5/503 (0%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WWRG IYQIYPRS DS GDG+GDL GI E+LDY+ASLNVD IW+SPFF SPM DFGYD Sbjct: 6 WWRGAAIYQIYPRSLKDSNGDGIGDLQGIIERLDYIASLNVDAIWISPFFRSPMKDFGYD 65 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 +SDY DVDPMFGT++DF L+ KAHSLGLKV+IDQV+SHTSD+H WF ESRQ+R NPKAD Sbjct: 66 ISDYLDVDPMFGTMDDFDELIAKAHSLGLKVVIDQVLSHTSDEHAWFAESRQSRDNPKAD 125 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 W+VWADP+ DGTPPNNWL+IFGG AW ++ RRQQYYLHNFL SQPD+NFH RQA L+ Sbjct: 126 WYVWADPREDGTPPNNWLAIFGGCAWEWEPRRQQYYLHNFLKSQPDLNFHCEAVRQAVLN 185 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 N+ FWL GVDGFRLD + F FHD LRDNP P + + G E NPY +Q H Y+ R Sbjct: 186 NVEFWLKKGVDGFRLDAITFCFHDKALRDNPAKPADKRQGRGFSEDNPYAYQYHWYNNER 245 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPHSA 306 PE L F++DLRAL+D YPG T+GE+ ++ L MAEYT G ++LHMAY+F+LL +SA Sbjct: 246 PETLGFIEDLRALIDRYPGAVTLGEVSSEDSLATMAEYTRGDNRLHMAYSFELLTKDYSA 305 Query: 307 SYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGSVC 366 Y+R +E + GD WPCWA NHDV R +RWG + K++ A+L LRGS+C Sbjct: 306 GYIRSTVEALEGAIGDGWPCWAIGNHDVERVISRWGQGKGTPQMAKMLSAMLGCLRGSLC 365 Query: 367 LYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGF----SPVE 421 +YQGEELGL EAD+PF+ +QDP+G WP FKGRDGCRTPMPW +GE GF S Sbjct: 366 VYQGEELGLTEADIPFDALQDPFGIAFWPNFKGRDGCRTPMPWQAEGEYMGFGATASGAM 425 Query: 422 PWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTR 481 PWLP+ H L V+ Q +P++ LN +A+RR+ PAL G++ +D + +L F R Sbjct: 426 PWLPLPEEHRALNVAAQSANPDSVLNQFSRFMAWRRTQPALVTGEIKFIDSKEPVLAFER 485 Query: 482 QKGDETLLCVFNLTGQEQQTTLP 504 D+ +LCVFNL+ + Q T+P Sbjct: 486 VSSDKKVLCVFNLSDKPQTMTVP 508 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: 1032 Number of extensions: 46 Number of successful extensions: 2 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: 544 Length adjustment: 35 Effective length of query: 503 Effective length of database: 509 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 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